mothur →
1.39.5-1 →
armhf → 2017-06-22 21:47:58
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| mothur 1.39.5-1 (armhf) Thu, 22 Jun 2017 20:12:59 +0000 |
+==============================================================================+
Package: mothur
Version: 1.39.5-1
Source Version: 1.39.5-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-ec36975c-baf6-4d46-ae99-27f56de04b31' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [9974 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 21.8 MB in 7s (2792 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'mothur' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/mothur.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/mothur.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1824 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main mothur 1.39.5-1 (dsc) [1796 B]
Get:2 http://172.17.0.1/private buster-staging/main mothur 1.39.5-1 (tar) [1810 kB]
Get:3 http://172.17.0.1/private buster-staging/main mothur 1.39.5-1 (diff) [12.1 kB]
Fetched 1824 kB in 0s (6177 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mothur-0fbCHZ/mothur-1.39.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mothur-0fbCHZ' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-jqo90Y/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-jqo90Y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-jqo90Y/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (5760 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12654 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), gfortran, libboost-iostreams-dev, libopenmpi-dev, libreadline-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), gfortran, libboost-iostreams-dev, libopenmpi-dev, libreadline-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-mothur-dummy' in '/<<BUILDDIR>>/resolver-jqo90Y/apt_archive/sbuild-build-depends-mothur-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-mothur-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Sources [530 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ Packages [611 B]
Fetched 2474 B in 0s (5994 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install mothur build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.62-dev libboost-iostreams1.62.0
libboost-regex1.62-dev libboost-regex1.62.0 libboost1.62-dev libbsd0
libcroco3 libffi6 libfile-stripnondeterminism-perl libgfortran-6-dev
libgfortran3 libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu-dev libicu57 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libreadline-dev libsigsegv2
libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
ocl-icd-libopencl1 openmpi-common po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-6-doc libgfortran3-dbg libcoarrays-dev groff libboost1.62-doc
libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev
libboost-coroutine1.62-dev libboost-date-time1.62-dev
libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-serialization1.62-dev
libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev
libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev
libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev
libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils
readline-doc gcj-jdk m4-doc less www-browser opencl-icd libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
openmpi-bin xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.62-dev libboost-iostreams1.62.0
libboost-regex1.62-dev libboost-regex1.62.0 libboost1.62-dev libbsd0
libcroco3 libffi6 libfile-stripnondeterminism-perl libgfortran-6-dev
libgfortran3 libglib2.0-0 libhwloc-dev libhwloc-plugins libhwloc5
libibverbs-dev libibverbs1 libicu-dev libicu57 libltdl-dev libltdl7
libmagic-mgc libmagic1 libnl-3-200 libnl-route-3-200 libopenmpi-dev
libopenmpi2 libpciaccess0 libpipeline1 libreadline-dev libsigsegv2
libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
ocl-icd-libopencl1 openmpi-common po-debconf
sbuild-build-depends-mothur-dummy zlib1g-dev
0 upgraded, 61 newly installed, 0 to remove and 1 not upgraded.
Need to get 53.0 MB of archives.
After this operation, 293 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jqo90Y/apt_archive ./ sbuild-build-depends-mothur-dummy 0.invalid.0 [814 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.034-1 [16.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.034-1 [10.5 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libffi6 armhf 3.2.1-6 [18.7 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.11-3 [131 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.3.0-18+rpi1 [166 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libgfortran-6-dev armhf 6.3.0-18+rpi1 [199 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gfortran-6 armhf 6.3.0-18+rpi1 [5422 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:6.3.0-4 [1352 B]
Get:37 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 57.1-6 [156 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-4 [232 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 57.1-6 [15.8 MB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-4 [325 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-4 [48.7 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-4 [57.7 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b4 [3694 B]
Get:45 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.2.27-2 [53.7 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.2.27-2 [113 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.0+20161126-1 [65.3 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-3 [109 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.5-1+rpi1 [83.2 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.5-1+rpi1 [136 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf ocl-icd-libopencl1 armhf 2.2.11-1 [35.5 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.5-1+rpi1 [14.9 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libopenmpi2 armhf 2.0.2-2 [1702 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 2.0.2-2 [149 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 2.0.2-2 [1007 kB]
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libgfortran3:armhf (6.3.0-18+rpi1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libgfortran-6-dev:armhf (6.3.0-18+rpi1) ...
Setting up libtinfo-dev:armhf (6.0+20161126-1) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
Setting up libmagic-mgc (1:5.30-1) ...
Setting up libmagic1:armhf (1:5.30-1) ...
Setting up libboost-iostreams1.62.0:armhf (1.62.0+dfsg-4) ...
Setting up openmpi-common (2.0.2-2) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libltdl7:armhf (2.4.6-2) ...
Setting up libreadline-dev:armhf (7.0-3) ...
Setting up libpciaccess0:armhf (0.13.4-1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up icu-devtools (57.1-6) ...
Setting up ocl-icd-libopencl1:armhf (2.2.11-1) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libnl-3-200:armhf (3.2.27-2) ...
Setting up autopoint (0.19.8.1-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.034-1) ...
Setting up gfortran-6 (6.3.0-18+rpi1) ...
Setting up libltdl-dev:armhf (2.4.6-2) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-4) ...
Setting up libnl-route-3-200:armhf (3.2.27-2) ...
Setting up autoconf (2.69-10) ...
Setting up libicu-dev (57.1-6) ...
Setting up file (1:5.30-1) ...
Setting up libhwloc5:armhf (1.11.5-1+rpi1) ...
Setting up libcroco3:armhf (0.6.11-3) ...
Setting up libhwloc-plugins (1.11.5-1+rpi1) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.3.0-4) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libibverbs1 (1.2.1-2) ...
Setting up libhwloc-dev:armhf (1.11.5-1+rpi1) ...
Setting up gettext (0.19.8.1-2) ...
Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b4) ...
Setting up libopenmpi2:armhf (2.0.2-2) ...
Setting up libibverbs-dev (1.2.1-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libopenmpi-dev (2.0.2-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.034-1) ...
Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-mothur-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-11+deb9u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.28-5 dpkg-dev_1.18.24 g++-6_6.3.0-18+rpi1 gcc-6_6.3.0-18+rpi1 libc6-dev_2.24-11+deb9u1 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.4.6 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-5 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.3.0-18+rpi1 dash_0.5.8-2.4 debconf_1.5.61 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.034-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20161106-2 g++_4:6.3.0-4 g++-6_6.3.0-18+rpi1 gcc_4:6.3.0-4 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.3.0-18+rpi1 gcc-6-base_6.3.0-18+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gfortran_4:6.3.0-4 gfortran-6_6.3.0-18+rpi1 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-6 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libasan3_6.3.0-18+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-18+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-2 libaudit1_1:2.6.7-2 libblkid1_2.29.2-1 libboost-iostreams-dev_1.62.0.1+b4 libboost-iostreams1.62-dev_1.62.0+dfsg-4 libboost-iostreams1.62.0_1.62.0+dfsg-4 libboost-regex1.62-dev_1.62.0+dfsg-4 libboost-regex1.62.0_1.62.0+dfsg-4 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-11+deb9u1 libc-dev-bin_2.24-11+deb9u1 libc6_2.24-11+deb9u1 libc6-dev_2.24-11+deb9u1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.3.0-18+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.74-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.034-1 libgcc-6-dev_6.3.0-18+rpi1 libgcc1_1:6.3.0-18+rpi1 libgcrypt20_1.7.6-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.3.0-18+rpi1 libgfortran3_6.3.0-18+rpi1 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgomp1_6.3.0-18+rpi1 libgpg-error0_1.26-2 libhwloc-dev_1.11.5-1+rpi1 libhwloc-plugins_1.11.5-1+rpi1 libhwloc5_1.11.5-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu-dev_57.1-6 libicu57_57.1-6 libidn11_1.33-1 libip4tc0_1.6.0+snapshot20161117-6 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libksba8_1.3.5-2 liblocale-gettext-perl_1.07-3+b1 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.3-1 libopenmpi-dev_2.0.2-2 libopenmpi2_2.0.2-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpciaccess0_0.13.4-1 libpcre3_2:8.39-3 libperl5.24_5.24.1-3 libpipeline1_1.4.1-2 libplymouth4_0.9.2-4 libpng16-16_1.6.28-1 libprocps6_2:3.3.12-3 libreadline-dev_7.0-3 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 libsystemd0_232-25 libtext-charwidth-perl_0.04-7+b7 libtext-iconv-perl_1.7-5+b8 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20161126-1 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-18+rpi1 libudev1_232-25 libunistring0_0.9.6+really0.9.3-0.1 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-2.2 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-1 mountall_2.54 multiarch-support_2.24-11+deb9u1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 ocl-icd-libopencl1_2.2.11-1 openmpi-common_2.0.2-2 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.24.1-3 perl-base_5.24.1-3 perl-modules-5.24_5.24.1-3 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mothur-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 systemd_232-25 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-1 udev_232-25 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Mar 25 11:31:49 2017 UTC
gpgv: using RSA key B3B8BD50E7CE8F0EE93818A582C20A4A29CBBFD5
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./mothur_1.39.5-1.dsc
dpkg-source: info: extracting mothur in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mothur_1.39.5.orig.tar.gz
dpkg-source: info: unpacking mothur_1.39.5-1.debian.tar.xz
dpkg-source: info: applying 0001-Add-hardening-flags.patch
dpkg-source: info: applying 0002-Fix-catchall-command.patch
dpkg-source: info: applying 0003-Update-version-numbers-everywhere.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-ec36975c-baf6-4d46-ae99-27f56de04b31
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package mothur
dpkg-buildpackage: info: source version 1.39.5-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build mothur-1.39.5
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f mothur mothur-mpi
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
( cd source/uchime_src && rm -f *.o mk.stdout mk.stderr tmp.stderr )
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- 64BIT_VERSION=no USEMPI=yes
make -j4 64BIT_VERSION=no USEMPI=yes
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp
source/mothur.cpp: In function 'int main(int, char**)':
source/mothur.cpp:46:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("clear");
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nastreport.o source/nastreport.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engine.o source/engine.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/gotohoverlap.o source/gotohoverlap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmap.o source/heatmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/sharedutilities.o source/sharedutilities.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'double SLibshuff::sCalculate(int, int)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int seqNoise::countDiffs(std::vector<int>, std::vector<int>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/dlibshuff.o source/dlibshuff.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double RefChimeraTest::alignQueryToReferences(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, double&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/progress.o source/progress.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/subsample.o source/subsample.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmapsim.o source/heatmapsim.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/collectorscurvedata.h:4,
from source/collect.h:4,
from source/collect.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/collectorscurvedata.h:4,
from source/collect.h:4,
from source/collect.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/venn.h:12,
from source/venn.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/venn.h:12,
from source/venn.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomnumber.o source/randomnumber.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double TrialSwap2::calc_c_score(std::vector<std::vector<int> >&, std::vector<int>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/consensus.o source/consensus.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual void RareDisplay::close()':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double correctDist::getDist(std::vector<int>&, std::vector<int>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandfactory.o source/commandfactory.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarecalc.o source/rarecalc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothurout.o source/mothurout.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp
source/mothurout.cpp: In member function 'bool MothurOut::mkDir(std::__cxx11::string&)':
source/mothurout.cpp:1135:45: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(makeDirectoryCommand.c_str());
^
source/mothurout.cpp: In member function 'int MothurOut::renameFile(std::__cxx11::string, std::__cxx11::string)':
source/mothurout.cpp:1633:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
source/mothurout.cpp:1637:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
source/mothurout.cpp: In member function 'std::__cxx11::string MothurOut::sortFile(std::__cxx11::string, std::__cxx11::string)':
source/mothurout.cpp:1844:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'double MothurOut::median(std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'std::vector<std::vector<seqDist> > MothurOut::getAverages(std::vector<std::vector<std::vector<seqDist> > >&, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/completelinkage.o source/completelinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::lda(std::vector<std::vector<double> >&, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::vector<double> >&, bool&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/coverage.o source/calculators/coverage.cpp
source/venn.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > Venn::getPic(std::vector<SharedRAbundVector*>, std::vector<Calculator*>)':
source/venn.cpp:77:16: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
^~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetayc.h:16,
from source/calculators/sharedthetayc.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetayc.h:16,
from source/calculators/sharedthetayc.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput ThetaYC::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/coverage.h:13,
from source/calculators/coverage.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/coverage.h:13,
from source/calculators/coverage.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Coverage::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/qstat.o source/calculators/qstat.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/invsimpson.h:15,
from source/calculators/invsimpson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/invsimpson.h:15,
from source/calculators/invsimpson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput InvSimpson::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedjest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedjest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Jest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynski.h:13,
from source/calculators/sharedkulczynski.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynski.h:13,
from source/calculators/sharedkulczynski.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Kulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/qstat.h:11,
from source/calculators/qstat.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/qstat.h:11,
from source/calculators/qstat.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput QStat::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bergerparker.h:12,
from source/calculators/bergerparker.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bergerparker.h:12,
from source/calculators/bergerparker.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput BergerParker::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobs.h:16,
from source/calculators/sharedsobs.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobs.h:16,
from source/calculators/sharedsobs.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobscollectsummary.h:15,
from source/calculators/sharedsobscollectsummary.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobscollectsummary.h:15,
from source/calculators/sharedsobscollectsummary.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>, std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shen.h:13,
from source/calculators/shen.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shen.h:13,
from source/calculators/shen.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Shen::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/canberra.h:15,
from source/calculators/canberra.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/canberra.h:15,
from source/calculators/canberra.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Canberra::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/gower.h:14,
from source/calculators/gower.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/gower.h:14,
from source/calculators/gower.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Gower::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/smithwilson.h:13,
from source/calculators/smithwilson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/smithwilson.h:13,
from source/calculators/smithwilson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SmithWilson::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpson.h:16,
from source/calculators/simpson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpson.h:16,
from source/calculators/simpson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Simpson::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/mempearson.h:15,
from source/calculators/mempearson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/mempearson.h:15,
from source/calculators/mempearson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/logsd.h:12,
from source/calculators/logsd.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/logsd.h:12,
from source/calculators/logsd.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput LogSD::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/goodscoverage.h:12,
from source/calculators/goodscoverage.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/goodscoverage.h:12,
from source/calculators/goodscoverage.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput GoodsCoverage::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/geom.o source/calculators/geom.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchord.h:14,
from source/calculators/memchord.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchord.h:14,
from source/calculators/memchord.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/solow.h:13,
from source/calculators/solow.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/solow.h:13,
from source/calculators/solow.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Solow::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/whittaker.o source/calculators/whittaker.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/manhattan.h:14,
from source/calculators/manhattan.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/manhattan.h:14,
from source/calculators/manhattan.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Manhattan::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/weighted.o source/calculators/weighted.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/geom.h:12,
from source/calculators/geom.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/geom.h:12,
from source/calculators/geom.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Geom::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/jackknife.h:13,
from source/calculators/jackknife.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/jackknife.h:13,
from source/calculators/jackknife.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Jackknife::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/efron.h:13,
from source/calculators/efron.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/efron.h:13,
from source/calculators/efron.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Efron::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/6/bits/stl_map.h: In member function 'EstOutput Weighted::driver(Tree*, std::vector<std::vector<std::__cxx11::basic_string<char> > >, int, int, CountTable*)':
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bootstrap.h:15,
from source/calculators/bootstrap.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bootstrap.h:15,
from source/calculators/bootstrap.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Bootstrap::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual EstOutput Weighted::getValues(Tree*, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hamming.h:15,
from source/calculators/hamming.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hamming.h:15,
from source/calculators/hamming.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Hamming::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkstest.h:11,
from source/calculators/sharedkstest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkstest.h:11,
from source/calculators/sharedkstest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput KSTest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/prng.o source/calculators/prng.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetan.h:16,
from source/calculators/sharedthetan.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetan.h:16,
from source/calculators/sharedthetan.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput ThetaN::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorclass.h:16,
from source/calculators/sharedsorclass.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorclass.h:16,
from source/calculators/sharedsorclass.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SorClass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannon.h:16,
from source/calculators/shannon.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannon.h:16,
from source/calculators/shannon.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Shannon::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedchao1.o source/calculators/sharedchao1.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput RangeShannon::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/npshannon.h:16,
from source/calculators/npshannon.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/npshannon.h:16,
from source/calculators/npshannon.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NPShannon::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structeuclidean.h:15,
from source/calculators/structeuclidean.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structeuclidean.h:15,
from source/calculators/structeuclidean.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjabund.h:16,
from source/calculators/sharedjabund.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjabund.h:16,
from source/calculators/sharedjabund.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput JAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedchao1.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedchao1.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedChao1::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchord.o source/calculators/structchord.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/chao1.h:12,
from source/calculators/chao1.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/chao1.h:12,
from source/calculators/chao1.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Chao1::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpsoneven.h:13,
from source/calculators/simpsoneven.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpsoneven.h:13,
from source/calculators/simpsoneven.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SimpsonEven::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/spearman.h:15,
from source/calculators/spearman.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/spearman.h:15,
from source/calculators/spearman.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Spearman::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchord.h:14,
from source/calculators/structchord.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchord.h:14,
from source/calculators/structchord.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannoneven.h:13,
from source/calculators/shannoneven.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannoneven.h:13,
from source/calculators/shannoneven.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput ShannonEven::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedace.h:15,
from source/calculators/sharedace.cpp:11:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedace.h:15,
from source/calculators/sharedace.cpp:11:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedAce::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmorisitahorn.h:13,
from source/calculators/sharedmorisitahorn.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmorisitahorn.h:13,
from source/calculators/sharedmorisitahorn.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MorHorn::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bstick.h:11,
from source/calculators/bstick.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bstick.h:11,
from source/calculators/bstick.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput BStick::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjackknife.h:13,
from source/calculators/sharedjackknife.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjackknife.h:13,
from source/calculators/sharedjackknife.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedJackknife::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/uvest.o source/calculators/uvest.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorabund.h:16,
from source/calculators/sharedsorabund.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorabund.h:16,
from source/calculators/sharedsorabund.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SorAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedanderbergs.h:12,
from source/calculators/sharedanderbergs.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedanderbergs.h:12,
from source/calculators/sharedanderbergs.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Anderberg::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/odum.h:15,
from source/calculators/odum.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/odum.h:15,
from source/calculators/odum.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Odum::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'EstOutput UVEst::getUVest(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structpearson.h:15,
from source/calculators/structpearson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structpearson.h:15,
from source/calculators/structpearson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/heip.h:13,
from source/calculators/heip.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/heip.h:13,
from source/calculators/heip.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Heip::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/ace.h:16,
from source/calculators/ace.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/ace.h:16,
from source/calculators/ace.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Ace::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjsd.h:12,
from source/calculators/sharedjsd.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjsd.h:12,
from source/calculators/sharedjsd.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput JSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/unweighted.o source/calculators/unweighted.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memeuclidean.h:14,
from source/calculators/memeuclidean.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memeuclidean.h:14,
from source/calculators/memeuclidean.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchi2.h:15,
from source/calculators/memchi2.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchi2.h:15,
from source/calculators/memchi2.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchi2.h:14,
from source/calculators/structchi2.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchi2.h:14,
from source/calculators/structchi2.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/boneh.h:13,
from source/calculators/boneh.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/boneh.h:13,
from source/calculators/boneh.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Boneh::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/soergel.o source/calculators/soergel.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorest.h:16,
from source/calculators/sharedsorest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorest.h:16,
from source/calculators/sharedsorest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SorEst::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/speciesprofile.h:14,
from source/calculators/speciesprofile.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/speciesprofile.h:14,
from source/calculators/speciesprofile.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SpeciesProfile::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/soergel.h:14,
from source/calculators/soergel.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/soergel.h:14,
from source/calculators/soergel.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Soergel::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjclass.h:15,
from source/calculators/sharedjclass.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjclass.h:15,
from source/calculators/sharedjclass.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Jclass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynskicody.h:14,
from source/calculators/sharedkulczynskicody.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynskicody.h:14,
from source/calculators/sharedkulczynskicody.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput KulczynskiCody::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmarczewski.h:13,
from source/calculators/sharedmarczewski.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structkulczynski.h:14,
from source/calculators/structkulczynski.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmarczewski.h:13,
from source/calculators/sharedmarczewski.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedMarczewski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structkulczynski.h:14,
from source/calculators/structkulczynski.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructKulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedrjsd.h:12,
from source/calculators/sharedrjsd.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedrjsd.h:12,
from source/calculators/sharedrjsd.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput RJSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedbraycurtis.h:11,
from source/calculators/sharedbraycurtis.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedbraycurtis.h:11,
from source/calculators/sharedbraycurtis.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput BrayCurtis::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/calculator.o source/calculators/calculator.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedlennon.h:14,
from source/calculators/sharedlennon.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedlennon.h:14,
from source/calculators/sharedlennon.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Lennon::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hellinger.h:14,
from source/calculators/hellinger.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hellinger.h:14,
from source/calculators/hellinger.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Hellinger::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedochiai.h:12,
from source/calculators/sharedochiai.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedochiai.h:12,
from source/calculators/sharedochiai.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Ochiai::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/bellerophon.o source/chimera/bellerophon.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double Perseus::basicPairwiseAlignSeqs(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, pwModel)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'double Perseus::modeledPairwiseAlignSeqs(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/ccode.o source/chimera/ccode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimerarealigner.o source/chimera/chimerarealigner.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp
source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
source/clearcut/dmat.cpp: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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int CooccurrenceCommand::getCooccurrence(std::vector<SharedRAbundVector*>&, std::ofstream&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp
source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
source/commands/distancecommand.cpp:338:45: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/matrixoutputcommand.o source/commands/matrixoutputcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MatrixOutputCommand::process(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treegroupscommand.o source/commands/treegroupscommand.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, std::vector<int> >; _KeyOfValue = std::_Select1st<std::pair<const double, std::vector<int> > >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, std::vector<int> > >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/c++/6/bits/stl_map.h: In member function 'int LibShuffCommand::printCoverageFile()':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotulabelscommand.o source/commands/getotulabelscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int TreeGroupCommand::process(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp
source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::__cxx11::string)':
source/commands/makefilecommand.cpp:370:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(findCommand.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parselistscommand.o source/commands/parselistscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int GetCoreMicroBiomeCommand::createTable(std::vector<SharedRAbundFloatVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracWeightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, double>; _KeyOfValue = std::_Select1st<std::pair<const double, double> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_map.h: In member function 'void UnifracWeightedCommand::calculateFreqsCumuls()':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'void UnifracWeightedCommand::printWeightedFile()':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'int UnifracWeightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual int UnifracWeightedCommand::execute()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
source/commands/clustercommand.cpp:609:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int HeatMapSimCommand::runCommandDist()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracUnweightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual int UnifracUnweightedCommand::execute()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int RareFactSharedCommand::subsampleLookup(std::vector<SharedRAbundVector*>&, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotulabelscommand.o source/commands/removeotulabelscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/6/bits/stl_tree.h:1928:5: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'std::vector<std::vector<double> > AnosimCommand::convertToRanks(std::vector<std::vector<double> >)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/catchallcommand.o source/commands/catchallcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp
source/commands/catchallcommand.cpp: In member function 'virtual int CatchAllCommand::execute()':
source/commands/catchallcommand.cpp:332:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
source/commands/catchallcommand.cpp:395:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
source/commands/catchallcommand.cpp:480:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MakeLookupCommand::alignFlowGrams(std::vector<double>&, std::vector<double>&, double, std::vector<std::vector<double> >, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual int MakeLookupCommand::execute()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int SummarySharedCommand::process(std::vector<SharedRAbundVector*>, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int NMDSCommand::normalizeConfiguration(std::vector<std::vector<double> >&, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::nmdsCalc(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, double&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::readAxes(std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp
source/commands/chimeravsearchcommand.cpp: In member function 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)':
source/commands/chimeravsearchcommand.cpp:1363:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp
In file included from /usr/include/string.h:635:0,
from /usr/include/boost/range/detail/implementation_help.hpp:18,
from /usr/include/boost/range/end.hpp:24,
from /usr/include/boost/range/functions.hpp:19,
from /usr/include/boost/range/iterator_range_core.hpp:38,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/pipeline.hpp:18,
from /usr/include/boost/iostreams/detail/push.hpp:22,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
In function 'char* strncat(char*, const char*, size_t)',
inlined from 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimeravsearchcommand.cpp:1231:64:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:71: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^
In function 'char* strncat(char*, const char*, size_t)',
inlined from 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimeravsearchcommand.cpp:1312:70:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:71: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runKruskalWallis(std::vector<SharedRAbundFloatVector*>&, DesignMap&)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runWilcoxon(std::vector<SharedRAbundFloatVector*>&, DesignMap&, std::map<int, double>, std::map<std::__cxx11::basic_string<char>, std::set<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'int LefseCommand::printResults(std::vector<std::vector<double> >, std::map<int, double>, std::map<int, double>, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LefseCommand::lda(std::vector<std::vector<double> >&, std::vector<int>, std::map<int, std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LefseCommand::getMeans(std::vector<SharedRAbundFloatVector*>&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::map<int, double> LefseCommand::testLDA(std::vector<SharedRAbundFloatVector*>&, std::map<int, double>, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/secondarystructurecommand.o source/commands/secondarystructurecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int PCACommand::process(std::vector<SharedRAbundFloatVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/seqsummarycommand.h:13,
from source/commands/seqsummarycommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = int; _Val = std::pair<const int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const int, long long int> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, long long int> >]':
/usr/include/c++/6/bits/stl_tree.h:1928:5: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, long long int> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MetaStatsCommand::driver(long long unsigned int, long long unsigned int, std::vector<SharedRAbundVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int CorrAxesCommand::calcSpearman(std::map<std::__cxx11::basic_string<char>, std::vector<float> >&, std::ofstream&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int ShhherCommand::getUniques(int, int, std::vector<short int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<short int>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void ShhherCommand::getJointLookUp()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void ShhherCommand::calcNewDistances(int, int, std::vector<int>&, std::vector<double>&, std::vector<double>&, std::vector<short int>&, std::vector<int>&, std::vector<std::vector<int> >&, std::vector<double>&, std::vector<std::vector<int> >&, std::vector<int>&, std::vector<int>&, std::vector<short int>&, std::vector<short int>&, int, std::vector<int>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sharedcommand.o source/commands/sharedcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(std::vector<SharedRAbundVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::processDriver(std::vector<SharedRAbundVector*>&, std::vector<int>&, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Distance = int; _Tp = summaryData; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Distance = int; _Tp = summaryData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'int GetMetaCommunityCommand::generateSummaryFile(int, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double HomovaCommand::calcBValue(std::map<std::__cxx11::basic_string<char>, std::vector<int> >, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyrfsharedcommand.o source/commands/classifyrfsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp
source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
source/commands/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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
source/commands/chimerauchimecommand.cpp: In member function 'int ChimeraUchimeCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)':
source/commands/chimerauchimecommand.cpp:1501:32: 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:635:0,
from /usr/include/boost/range/detail/implementation_help.hpp:18,
from /usr/include/boost/range/end.hpp:24,
from /usr/include/boost/range/functions.hpp:19,
from /usr/include/boost/range/iterator_range_core.hpp:38,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/pipeline.hpp:18,
from /usr/include/boost/iostreams/detail/push.hpp:22,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
In function 'char* strcpy(char*, const char*)',
inlined from 'int ChimeraUchimeCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimerauchimecommand.cpp:1472:28:
/usr/include/arm-linux-gnueabihf/bits/string3.h:110:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer
return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp
source/commands/clustersplitcommand.cpp: In member function 'int ClusterSplitCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double)':
source/commands/clustersplitcommand.cpp:1605:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, int>; _KeyOfValue = std::_Select1st<std::pair<const double, int> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, int> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, int> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
source/commands/pairwiseseqscommand.cpp:342:46: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp
/usr/include/c++/6/bits/stl_algo.h: In member function 'std::map<double, int> ClusterSplitCommand::completeListFile(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, std::set<std::__cxx11::basic_string<char> >&, ListVector*&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, int> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, int> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int CommunityTypeFinder::findkMeans()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'double CommunityTypeFinder::rMedoid(std::vector<std::vector<double> >, std::vector<std::vector<double> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > CommunityTypeFinder::calcCenters(std::vector<std::vector<double> >&, std::map<int, int>, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual std::vector<double> CommunityTypeFinder::calcSilhouettes(std::vector<std::vector<double> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/qFinderDMM.h:12,
from source/communitytype/qFinderDMM.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/qFinderDMM.h:12,
from source/communitytype/qFinderDMM.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void qFinderDMM::negativeLogDerivEvidenceLambdaPi(std::vector<double>&, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int qFinderDMM::lineMinimizeFletcher(std::vector<double>&, std::vector<double>&, double, double, double, double&, double&, std::vector<double>&, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::__cxx11::string, std::__cxx11::string)':
source/datastructures/blastalign.cpp:62:30: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual std::vector<int> DistanceDB::findClosestSequences(Sequence*, int)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/database.o source/datastructures/database.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedsabundvector.o source/datastructures/sharedsabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int)':
source/datastructures/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());
^
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int, int)':
source/datastructures/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());
^
source/datastructures/blastdb.cpp: In member function 'virtual void BlastDB::generateDB()':
source/datastructures/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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permute_and_calc_ts(std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permuted_pvalues(std::vector<std::vector<double> >&, std::vector<double>&, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MothurMetastats::runMetastats(std::__cxx11::string, std::vector<std::vector<double> >&, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/forest.o source/randomforest/forest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Distance = int; _Tp = std::pair<int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual int RandomForest::calcForrestVariableImportance(std::__cxx11::string)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp
source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)':
source/read/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());
^
source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(CountTable*)':
source/read/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());
^
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'int ReadBlast::read(NameAssignment*)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatphylip.o source/read/formatphylip.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp
source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
source/read/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());
^
source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)':
source/read/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());
^
cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
+ CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit'
+ ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o'
+ rm -f '*.o' mk.stdout mk.stderr tmp.stderr
+ for CPPName in $CPPNames
+ echo addtargets2
addtargets2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 addtargets2.cpp -o addtargets2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alignchime
alignchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchime.cpp -o alignchime.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alignchimel
alignchimel
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchimel.cpp -o alignchimel.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alnparams
alnparams
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alnparams.cpp -o alnparams.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alpha
alpha
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha.cpp -o alpha.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alpha2
alpha2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha2.cpp -o alpha2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo fractid
fractid
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 fractid.cpp -o fractid.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo getparents
getparents
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 getparents.cpp -o getparents.o
In file included from /usr/include/c++/6/map:60:0,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/6/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo globalalign2
globalalign2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 globalalign2.cpp -o globalalign2.o
/usr/include/c++/6/bits/stl_map.h: In member function 'void SmoTrainer::assignNumericLabels(std::vector<double>&, const LabeledObservationVector&, NumericClassToLabel&)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo make3way
make3way
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 make3way.cpp -o make3way.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo mx
mx
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 mx.cpp -o mx.o
/usr/include/c++/6/bits/stl_map.h: In constructor 'ParameterSetBuilder::ParameterSetBuilder(const ParameterRangeMap&)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo myutils
myutils
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 myutils.cpp -o myutils.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo path
path
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 path.cpp -o path.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo searchchime
searchchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 searchchime.cpp -o searchchime.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo seqdb
seqdb
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 seqdb.cpp -o seqdb.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo setnucmx
setnucmx
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 setnucmx.cpp -o setnucmx.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo sfasta
sfasta
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 sfasta.cpp -o sfasta.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo tracebackbit
tracebackbit
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 tracebackbit.cpp -o tracebackbit.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo uchime_main
uchime_main
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 uchime_main.cpp -o uchime_main.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo usort
usort
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 usort.cpp -o usort.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo viterbifast
viterbifast
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 viterbifast.cpp -o viterbifast.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo writechhit
writechhit
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 writechhit.cpp -o writechhit.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ LINK_OPTS=
+ g++ -g -o uchime addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o -Wl,-z,relro -Wl,-z,now -std=c++0x -L '"\"Enter_your_boost_library_path_here\""' -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ ls -lh uchime
-rwxrwxr-x 1 buildd buildd 2.4M Jun 22 21:00 uchime
+ sum uchime
27553 2371
g++ -Wl,-z,relro -Wl,-z,now -std=c++0x -L "\"Enter_your_boost_library_path_here\"" -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/randomnumber.o source/gotohoverlap.o source/validparameter.o source/opticluster.o source/nast.o source/averagelinkage.o source/mothurout.o source/completelinkage.o source/collect.o source/seqnoise.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/vsearchfileparser.o source/refchimeratest.o source/slibshuff.o source/trialSwap2.o source/sharedutilities.o source/consensus.o source/nastreport.o source/fileoutput.o source/cluster.o source/needlemanoverlap.o source/myseqdist.o source/subsample.o source/commandfactory.o source/rarecalc.o source/heatmap.o source/rarefact.o source/weightedlinkage.o source/wilcox.o source/progress.o source/linearalgebra.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/engine.o source/mothur.o source/dlibshuff.o source/heatmapsim.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/noalign.o source/overlap.o source/calculators/sharedthetayc.o source/calculators/coverage.o source/calculators/invsimpson.o source/calculators/sharedjest.o source/calculators/sharedkulczynski.o source/calculators/qstat.o source/calculators/bergerparker.o source/calculators/sharedsobs.o source/calculators/sharedsobscollectsummary.o source/calculators/shen.o source/calculators/canberra.o source/calculators/parsimony.o source/calculators/gower.o source/calculators/smithwilson.o source/calculators/simpson.o source/calculators/mempearson.o source/calculators/logsd.o source/calculators/goodscoverage.o source/calculators/memchord.o source/calculators/solow.o source/calculators/manhattan.o source/calculators/geom.o source/calculators/jackknife.o source/calculators/whittaker.o source/calculators/weighted.o source/calculators/efron.o source/calculators/bootstrap.o source/calculators/hamming.o source/calculators/sharedkstest.o source/calculators/sharedthetan.o source/calculators/sharedsorclass.o source/calculators/shannon.o source/calculators/prng.o source/calculators/shannonrange.o source/calculators/npshannon.o source/calculators/structeuclidean.o source/calculators/sharedchao1.o source/calculators/sharedjabund.o source/calculators/chao1.o source/calculators/simpsoneven.o source/calculators/spearman.o source/calculators/structchord.o source/calculators/shannoneven.o source/calculators/sharedace.o source/calculators/sharedmorisitahorn.o source/calculators/bstick.o source/calculators/sharedjackknife.o source/calculators/sharedsorabund.o source/calculators/sharedanderbergs.o source/calculators/odum.o source/calculators/uvest.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedjsd.o source/calculators/memeuclidean.o source/calculators/memchi2.o source/calculators/structchi2.o source/calculators/unweighted.o source/calculators/boneh.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedjclass.o source/calculators/sharedkulczynskicody.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/sharedrjsd.o source/calculators/sharedbraycurtis.o source/calculators/hellinger.o source/calculators/sharedlennon.o source/calculators/sharedochiai.o source/calculators/calculator.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimerarealigner.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/cmdargs.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/clearcut/getopt_long.o source/commands/getcurrentcommand.o source/commands/collectcommand.o source/commands/cooccurrencecommand.o source/commands/clearcutcommand.o source/commands/listseqscommand.o source/commands/clusterdoturcommand.o source/commands/distancecommand.o source/commands/binsequencecommand.o source/commands/quitcommand.o source/commands/matrixoutputcommand.o source/commands/subsamplecommand.o source/commands/indicatorcommand.o source/commands/removegroupscommand.o source/commands/libshuffcommand.o source/commands/clusterfragmentscommand.o source/commands/treegroupscommand.o source/commands/kruskalwalliscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/mimarksattributescommand.o source/commands/renameseqscommand.o source/commands/makegroupcommand.o source/commands/removerarecommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/splitgroupscommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/rarefactsharedcommand.o source/commands/aligncommand.o source/commands/chimerabellerophoncommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/venncommand.o source/commands/getsharedotucommand.o source/commands/classifyseqscommand.o source/commands/removeotulabelscommand.o source/commands/screenseqscommand.o source/commands/setdircommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/mgclustercommand.o source/commands/anosimcommand.o source/commands/sffmultiplecommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getrabundcommand.o source/commands/catchallcommand.o source/commands/getgroupscommand.o source/commands/heatmapcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/mergetaxsummarycommand.o source/commands/makelookupcommand.o source/commands/rarefactcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/trimseqscommand.o source/commands/listotulabelscommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/phylodiversitycommand.o source/commands/makelefsecommand.o source/commands/filtersharedcommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/pcacommand.o source/commands/seqsummarycommand.o source/commands/metastatscommand.o source/commands/chimeraslayercommand.o source/commands/chopseqscommand.o source/commands/sffinfocommand.o source/commands/makebiomcommand.o source/commands/seqerrorcommand.o source/commands/getlistcountcommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/corraxescommand.o source/commands/preclustercommand.o source/commands/shhhercommand.o source/commands/chimeraccodecommand.o source/commands/classifytreecommand.o source/commands/getseqscommand.o source/commands/collectsharedcommand.o source/commands/deuniqueseqscommand.o source/commands/getmimarkspackagecommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/setseedcommand.o source/commands/sharedcommand.o source/commands/makecontigscommand.o source/commands/mergefilecommand.o source/commands/homovacommand.o source/commands/getcommandinfocommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/helpcommand.o source/commands/mergegroupscommand.o source/commands/pcrseqscommand.o source/commands/systemcommand.o source/commands/chimeraperseuscommand.o source/commands/deuniquetreecommand.o source/commands/makefastqcommand.o source/commands/classifyotucommand.o source/commands/createdatabasecommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/removedistscommand.o source/commands/parsefastaqcommand.o source/commands/amovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/getgroupcommand.o source/commands/chimeracheckcommand.o source/commands/clustersplitcommand.o source/commands/pairwiseseqscommand.o source/commands/nocommands.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/setlogfilecommand.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/newcommandtemplate.o source/commands/pcoacommand.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/commands/reversecommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/sharedlistvector.o source/datastructures/optimatrix.o source/datastructures/fastamap.o source/datastructures/distancedb.o source/datastructures/alignment.o source/datastructures/kmer.o source/datastructures/sharedordervector.o source/datastructures/nameassignment.o source/datastructures/fastqread.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/tree.o source/datastructures/oligos.o source/datastructures/listvector.o source/datastructures/kmeralign.o source/datastructures/sparsematrix.o source/datastructures/alignmentdb.o source/datastructures/fullmatrix.o source/datastructures/blastalign.o source/datastructures/treenode.o source/datastructures/alignmentcell.o source/datastructures/suffixdb.o source/datastructures/sabundvector.o source/datastructures/rabundvector.o source/datastructures/suffixtree.o source/datastructures/qualityscores.o source/datastructures/groupmap.o source/datastructures/sequenceparser.o source/datastructures/sparsedistancematrix.o source/datastructures/sequencecountparser.o source/datastructures/counttable.o source/datastructures/treemap.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/ordervector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/database.o source/datastructures/designmap.o source/datastructures/sharedsabundvector.o source/datastructures/reportfile.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/decisiontree.o source/randomforest/abstractdecisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/readblast.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readcolumn.o source/read/readcluster.o source/read/readtree.o source/read/formatphylip.o source/read/treereader.o source/read/readphylip.o source/svm/svm.o -lreadline -lboost_iostreams -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
mv mothur mothur-mpi
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -- 64BIT_VERSION=no USEMPI=no
make -j4 64BIT_VERSION=no USEMPI=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp
source/mothur.cpp: In function 'int main(int, char**)':
source/mothur.cpp:46:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("clear");
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nastreport.o source/nastreport.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engine.o source/engine.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/gotohoverlap.o source/gotohoverlap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmap.o source/heatmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/sharedutilities.o source/sharedutilities.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'double SLibshuff::sCalculate(int, int)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int seqNoise::countDiffs(std::vector<int>, std::vector<int>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/dlibshuff.o source/dlibshuff.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double RefChimeraTest::alignQueryToReferences(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, double&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/progress.o source/progress.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/subsample.o source/subsample.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmapsim.o source/heatmapsim.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/collectorscurvedata.h:4,
from source/collect.h:4,
from source/collect.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/venn.h:12,
from source/venn.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/venn.h:12,
from source/venn.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/collectorscurvedata.h:4,
from source/collect.h:4,
from source/collect.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double TrialSwap2::calc_c_score(std::vector<std::vector<int> >&, std::vector<int>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomnumber.o source/randomnumber.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/consensus.o source/consensus.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/datavector.hpp:5,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual void RareDisplay::close()':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double correctDist::getDist(std::vector<int>&, std::vector<int>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandfactory.o source/commandfactory.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarecalc.o source/rarecalc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothurout.o source/mothurout.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp
source/mothurout.cpp: In member function 'bool MothurOut::mkDir(std::__cxx11::string&)':
source/mothurout.cpp:1135:45: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(makeDirectoryCommand.c_str());
^
source/mothurout.cpp: In member function 'int MothurOut::renameFile(std::__cxx11::string, std::__cxx11::string)':
source/mothurout.cpp:1633:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
source/mothurout.cpp:1637:26: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
source/mothurout.cpp: In member function 'std::__cxx11::string MothurOut::sortFile(std::__cxx11::string, std::__cxx11::string)':
source/mothurout.cpp:1844:27: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'double MothurOut::median(std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'std::vector<std::vector<seqDist> > MothurOut::getAverages(std::vector<std::vector<std::vector<seqDist> > >&, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/completelinkage.o source/completelinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::lda(std::vector<std::vector<double> >&, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::vector<double> >&, bool&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/coverage.o source/calculators/coverage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp
source/venn.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > Venn::getPic(std::vector<SharedRAbundVector*>, std::vector<Calculator*>)':
source/venn.cpp:77:16: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
^~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/coverage.h:13,
from source/calculators/coverage.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/coverage.h:13,
from source/calculators/coverage.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Coverage::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/invsimpson.h:15,
from source/calculators/invsimpson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/invsimpson.h:15,
from source/calculators/invsimpson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput InvSimpson::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/qstat.o source/calculators/qstat.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedjest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedjest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Jest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynski.h:13,
from source/calculators/sharedkulczynski.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynski.h:13,
from source/calculators/sharedkulczynski.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Kulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/qstat.h:11,
from source/calculators/qstat.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/qstat.h:11,
from source/calculators/qstat.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput QStat::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bergerparker.h:12,
from source/calculators/bergerparker.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bergerparker.h:12,
from source/calculators/bergerparker.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput BergerParker::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobs.h:16,
from source/calculators/sharedsobs.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobs.h:16,
from source/calculators/sharedsobs.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobscollectsummary.h:15,
from source/calculators/sharedsobscollectsummary.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobscollectsummary.h:15,
from source/calculators/sharedsobscollectsummary.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>, std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shen.h:13,
from source/calculators/shen.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shen.h:13,
from source/calculators/shen.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Shen::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/canberra.h:15,
from source/calculators/canberra.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/canberra.h:15,
from source/calculators/canberra.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Canberra::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/gower.h:14,
from source/calculators/gower.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/gower.h:14,
from source/calculators/gower.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Gower::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/smithwilson.h:13,
from source/calculators/smithwilson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/smithwilson.h:13,
from source/calculators/smithwilson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SmithWilson::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpson.h:16,
from source/calculators/simpson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpson.h:16,
from source/calculators/simpson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Simpson::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/calculator.o source/calculators/calculator.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/mempearson.h:15,
from source/calculators/mempearson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/mempearson.h:15,
from source/calculators/mempearson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/logsd.h:12,
from source/calculators/logsd.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/logsd.h:12,
from source/calculators/logsd.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput LogSD::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/goodscoverage.h:12,
from source/calculators/goodscoverage.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/goodscoverage.h:12,
from source/calculators/goodscoverage.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput GoodsCoverage::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/geom.o source/calculators/geom.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchord.h:14,
from source/calculators/memchord.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchord.h:14,
from source/calculators/memchord.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/solow.h:13,
from source/calculators/solow.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/solow.h:13,
from source/calculators/solow.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Solow::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/manhattan.h:14,
from source/calculators/manhattan.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/manhattan.h:14,
from source/calculators/manhattan.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Manhattan::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/whittaker.o source/calculators/whittaker.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/weighted.o source/calculators/weighted.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/geom.h:12,
from source/calculators/geom.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/geom.h:12,
from source/calculators/geom.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Geom::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/jackknife.h:13,
from source/calculators/jackknife.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/jackknife.h:13,
from source/calculators/jackknife.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Jackknife::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/efron.h:13,
from source/calculators/efron.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/efron.h:13,
from source/calculators/efron.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Efron::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/6/bits/stl_map.h: In member function 'EstOutput Weighted::driver(Tree*, std::vector<std::vector<std::__cxx11::basic_string<char> > >, int, int, CountTable*)':
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual EstOutput Weighted::getValues(Tree*, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:502:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bootstrap.h:15,
from source/calculators/bootstrap.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bootstrap.h:15,
from source/calculators/bootstrap.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Bootstrap::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hamming.h:15,
from source/calculators/hamming.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hamming.h:15,
from source/calculators/hamming.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Hamming::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkstest.h:11,
from source/calculators/sharedkstest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkstest.h:11,
from source/calculators/sharedkstest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput KSTest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/prng.o source/calculators/prng.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetan.h:16,
from source/calculators/sharedthetan.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetan.h:16,
from source/calculators/sharedthetan.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput ThetaN::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorclass.h:16,
from source/calculators/sharedsorclass.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorclass.h:16,
from source/calculators/sharedsorclass.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SorClass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannon.h:16,
from source/calculators/shannon.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannon.h:16,
from source/calculators/shannon.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Shannon::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput RangeShannon::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedchao1.o source/calculators/sharedchao1.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/npshannon.h:16,
from source/calculators/npshannon.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/npshannon.h:16,
from source/calculators/npshannon.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NPShannon::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structeuclidean.h:15,
from source/calculators/structeuclidean.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structeuclidean.h:15,
from source/calculators/structeuclidean.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjabund.h:16,
from source/calculators/sharedjabund.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjabund.h:16,
from source/calculators/sharedjabund.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput JAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedchao1.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedchao1.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedChao1::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchord.o source/calculators/structchord.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/chao1.h:12,
from source/calculators/chao1.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/chao1.h:12,
from source/calculators/chao1.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Chao1::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpsoneven.h:13,
from source/calculators/simpsoneven.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/simpsoneven.h:13,
from source/calculators/simpsoneven.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SimpsonEven::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/spearman.h:15,
from source/calculators/spearman.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/spearman.h:15,
from source/calculators/spearman.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Spearman::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchord.h:14,
from source/calculators/structchord.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchord.h:14,
from source/calculators/structchord.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannoneven.h:13,
from source/calculators/shannoneven.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/shannoneven.h:13,
from source/calculators/shannoneven.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput ShannonEven::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedace.h:15,
from source/calculators/sharedace.cpp:11:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedace.h:15,
from source/calculators/sharedace.cpp:11:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedAce::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmorisitahorn.h:13,
from source/calculators/sharedmorisitahorn.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmorisitahorn.h:13,
from source/calculators/sharedmorisitahorn.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MorHorn::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bstick.h:11,
from source/calculators/bstick.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/bstick.h:11,
from source/calculators/bstick.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput BStick::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjackknife.h:13,
from source/calculators/sharedjackknife.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjackknife.h:13,
from source/calculators/sharedjackknife.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedJackknife::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/uvest.o source/calculators/uvest.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorabund.h:16,
from source/calculators/sharedsorabund.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorabund.h:16,
from source/calculators/sharedsorabund.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SorAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedanderbergs.h:12,
from source/calculators/sharedanderbergs.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedanderbergs.h:12,
from source/calculators/sharedanderbergs.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Anderberg::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/odum.h:15,
from source/calculators/odum.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/odum.h:15,
from source/calculators/odum.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Odum::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'EstOutput UVEst::getUVest(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structpearson.h:15,
from source/calculators/structpearson.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structpearson.h:15,
from source/calculators/structpearson.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/heip.h:13,
from source/calculators/heip.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/heip.h:13,
from source/calculators/heip.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Heip::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/ace.h:16,
from source/calculators/ace.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/ace.h:16,
from source/calculators/ace.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Ace::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjsd.h:12,
from source/calculators/sharedjsd.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjsd.h:12,
from source/calculators/sharedjsd.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput JSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/unweighted.o source/calculators/unweighted.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memeuclidean.h:14,
from source/calculators/memeuclidean.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memeuclidean.h:14,
from source/calculators/memeuclidean.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchi2.h:15,
from source/calculators/memchi2.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/memchi2.h:15,
from source/calculators/memchi2.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput MemChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchi2.h:14,
from source/calculators/structchi2.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structchi2.h:14,
from source/calculators/structchi2.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/boneh.h:13,
from source/calculators/boneh.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/boneh.h:13,
from source/calculators/boneh.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Boneh::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/soergel.o source/calculators/soergel.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorest.h:16,
from source/calculators/sharedsorest.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorest.h:16,
from source/calculators/sharedsorest.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SorEst::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/speciesprofile.h:14,
from source/calculators/speciesprofile.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/speciesprofile.h:14,
from source/calculators/speciesprofile.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SpeciesProfile::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/soergel.h:14,
from source/calculators/soergel.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/soergel.h:14,
from source/calculators/soergel.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Soergel::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjclass.h:15,
from source/calculators/sharedjclass.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedjclass.h:15,
from source/calculators/sharedjclass.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Jclass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynskicody.h:14,
from source/calculators/sharedkulczynskicody.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynskicody.h:14,
from source/calculators/sharedkulczynskicody.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput KulczynskiCody::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmarczewski.h:13,
from source/calculators/sharedmarczewski.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedmarczewski.h:13,
from source/calculators/sharedmarczewski.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedMarczewski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structkulczynski.h:14,
from source/calculators/structkulczynski.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/structkulczynski.h:14,
from source/calculators/structkulczynski.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput StructKulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedrjsd.h:12,
from source/calculators/sharedrjsd.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedrjsd.h:12,
from source/calculators/sharedrjsd.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput RJSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedbraycurtis.h:11,
from source/calculators/sharedbraycurtis.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedbraycurtis.h:11,
from source/calculators/sharedbraycurtis.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput BrayCurtis::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hellinger.h:14,
from source/calculators/hellinger.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/hellinger.h:14,
from source/calculators/hellinger.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Hellinger::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedlennon.h:14,
from source/calculators/sharedlennon.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedlennon.h:14,
from source/calculators/sharedlennon.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Lennon::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedochiai.h:12,
from source/calculators/sharedochiai.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedochiai.h:12,
from source/calculators/sharedochiai.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Ochiai::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/bellerophon.o source/chimera/bellerophon.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetayc.h:16,
from source/calculators/sharedthetayc.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetayc.h:16,
from source/calculators/sharedthetayc.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput ThetaYC::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double Perseus::basicPairwiseAlignSeqs(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, pwModel)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'double Perseus::modeledPairwiseAlignSeqs(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/ccode.o source/chimera/ccode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimerarealigner.o source/chimera/chimerarealigner.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp
source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
source/clearcut/dmat.cpp: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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int CooccurrenceCommand::getCooccurrence(std::vector<SharedRAbundVector*>&, std::ofstream&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp
source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
source/commands/distancecommand.cpp:338:45: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/matrixoutputcommand.o source/commands/matrixoutputcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MatrixOutputCommand::process(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treegroupscommand.o source/commands/treegroupscommand.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, std::vector<int> >; _KeyOfValue = std::_Select1st<std::pair<const double, std::vector<int> > >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, std::vector<int> > >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/c++/6/bits/stl_map.h: In member function 'int LibShuffCommand::printCoverageFile()':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotulabelscommand.o source/commands/getotulabelscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp
/usr/include/c++/6/bits/stl_vector.h: In member function 'int TreeGroupCommand::process(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp
source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::__cxx11::string)':
source/commands/makefilecommand.cpp:370:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(findCommand.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parselistscommand.o source/commands/parselistscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int GetCoreMicroBiomeCommand::createTable(std::vector<SharedRAbundFloatVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracWeightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, double>; _KeyOfValue = std::_Select1st<std::pair<const double, double> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_map.h: In member function 'void UnifracWeightedCommand::calculateFreqsCumuls()':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'void UnifracWeightedCommand::printWeightedFile()':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'int UnifracWeightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual int UnifracWeightedCommand::execute()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
source/commands/clustercommand.cpp:609:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int HeatMapSimCommand::runCommandDist()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracUnweightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual int UnifracUnweightedCommand::execute()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int RareFactSharedCommand::subsampleLookup(std::vector<SharedRAbundVector*>&, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotulabelscommand.o source/commands/removeotulabelscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/6/bits/stl_tree.h:1928:5: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'std::vector<std::vector<double> > AnosimCommand::convertToRanks(std::vector<std::vector<double> >)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/catchallcommand.o source/commands/catchallcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp
source/commands/catchallcommand.cpp: In member function 'virtual int CatchAllCommand::execute()':
source/commands/catchallcommand.cpp:332:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
source/commands/catchallcommand.cpp:395:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
source/commands/catchallcommand.cpp:480:36: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MakeLookupCommand::alignFlowGrams(std::vector<double>&, std::vector<double>&, double, std::vector<std::vector<double> >, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual int MakeLookupCommand::execute()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int SummarySharedCommand::process(std::vector<SharedRAbundVector*>, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int NMDSCommand::normalizeConfiguration(std::vector<std::vector<double> >&, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::nmdsCalc(std::vector<std::vector<double> >&, std::vector<std::vector<double> >&, double&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::readAxes(std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp
source/commands/chimeravsearchcommand.cpp: In member function 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)':
source/commands/chimeravsearchcommand.cpp:1363:38: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp
In file included from /usr/include/string.h:635:0,
from /usr/include/boost/range/detail/implementation_help.hpp:18,
from /usr/include/boost/range/end.hpp:24,
from /usr/include/boost/range/functions.hpp:19,
from /usr/include/boost/range/iterator_range_core.hpp:38,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/pipeline.hpp:18,
from /usr/include/boost/iostreams/detail/push.hpp:22,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
In function 'char* strncat(char*, const char*, size_t)',
inlined from 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimeravsearchcommand.cpp:1231:64:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:71: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^
In function 'char* strncat(char*, const char*, size_t)',
inlined from 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimeravsearchcommand.cpp:1312:70:
/usr/include/arm-linux-gnueabihf/bits/string3.h:156:71: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runKruskalWallis(std::vector<SharedRAbundFloatVector*>&, DesignMap&)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runWilcoxon(std::vector<SharedRAbundFloatVector*>&, DesignMap&, std::map<int, double>, std::map<std::__cxx11::basic_string<char>, std::set<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'int LefseCommand::printResults(std::vector<std::vector<double> >, std::map<int, double>, std::map<int, double>, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LefseCommand::lda(std::vector<std::vector<double> >&, std::vector<int>, std::map<int, std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LefseCommand::getMeans(std::vector<SharedRAbundFloatVector*>&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::map<int, double> LefseCommand::testLDA(std::vector<SharedRAbundFloatVector*>&, std::map<int, double>, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/secondarystructurecommand.o source/commands/secondarystructurecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int PCACommand::process(std::vector<SharedRAbundFloatVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp
In file included from /usr/include/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/seqsummarycommand.h:13,
from source/commands/seqsummarycommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = int; _Val = std::pair<const int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const int, long long int> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, long long int> >]':
/usr/include/c++/6/bits/stl_tree.h:1928:5: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, long long int> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MetaStatsCommand::driver(long long unsigned int, long long unsigned int, std::vector<SharedRAbundVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int CorrAxesCommand::calcSpearman(std::map<std::__cxx11::basic_string<char>, std::vector<float> >&, std::ofstream&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int ShhherCommand::getUniques(int, int, std::vector<short int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<int>&, std::vector<double>&, std::vector<short int>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void ShhherCommand::getJointLookUp()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void ShhherCommand::calcNewDistances(int, int, std::vector<int>&, std::vector<double>&, std::vector<double>&, std::vector<short int>&, std::vector<int>&, std::vector<std::vector<int> >&, std::vector<double>&, std::vector<std::vector<int> >&, std::vector<int>&, std::vector<int>&, std::vector<short int>&, std::vector<short int>&, int, std::vector<int>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sharedcommand.o source/commands/sharedcommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(std::vector<SharedRAbundVector*>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::processDriver(std::vector<SharedRAbundVector*>&, std::vector<int>&, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Distance = int; _Tp = summaryData; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Distance = int; _Tp = summaryData; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'int GetMetaCommunityCommand::generateSummaryFile(int, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'double HomovaCommand::calcBValue(std::map<std::__cxx11::basic_string<char>, std::vector<int> >, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyrfsharedcommand.o source/commands/classifyrfsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp
source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
source/commands/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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp
source/commands/chimerauchimecommand.cpp: In member function 'int ChimeraUchimeCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)':
source/commands/chimerauchimecommand.cpp:1501:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
In file included from /usr/include/string.h:635:0,
from /usr/include/boost/range/detail/implementation_help.hpp:18,
from /usr/include/boost/range/end.hpp:24,
from /usr/include/boost/range/functions.hpp:19,
from /usr/include/boost/range/iterator_range_core.hpp:38,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/pipeline.hpp:18,
from /usr/include/boost/iostreams/detail/push.hpp:22,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
In function 'char* strcpy(char*, const char*)',
inlined from 'int ChimeraUchimeCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimerauchimecommand.cpp:1472:28:
/usr/include/arm-linux-gnueabihf/bits/string3.h:110:63: warning: call to void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int) will always overflow destination buffer
return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
source/commands/clustersplitcommand.cpp: In member function 'int ClusterSplitCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double)':
source/commands/clustersplitcommand.cpp:1605:38: 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/c++/6/set:60:0,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, int>; _KeyOfValue = std::_Select1st<std::pair<const double, int> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, int> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, int> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
source/commands/pairwiseseqscommand.cpp:342:46: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'std::map<double, int> ClusterSplitCommand::completeListFile(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, std::set<std::__cxx11::basic_string<char> >&, ListVector*&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
In file included from /usr/include/c++/6/map:61:0,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, int> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const double, int> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int CommunityTypeFinder::findkMeans()':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'double CommunityTypeFinder::rMedoid(std::vector<std::vector<double> >, std::vector<std::vector<double> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > CommunityTypeFinder::calcCenters(std::vector<std::vector<double> >&, std::map<int, int>, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual std::vector<double> CommunityTypeFinder::calcSilhouettes(std::vector<std::vector<double> >)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/qFinderDMM.h:12,
from source/communitytype/qFinderDMM.cpp:9:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/qFinderDMM.h:12,
from source/communitytype/qFinderDMM.cpp:9:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void qFinderDMM::negativeLogDerivEvidenceLambdaPi(std::vector<double>&, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int qFinderDMM::lineMinimizeFletcher(std::vector<double>&, std::vector<double>&, double, double, double, double&, double&, std::vector<double>&, std::vector<double>&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::__cxx11::string, std::__cxx11::string)':
source/datastructures/blastalign.cpp:62:30: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual std::vector<int> DistanceDB::findClosestSequences(Sequence*, int)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/database.o source/datastructures/database.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedsabundvector.o source/datastructures/sharedsabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int)':
source/datastructures/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());
^
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int, int)':
source/datastructures/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());
^
source/datastructures/blastdb.cpp: In member function 'virtual void BlastDB::generateDB()':
source/datastructures/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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp
In file included from /usr/include/c++/6/vector:69:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permute_and_calc_ts(std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permuted_pvalues(std::vector<std::vector<double> >&, std::vector<double>&, std::vector<std::vector<double> >&)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'int MothurMetastats::runMetastats(std::__cxx11::string, std::vector<std::vector<double> >&, int)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/forest.o source/randomforest/forest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Distance = int; _Tp = std::pair<int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual int RandomForest::calcForrestVariableImportance(std::__cxx11::string)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp
source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)':
source/read/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());
^
source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(CountTable*)':
source/read/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());
^
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:124:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Distance = int; _Tp = seqDist; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'int ReadBlast::read(NameAssignment*)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatphylip.o source/read/formatphylip.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -DRELEASE_DATE="\"3/20/2017\"" -DVERSION="\"1.39.5\"" -std=c++0x -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp
source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
source/read/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());
^
source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)':
source/read/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());
^
cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
+ CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit'
+ ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o'
+ rm -f addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o mk.stdout mk.stderr tmp.stderr
+ for CPPName in $CPPNames
+ echo addtargets2
addtargets2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 addtargets2.cpp -o addtargets2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alignchime
alignchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchime.cpp -o alignchime.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alignchimel
alignchimel
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchimel.cpp -o alignchimel.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alnparams
alnparams
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alnparams.cpp -o alnparams.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alpha
alpha
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha.cpp -o alpha.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alpha2
alpha2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha2.cpp -o alpha2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo fractid
fractid
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 fractid.cpp -o fractid.o
In file included from /usr/include/c++/6/map:60:0,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/6/bits/stl_tree.h:2193:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/6/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo getparents
getparents
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 getparents.cpp -o getparents.o
/usr/include/c++/6/bits/stl_map.h: In member function 'void SmoTrainer::assignNumericLabels(std::vector<double>&, const LabeledObservationVector&, NumericClassToLabel&)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo globalalign2
globalalign2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 globalalign2.cpp -o globalalign2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo make3way
make3way
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 make3way.cpp -o make3way.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo mx
mx
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 mx.cpp -o mx.o
/usr/include/c++/6/bits/stl_map.h: In constructor 'ParameterSetBuilder::ParameterSetBuilder(const ParameterRangeMap&)':
/usr/include/c++/6/bits/stl_map.h:483:4: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo myutils
myutils
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 myutils.cpp -o myutils.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo path
path
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 path.cpp -o path.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo searchchime
searchchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 searchchime.cpp -o searchchime.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo seqdb
seqdb
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 seqdb.cpp -o seqdb.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo setnucmx
setnucmx
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 setnucmx.cpp -o setnucmx.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo sfasta
sfasta
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 sfasta.cpp -o sfasta.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo tracebackbit
tracebackbit
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 tracebackbit.cpp -o tracebackbit.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo uchime_main
uchime_main
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 uchime_main.cpp -o uchime_main.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo usort
usort
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 usort.cpp -o usort.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo viterbifast
viterbifast
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 viterbifast.cpp -o viterbifast.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo writechhit
writechhit
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 '-DRELEASE_DATE="\"3/20/2017\""' '-DVERSION="\"1.39.5\""' -std=c++0x -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 writechhit.cpp -o writechhit.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ LINK_OPTS=
+ g++ -g -o uchime addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o -Wl,-z,relro -Wl,-z,now -std=c++0x -L '"\"Enter_your_boost_library_path_here\""' -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ ls -lh uchime
-rwxrwxr-x 1 buildd buildd 2.4M Jun 22 21:45 uchime
+ sum uchime
27553 2371
g++ -Wl,-z,relro -Wl,-z,now -std=c++0x -L "\"Enter_your_boost_library_path_here\"" -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/randomnumber.o source/gotohoverlap.o source/validparameter.o source/opticluster.o source/nast.o source/averagelinkage.o source/mothurout.o source/completelinkage.o source/collect.o source/seqnoise.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/vsearchfileparser.o source/refchimeratest.o source/slibshuff.o source/trialSwap2.o source/sharedutilities.o source/consensus.o source/nastreport.o source/fileoutput.o source/cluster.o source/needlemanoverlap.o source/myseqdist.o source/subsample.o source/commandfactory.o source/rarecalc.o source/heatmap.o source/rarefact.o source/weightedlinkage.o source/wilcox.o source/progress.o source/linearalgebra.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/engine.o source/mothur.o source/dlibshuff.o source/heatmapsim.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/noalign.o source/overlap.o source/calculators/coverage.o source/calculators/invsimpson.o source/calculators/sharedjest.o source/calculators/sharedkulczynski.o source/calculators/qstat.o source/calculators/bergerparker.o source/calculators/sharedsobs.o source/calculators/sharedsobscollectsummary.o source/calculators/shen.o source/calculators/canberra.o source/calculators/parsimony.o source/calculators/gower.o source/calculators/smithwilson.o source/calculators/simpson.o source/calculators/mempearson.o source/calculators/logsd.o source/calculators/calculator.o source/calculators/goodscoverage.o source/calculators/memchord.o source/calculators/solow.o source/calculators/manhattan.o source/calculators/geom.o source/calculators/jackknife.o source/calculators/whittaker.o source/calculators/weighted.o source/calculators/efron.o source/calculators/bootstrap.o source/calculators/hamming.o source/calculators/sharedkstest.o source/calculators/sharedthetan.o source/calculators/sharedsorclass.o source/calculators/shannon.o source/calculators/prng.o source/calculators/shannonrange.o source/calculators/npshannon.o source/calculators/structeuclidean.o source/calculators/sharedchao1.o source/calculators/sharedjabund.o source/calculators/chao1.o source/calculators/simpsoneven.o source/calculators/spearman.o source/calculators/structchord.o source/calculators/shannoneven.o source/calculators/sharedace.o source/calculators/sharedmorisitahorn.o source/calculators/bstick.o source/calculators/sharedjackknife.o source/calculators/sharedsorabund.o source/calculators/sharedanderbergs.o source/calculators/odum.o source/calculators/uvest.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedjsd.o source/calculators/memeuclidean.o source/calculators/memchi2.o source/calculators/structchi2.o source/calculators/unweighted.o source/calculators/boneh.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedjclass.o source/calculators/sharedkulczynskicody.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/sharedrjsd.o source/calculators/sharedbraycurtis.o source/calculators/hellinger.o source/calculators/sharedlennon.o source/calculators/sharedochiai.o source/calculators/sharedthetayc.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimerarealigner.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/cmdargs.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/clearcut/getopt_long.o source/commands/getcurrentcommand.o source/commands/collectcommand.o source/commands/cooccurrencecommand.o source/commands/clearcutcommand.o source/commands/listseqscommand.o source/commands/clusterdoturcommand.o source/commands/distancecommand.o source/commands/binsequencecommand.o source/commands/quitcommand.o source/commands/matrixoutputcommand.o source/commands/subsamplecommand.o source/commands/indicatorcommand.o source/commands/removegroupscommand.o source/commands/libshuffcommand.o source/commands/clusterfragmentscommand.o source/commands/treegroupscommand.o source/commands/kruskalwalliscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/mimarksattributescommand.o source/commands/renameseqscommand.o source/commands/makegroupcommand.o source/commands/removerarecommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/splitgroupscommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/rarefactsharedcommand.o source/commands/aligncommand.o source/commands/chimerabellerophoncommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/venncommand.o source/commands/getsharedotucommand.o source/commands/classifyseqscommand.o source/commands/removeotulabelscommand.o source/commands/screenseqscommand.o source/commands/setdircommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/mgclustercommand.o source/commands/anosimcommand.o source/commands/sffmultiplecommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getrabundcommand.o source/commands/catchallcommand.o source/commands/getgroupscommand.o source/commands/heatmapcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/mergetaxsummarycommand.o source/commands/makelookupcommand.o source/commands/rarefactcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/trimseqscommand.o source/commands/listotulabelscommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/phylodiversitycommand.o source/commands/makelefsecommand.o source/commands/filtersharedcommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/pcacommand.o source/commands/seqsummarycommand.o source/commands/metastatscommand.o source/commands/chimeraslayercommand.o source/commands/chopseqscommand.o source/commands/sffinfocommand.o source/commands/makebiomcommand.o source/commands/seqerrorcommand.o source/commands/getlistcountcommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/corraxescommand.o source/commands/preclustercommand.o source/commands/shhhercommand.o source/commands/chimeraccodecommand.o source/commands/classifytreecommand.o source/commands/getseqscommand.o source/commands/collectsharedcommand.o source/commands/deuniqueseqscommand.o source/commands/getmimarkspackagecommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/setseedcommand.o source/commands/sharedcommand.o source/commands/makecontigscommand.o source/commands/mergefilecommand.o source/commands/homovacommand.o source/commands/getcommandinfocommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/helpcommand.o source/commands/mergegroupscommand.o source/commands/pcrseqscommand.o source/commands/systemcommand.o source/commands/chimeraperseuscommand.o source/commands/deuniquetreecommand.o source/commands/makefastqcommand.o source/commands/classifyotucommand.o source/commands/createdatabasecommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/removedistscommand.o source/commands/parsefastaqcommand.o source/commands/amovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/getgroupcommand.o source/commands/chimeracheckcommand.o source/commands/clustersplitcommand.o source/commands/pairwiseseqscommand.o source/commands/nocommands.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/setlogfilecommand.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/newcommandtemplate.o source/commands/pcoacommand.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/commands/reversecommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/sharedlistvector.o source/datastructures/optimatrix.o source/datastructures/fastamap.o source/datastructures/distancedb.o source/datastructures/alignment.o source/datastructures/kmer.o source/datastructures/sharedordervector.o source/datastructures/nameassignment.o source/datastructures/fastqread.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/tree.o source/datastructures/oligos.o source/datastructures/listvector.o source/datastructures/kmeralign.o source/datastructures/sparsematrix.o source/datastructures/alignmentdb.o source/datastructures/fullmatrix.o source/datastructures/blastalign.o source/datastructures/treenode.o source/datastructures/alignmentcell.o source/datastructures/suffixdb.o source/datastructures/sabundvector.o source/datastructures/rabundvector.o source/datastructures/suffixtree.o source/datastructures/qualityscores.o source/datastructures/groupmap.o source/datastructures/sequenceparser.o source/datastructures/sparsedistancematrix.o source/datastructures/sequencecountparser.o source/datastructures/counttable.o source/datastructures/treemap.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/ordervector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/database.o source/datastructures/designmap.o source/datastructures/sharedsabundvector.o source/datastructures/reportfile.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/decisiontree.o source/randomforest/abstractdecisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/readblast.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readcolumn.o source/read/readcluster.o source/read/readtree.o source/read/formatphylip.o source/read/treereader.o source/read/readphylip.o source/svm/svm.o -lreadline -lboost_iostreams -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# cp mothur mothur-mpi # XXX: debug
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
true
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_installmenu -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/mothur/usr/bin/uchime contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/mothur/usr/bin/mothur contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mothur/usr/bin/uchime debian/mothur/usr/bin/mothur were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mothur/usr/bin/mothur was not linked against libz.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: debian/mothur-mpi/usr/bin/mothur-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mothur-mpi/usr/bin/mothur-mpi was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mothur-mpi/usr/bin/mothur-mpi was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'mothur-mpi-dbgsym' in '../mothur-mpi-dbgsym_1.39.5-1_armhf.deb'.
dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.39.5-1_armhf.deb'.
dpkg-deb: building package 'mothur' in '../mothur_1.39.5-1_armhf.deb'.
dpkg-deb: building package 'mothur-mpi' in '../mothur-mpi_1.39.5-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../mothur_1.39.5-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build mothur-1.39.5
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-06-22T21:47:41Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mothur_1.39.5-1_armhf.changes:
------------------------------
Format: 1.8
Date: Sat, 25 Mar 2017 12:02:56 +0100
Source: mothur
Binary: mothur mothur-mpi
Architecture: armhf
Version: 1.39.5-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Tomasz Buchert <tomasz@debian.org>
Description:
mothur - sequence analysis suite for research on microbiota
mothur-mpi - mpi-enabled binary for mothur
Changes:
mothur (1.39.5-1) unstable; urgency=medium
.
* New upstream version 1.39.5
* d/patches: refresh
Checksums-Sha1:
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Checksums-Sha256:
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Files:
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935dc783ccabcccfd0684d59fbb74e1a 3854338 science optional mothur_1.39.5-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mothur-dbgsym_1.39.5-1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 71034444 bytes: control archive=535 bytes.
440 bytes, 13 lines control
212 bytes, 2 lines md5sums
Package: mothur-dbgsym
Source: mothur
Version: 1.39.5-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 71256
Depends: mothur (= 1.39.5-1)
Section: debug
Priority: extra
Homepage: http://www.mothur.org
Description: Debug symbols for mothur
Build-Ids: 07dc5f74414eecc3b69bb108f1fdfb07ebb26211 7d939a51126338af974d5960b8effddfcd2f5892
drwxr-xr-x root/root 0 2017-03-25 11:02 ./
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/.build-id/07/
-rw-r--r-- root/root 72133236 2017-03-25 11:02 ./usr/lib/debug/.build-id/07/dc5f74414eecc3b69bb108f1fdfb07ebb26211.debug
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 820232 2017-03-25 11:02 ./usr/lib/debug/.build-id/7d/939a51126338af974d5960b8effddfcd2f5892.debug
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-03-25 11:02 ./usr/share/doc/mothur-dbgsym -> mothur
mothur-mpi-dbgsym_1.39.5-1_armhf.deb
------------------------------------
new debian package, version 2.0.
size 70277142 bytes: control archive=482 bytes.
411 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: mothur-mpi-dbgsym
Source: mothur
Version: 1.39.5-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 70453
Depends: mothur-mpi (= 1.39.5-1)
Section: debug
Priority: extra
Homepage: http://www.mothur.org
Description: Debug symbols for mothur-mpi
Build-Ids: 2b10136cb28e31625c313f0bcec4c0235d0e7c3e
drwxr-xr-x root/root 0 2017-03-25 11:02 ./
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 72133580 2017-03-25 11:02 ./usr/lib/debug/.build-id/2b/10136cb28e31625c313f0bcec4c0235d0e7c3e.debug
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-03-25 11:02 ./usr/share/doc/mothur-mpi-dbgsym -> mothur-mpi
mothur-mpi_1.39.5-1_armhf.deb
-----------------------------
new debian package, version 2.0.
size 3792718 bytes: control archive=881 bytes.
995 bytes, 21 lines control
201 bytes, 3 lines md5sums
Package: mothur-mpi
Source: mothur
Version: 1.39.5-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13330
Depends: mothur, openmpi-bin, libboost-iostreams1.62.0, libc6 (>= 2.23), libgcc1 (>= 1:3.5), libreadline7 (>= 6.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://www.mothur.org
Description: mpi-enabled binary for mothur
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.
.
Provides the MPI-enabled binary for Mothur
This is recommended for operations like shhh.flows which will be
very slow on a single processor.
drwxr-xr-x root/root 0 2017-03-25 11:02 ./
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/bin/
-rwxr-xr-x root/root 13629852 2017-03-25 11:02 ./usr/bin/mothur-mpi
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/doc/mothur-mpi/
-rw-r--r-- root/root 3134 2017-03-25 11:02 ./usr/share/doc/mothur-mpi/changelog.Debian.gz
-rw-r--r-- root/root 4543 2017-02-26 14:45 ./usr/share/doc/mothur-mpi/copyright
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/man/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2017-03-25 11:02 ./usr/share/man/man1/mothur-mpi.1.gz -> mothur.1.gz
mothur_1.39.5-1_armhf.deb
-------------------------
new debian package, version 2.0.
size 3854338 bytes: control archive=1145 bytes.
864 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: 1.39.5-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13515
Depends: libboost-iostreams1.62.0, libc6 (>= 2.23), libgcc1 (>= 1:3.5), libreadline7 (>= 6.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
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 2017-03-25 11:02 ./
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/bin/
-rwxr-xr-x root/root 13629852 2017-03-25 11:02 ./usr/bin/mothur
-rwxr-xr-x root/root 179668 2017-03-25 11:02 ./usr/bin/uchime
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/doc/mothur/
-rw-r--r-- root/root 259 2017-02-26 14:45 ./usr/share/doc/mothur/README.Debian
-rw-r--r-- root/root 3134 2017-03-25 11:02 ./usr/share/doc/mothur/changelog.Debian.gz
-rw-r--r-- root/root 4543 2017-02-26 14:45 ./usr/share/doc/mothur/copyright
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/man/
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/man/man1/
-rw-r--r-- root/root 566 2017-03-25 11:02 ./usr/share/man/man1/mothur.1.gz
-rw-r--r-- root/root 3393 2017-03-25 11:02 ./usr/share/man/man1/uchime.1.gz
drwxr-xr-x root/root 0 2017-03-25 11:02 ./usr/share/menu/
-rw-r--r-- root/root 176 2017-02-26 14:45 ./usr/share/menu/mothur
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1136892
Build-Time: 5488
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 178
Job: mothur_1.39.5-1
Machine Architecture: armhf
Package: mothur
Package-Time: 5682
Source-Version: 1.39.5-1
Space: 1136892
Status: successful
Version: 1.39.5-1
--------------------------------------------------------------------------------
Finished at 2017-06-22T21:47:41Z
Build needed 01:34:42, 1136892k disk space