mothur →
1.46.1-1 →
armhf → 2021-11-11 09:57:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| mothur 1.46.1-1 (armhf) Thu, 11 Nov 2021 07:38:57 +0000 |
+==============================================================================+
Package: mothur
Version: 1.46.1-1
Source Version: 1.46.1-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-fefe9fe4-6d81-4d84-9537-71e86daf4268' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.9 MB in 31s (823 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://salsa.debian.org/med-team/mothur.git
Please use:
git clone https://salsa.debian.org/med-team/mothur.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1661 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main mothur 1.46.1-1 (dsc) [2075 B]
Get:2 http://172.17.0.1/private bookworm-staging/main mothur 1.46.1-1 (tar) [1638 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main mothur 1.46.1-1 (diff) [21.1 kB]
Fetched 1661 kB in 1s (1959 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mothur-t2N9Jc/mothur-1.46.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mothur-t2N9Jc' 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-fajAiS/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-fajAiS/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-fajAiS/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-fajAiS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2702 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...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 13 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (21.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12500 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-compat (= 13), gfortran, libboost-iostreams-dev, libreadline-dev, zlib1g-dev
Filtered Build-Depends: debhelper-compat (= 13), gfortran, libboost-iostreams-dev, libreadline-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-mothur-dummy' in '/<<BUILDDIR>>/resolver-fajAiS/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-fajAiS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Sources [527 B]
Get:5 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ Packages [605 B]
Fetched 2465 B in 1s (3344 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cpp cpp-11 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++ g++-11 gcc gcc-11 gettext
gettext-base gfortran gfortran-11 groff-base icu-devtools intltool-debian
libarchive-zip-perl libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libdebhelper-perl libelf1 libfile-stripnondeterminism-perl
libgcc-11-dev libgfortran-11-dev libgfortran5 libicu-dev libicu67
libmagic-mgc libmagic1 libncurses-dev libncurses6 libpipeline1
libreadline-dev libsigsegv2 libstdc++-11-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cpp-doc gcc-11-locales dh-make
gcc-11-doc gcc-multilib manpages-dev flex bison gdb gcc-doc gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-11-doc
libcoarrays-dev groff libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
icu-doc ncurses-doc readline-doc libstdc++-11-doc libtool-doc gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libgpm2 libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cpp-11 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-11 gcc-11 gettext
gettext-base gfortran gfortran-11 groff-base icu-devtools intltool-debian
libarchive-zip-perl libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libdebhelper-perl libelf1 libfile-stripnondeterminism-perl
libgcc-11-dev libgfortran-11-dev libgfortran5 libicu-dev libicu67
libmagic-mgc libmagic1 libncurses-dev libncurses6 libpipeline1
libreadline-dev libsigsegv2 libstdc++-11-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-mothur-dummy
sensible-utils zlib1g-dev
The following packages will be upgraded:
cpp g++ gcc
3 upgraded, 53 newly installed, 0 to remove and 10 not upgraded.
Need to get 222 MB of archives.
After this operation, 855 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-fajAiS/apt_archive ./ sbuild-build-depends-mothur-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1 [823 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf cpp-11 armhf 11.2.0-10+rpi1 [42.3 MB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libgcc-11-dev armhf 11.2.0-10+rpi1 [697 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf gcc-11 armhf 11.2.0-10+rpi1 [48.3 MB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf g++ armhf 4:11.2.0-2+rpi1 [1636 B]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf gcc armhf 4:11.2.0-2+rpi1 [5192 B]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libstdc++-11-dev armhf 11.2.0-10+rpi1 [1956 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf g++-11 armhf 11.2.0-10+rpi1 [46.1 MB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf cpp armhf 4:11.2.0-2+rpi1 [20.1 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-10+rpi1 [234 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libgfortran-11-dev armhf 11.2.0-10+rpi1 [280 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf gfortran-11 armhf 11.2.0-10+rpi1 [43.8 MB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf gfortran armhf 4:11.2.0-2+rpi1 [1428 B]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf icu-devtools armhf 67.1-7 [172 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-9 [448 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libicu-dev armhf 67.1-7 [9228 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-9 [553 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-9 [260 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-9 [269 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b1 [4588 B]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libncurses-dev armhf 6.2+20201114-4 [288 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf libreadline-dev armhf 8.1-2 [121 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 222 MB in 1min 59s (1865 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12500 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-4_armhf.deb ...
Unpacking bsdextrautils (2.37.2-4) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.4-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.4-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../07-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.5-1_all.deb ...
Unpacking automake (1:1.16.5-1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package cpp-11.
Preparing to unpack .../16-cpp-11_11.2.0-10+rpi1_armhf.deb ...
Unpacking cpp-11 (11.2.0-10+rpi1) ...
Selecting previously unselected package libgcc-11-dev:armhf.
Preparing to unpack .../17-libgcc-11-dev_11.2.0-10+rpi1_armhf.deb ...
Unpacking libgcc-11-dev:armhf (11.2.0-10+rpi1) ...
Selecting previously unselected package gcc-11.
Preparing to unpack .../18-gcc-11_11.2.0-10+rpi1_armhf.deb ...
Unpacking gcc-11 (11.2.0-10+rpi1) ...
Preparing to unpack .../19-g++_4%3a11.2.0-2+rpi1_armhf.deb ...
Unpacking g++ (4:11.2.0-2+rpi1) over (4:10.2.1-1+rpi1) ...
Preparing to unpack .../20-gcc_4%3a11.2.0-2+rpi1_armhf.deb ...
Unpacking gcc (4:11.2.0-2+rpi1) over (4:10.2.1-1+rpi1) ...
Selecting previously unselected package libstdc++-11-dev:armhf.
Preparing to unpack .../21-libstdc++-11-dev_11.2.0-10+rpi1_armhf.deb ...
Unpacking libstdc++-11-dev:armhf (11.2.0-10+rpi1) ...
Selecting previously unselected package g++-11.
Preparing to unpack .../22-g++-11_11.2.0-10+rpi1_armhf.deb ...
Unpacking g++-11 (11.2.0-10+rpi1) ...
Preparing to unpack .../23-cpp_4%3a11.2.0-2+rpi1_armhf.deb ...
Unpacking cpp (4:11.2.0-2+rpi1) over (4:10.2.1-1+rpi1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../24-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../25-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../26-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../27-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../28-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../29-libfile-stripnondeterminism-perl_1.12.0-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../30-dh-strip-nondeterminism_1.12.0-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-2) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../31-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../32-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../33-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../34-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
Preparing to unpack .../35-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../36-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../37-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../38-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../39-libgfortran5_11.2.0-10+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (11.2.0-10+rpi1) ...
Selecting previously unselected package libgfortran-11-dev:armhf.
Preparing to unpack .../40-libgfortran-11-dev_11.2.0-10+rpi1_armhf.deb ...
Unpacking libgfortran-11-dev:armhf (11.2.0-10+rpi1) ...
Selecting previously unselected package gfortran-11.
Preparing to unpack .../41-gfortran-11_11.2.0-10+rpi1_armhf.deb ...
Unpacking gfortran-11 (11.2.0-10+rpi1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../42-gfortran_4%3a11.2.0-2+rpi1_armhf.deb ...
Unpacking gfortran (4:11.2.0-2+rpi1) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../43-icu-devtools_67.1-7_armhf.deb ...
Unpacking icu-devtools (67.1-7) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../44-libboost1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-regex1.74.0:armhf.
Preparing to unpack .../45-libboost-regex1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-regex1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libicu-dev:armhf.
Preparing to unpack .../46-libicu-dev_67.1-7_armhf.deb ...
Unpacking libicu-dev:armhf (67.1-7) ...
Selecting previously unselected package libboost-regex1.74-dev:armhf.
Preparing to unpack .../47-libboost-regex1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost-regex1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-iostreams1.74.0:armhf.
Preparing to unpack .../48-libboost-iostreams1.74.0_1.74.0-9_armhf.deb ...
Unpacking libboost-iostreams1.74.0:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-iostreams1.74-dev:armhf.
Preparing to unpack .../49-libboost-iostreams1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost-iostreams1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-iostreams-dev:armhf.
Preparing to unpack .../50-libboost-iostreams-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-iostreams-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../51-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../52-libncurses-dev_6.2+20201114-4_armhf.deb ...
Unpacking libncurses-dev:armhf (6.2+20201114-4) ...
Selecting previously unselected package libreadline-dev:armhf.
Preparing to unpack .../53-libreadline-dev_8.1-2_armhf.deb ...
Unpacking libreadline-dev:armhf (8.1-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../54-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package sbuild-build-depends-mothur-dummy.
Preparing to unpack .../55-sbuild-build-depends-mothur-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-mothur-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.4-1) ...
Setting up cpp-11 (11.2.0-10+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-9) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0-9) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libboost-regex1.74.0:armhf (1.74.0-9) ...
Setting up autopoint (0.21-4) ...
Setting up icu-devtools (67.1-7) ...
Setting up libgfortran5:armhf (11.2.0-10+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libgcc-11-dev:armhf (11.2.0-10+rpi1) ...
Setting up gcc-11 (11.2.0-10+rpi1) ...
Setting up sensible-utils (0.0.17) ...
Setting up cpp (4:11.2.0-2+rpi1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libicu-dev:armhf (67.1-7) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up libncurses-dev:armhf (6.2+20201114-4) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libgfortran-11-dev:armhf (11.2.0-10+rpi1) ...
Setting up m4 (1.4.18-5) ...
Setting up libreadline-dev:armhf (8.1-2) ...
Setting up gcc (4:11.2.0-2+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up gfortran-11 (11.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up libstdc++-11-dev:armhf (11.2.0-10+rpi1) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-9) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.5-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up g++-11 (11.2.0-10+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:11.2.0-2+rpi1) ...
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 libboost-iostreams1.74-dev:armhf (1.74.0-9) ...
Setting up dh-autoreconf (20) ...
Setting up g++ (4:11.2.0-2+rpi1) ...
Setting up debhelper (13.5.2) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b1) ...
Setting up sbuild-build-depends-mothur-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 g++-11_11.2.0-10+rpi1 gcc-10_10.3.0-11+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:11.2.0-2+rpi1 cpp-10_10.3.0-11+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-1 debconf_1.5.78 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-10_10.3.0-11+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran_4:11.2.0-2+rpi1 gfortran-11_11.2.0-10+rpi1 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 icu-devtools_67.1-7 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libboost-iostreams-dev_1.74.0.3+b1 libboost-iostreams1.74-dev_1.74.0-9 libboost-iostreams1.74.0_1.74.0-9 libboost-regex1.74-dev_1.74.0-9 libboost-regex1.74.0_1.74.0-9 libboost1.74-dev_1.74.0-9 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran-11-dev_11.2.0-10+rpi1 libgfortran5_11.2.0-10+rpi1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu-dev_67.1-7 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20201114-4 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libreadline-dev_8.1-2 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mothur-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.ovzaEVuL/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 8 17:23:00 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./mothur_1.46.1-1.dsc
dpkg-source: info: extracting mothur in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mothur_1.46.1.orig.tar.gz
dpkg-source: info: unpacking mothur_1.46.1-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0002-Fix-include.patch
dpkg-source: info: applying drop_sys_sysctl.h.patch
dpkg-source: info: applying gcc-11.patch
dpkg-source: info: applying c++14.patch
dpkg-source: info: applying fix_linking.patch
Check disc 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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-fefe9fe4-6d81-4d84-9537-71e86daf4268
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package mothur
dpkg-buildpackage: info: source version 1.46.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f mothur uchime
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_clean
debian/rules binary-arch
dh binary-arch
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
make -j4 "INSTALL=install --strip-program=true" 64BIT_VERSION=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/bergerparker.h:12,
from source/calculators/bergerparker.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/boneh.h:13,
from source/calculators/boneh.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/bergerparker.h:12,
from source/calculators/bergerparker.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput BergerParker::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/ace.h:16,
from source/calculators/ace.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/boneh.h:13,
from source/calculators/boneh.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Boneh::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/ace.h:16,
from source/calculators/ace.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Ace::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/calculator.o source/calculators/calculator.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/bootstrap.h:15,
from source/calculators/bootstrap.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/bootstrap.h:15,
from source/calculators/bootstrap.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Bootstrap::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/bstick.h:11,
from source/calculators/bstick.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/canberra.h:15,
from source/calculators/canberra.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/canberra.h:15,
from source/calculators/canberra.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Canberra::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/bstick.h:11,
from source/calculators/bstick.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput BStick::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/coverage.o source/calculators/coverage.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/diversityutils.o source/calculators/diversityutils.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapdist.o source/calculators/eachgapdist.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/chao1.h:12,
from source/calculators/chao1.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/chao1.h:12,
from source/calculators/chao1.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Chao1::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapignore.o source/calculators/eachgapignore.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/coverage.h:13,
from source/calculators/coverage.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/coverage.h:13,
from source/calculators/coverage.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Coverage::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/erarefaction.o source/calculators/erarefaction.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/f1score.o source/calculators/f1score.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/efron.h:13,
from source/calculators/efron.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/efron.h:13,
from source/calculators/efron.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Efron::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/erarefaction.hpp:12,
from source/calculators/erarefaction.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/erarefaction.hpp:12,
from source/calculators/erarefaction.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void ERarefaction::getValues(SAbundVector*, std::vector<double>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fdr.o source/calculators/fdr.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fn.o source/calculators/fn.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fp.o source/calculators/fp.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fpfn.o source/calculators/fpfn.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/geom.o source/calculators/geom.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/goodscoverage.h:12,
from source/calculators/goodscoverage.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/goodscoverage.h:12,
from source/calculators/goodscoverage.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput GoodsCoverage::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/geom.h:12,
from source/calculators/geom.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/geom.h:12,
from source/calculators/geom.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Geom::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/gower.h:14,
from source/calculators/gower.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/gower.h:14,
from source/calculators/gower.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Gower::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igabundance.o source/calculators/igabundance.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/hamming.h:15,
from source/calculators/hamming.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/hamming.h:15,
from source/calculators/hamming.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Hamming::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ignoregaps.o source/calculators/ignoregaps.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/heip.h:13,
from source/calculators/heip.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/heip.h:13,
from source/calculators/heip.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Heip::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igrarefaction.o source/calculators/igrarefaction.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/hellinger.h:14,
from source/calculators/hellinger.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/hellinger.h:14,
from source/calculators/hellinger.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Hellinger::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/igabundance.hpp:12,
from source/calculators/igabundance.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/igabundance.hpp:12,
from source/calculators/igabundance.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<double> IGAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/kimura.o source/calculators/kimura.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/invsimpson.h:15,
from source/calculators/invsimpson.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/kmerdist.o source/calculators/kmerdist.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/invsimpson.h:15,
from source/calculators/invsimpson.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput InvSimpson::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnabundance.o source/calculators/lnabundance.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/jackknife.h:13,
from source/calculators/jackknife.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/jackknife.h:13,
from source/calculators/jackknife.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Jackknife::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnrarefaction.o source/calculators/lnrarefaction.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/kmerdist.hpp:12,
from source/calculators/kmerdist.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnshift.o source/calculators/lnshift.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/kmerdist.hpp:12,
from source/calculators/kmerdist.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<double> KmerDist::calcDist(std::vector<kmerCount>, std::vector<int>, int)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lnabundance.hpp:12,
from source/calculators/lnabundance.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lnabundance.hpp:12,
from source/calculators/lnabundance.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<double> LNAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsabundance.o source/calculators/lsabundance.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsrarefaction.o source/calculators/lsrarefaction.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lnshift.hpp:12,
from source/calculators/lnshift.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lnshift.hpp:12,
from source/calculators/lnshift.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<double> LNShift::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/logsd.h:12,
from source/calculators/logsd.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/logsd.h:12,
from source/calculators/logsd.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput LogSD::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mcc.o source/calculators/mcc.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lsabundance.hpp:12,
from source/calculators/lsabundance.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lsabundance.hpp:12,
from source/calculators/lsabundance.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<double> LSAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/manhattan.h:14,
from source/calculators/manhattan.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/manhattan.h:14,
from source/calculators/manhattan.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Manhattan::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/memchi2.h:15,
from source/calculators/memchi2.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/memchi2.h:15,
from source/calculators/memchi2.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput MemChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metroig.o source/calculators/metroig.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/memchord.h:14,
from source/calculators/memchord.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/memchord.h:14,
from source/calculators/memchord.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput MemChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrolognormal.o source/calculators/metrolognormal.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/memeuclidean.h:14,
from source/calculators/memeuclidean.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/memeuclidean.h:14,
from source/calculators/memeuclidean.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput MemEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/mempearson.h:15,
from source/calculators/mempearson.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/mempearson.h:15,
from source/calculators/mempearson.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput MemPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrologstudent.o source/calculators/metrologstudent.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrosichel.o source/calculators/metrosichel.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npv.o source/calculators/npv.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapdist.o source/calculators/onegapdist.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/npshannon.h:16,
from source/calculators/npshannon.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/npshannon.h:16,
from source/calculators/npshannon.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NPShannon::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapignore.o source/calculators/onegapignore.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/odum.h:15,
from source/calculators/odum.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/odum.h:15,
from source/calculators/odum.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Odum::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ppv.o source/calculators/ppv.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/prng.o source/calculators/prng.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/qstat.o source/calculators/qstat.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sensitivity.o source/calculators/sensitivity.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/parsimony.h:14,
from source/calculators/parsimony.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'EstOutput Parsimony::createProcesses(Tree*, CountTable*)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/parsimony.h:14,
from source/calculators/parsimony.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/qstat.h:11,
from source/calculators/qstat.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/qstat.h:11,
from source/calculators/qstat.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput QStat::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannon.h:16,
from source/calculators/shannon.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannon.h:16,
from source/calculators/shannon.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Shannon::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannoneven.h:13,
from source/calculators/shannoneven.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannoneven.h:13,
from source/calculators/shannoneven.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput ShannonEven::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput RangeShannon::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shannonrange.h:19,
from source/calculators/shannonrange.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedace.h:15,
from source/calculators/sharedace.cpp:11:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedchao1.o source/calculators/sharedchao1.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedace.h:15,
from source/calculators/sharedace.cpp:11:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedAce::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedanderbergs.h:12,
from source/calculators/sharedanderbergs.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedanderbergs.h:12,
from source/calculators/sharedanderbergs.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Anderberg::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedbraycurtis.h:11,
from source/calculators/sharedbraycurtis.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedbraycurtis.h:11,
from source/calculators/sharedbraycurtis.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput BrayCurtis::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjabund.h:16,
from source/calculators/sharedjabund.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjabund.h:16,
from source/calculators/sharedjabund.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput JAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjackknife.h:13,
from source/calculators/sharedjackknife.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedchao1.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjackknife.h:13,
from source/calculators/sharedjackknife.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedJackknife::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedchao1.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedChao1::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjclass.h:15,
from source/calculators/sharedjclass.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjclass.h:15,
from source/calculators/sharedjclass.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Jclass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjsd.h:12,
from source/calculators/sharedjsd.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedjsd.h:12,
from source/calculators/sharedjsd.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput JSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedjest.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedchao1.h:16,
from source/calculators/sharedjest.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Jest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedkstest.h:11,
from source/calculators/sharedkstest.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedkstest.h:11,
from source/calculators/sharedkstest.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput KSTest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynski.h:13,
from source/calculators/sharedkulczynski.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynski.h:13,
from source/calculators/sharedkulczynski.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Kulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynskicody.h:14,
from source/calculators/sharedkulczynskicody.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedkulczynskicody.h:14,
from source/calculators/sharedkulczynskicody.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput KulczynskiCody::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedlennon.h:14,
from source/calculators/sharedlennon.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedlennon.h:14,
from source/calculators/sharedlennon.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Lennon::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedmarczewski.h:13,
from source/calculators/sharedmarczewski.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedmarczewski.h:13,
from source/calculators/sharedmarczewski.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedMarczewski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedmorisitahorn.h:13,
from source/calculators/sharedmorisitahorn.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedmorisitahorn.h:13,
from source/calculators/sharedmorisitahorn.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput MorHorn::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedochiai.h:12,
from source/calculators/sharedochiai.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedochiai.h:12,
from source/calculators/sharedochiai.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Ochiai::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedrjsd.h:12,
from source/calculators/sharedrjsd.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedrjsd.h:12,
from source/calculators/sharedrjsd.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput RJSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobs.h:16,
from source/calculators/sharedsobs.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobs.h:16,
from source/calculators/sharedsobs.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobscollectsummary.h:15,
from source/calculators/sharedsobscollectsummary.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsobscollectsummary.h:15,
from source/calculators/sharedsobscollectsummary.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorabund.h:16,
from source/calculators/sharedsorabund.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorabund.h:16,
from source/calculators/sharedsorabund.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SorAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorclass.h:16,
from source/calculators/sharedsorclass.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorclass.h:16,
from source/calculators/sharedsorclass.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SorClass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorest.h:16,
from source/calculators/sharedsorest.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedsorest.h:16,
from source/calculators/sharedsorest.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SorEst::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetan.h:16,
from source/calculators/sharedthetan.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetan.h:16,
from source/calculators/sharedthetan.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput ThetaN::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/siabundance.o source/calculators/siabundance.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetayc.h:16,
from source/calculators/sharedthetayc.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/sharedthetayc.h:16,
from source/calculators/sharedthetayc.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput ThetaYC::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shen.h:13,
from source/calculators/shen.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/shen.h:13,
from source/calculators/shen.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Shen::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sirarefaction.o source/calculators/sirarefaction.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/siabundance.hpp:12,
from source/calculators/siabundance.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/siabundance.hpp:12,
from source/calculators/siabundance.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<double> SIAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/simpson.h:16,
from source/calculators/simpson.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sishift.o source/calculators/sishift.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/simpson.h:16,
from source/calculators/simpson.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Simpson::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/simpsoneven.h:13,
from source/calculators/simpsoneven.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/simpsoneven.h:13,
from source/calculators/simpsoneven.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SimpsonEven::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/soergel.o source/calculators/soergel.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/sishift.hpp:12,
from source/calculators/sishift.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/sishift.hpp:12,
from source/calculators/sishift.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<double> SIShift::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/smithwilson.h:13,
from source/calculators/smithwilson.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/smithwilson.h:13,
from source/calculators/smithwilson.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SmithWilson::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/soergel.h:14,
from source/calculators/soergel.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/soergel.h:14,
from source/calculators/soergel.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Soergel::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/specificity.o source/calculators/specificity.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/solow.h:13,
from source/calculators/solow.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/solow.h:13,
from source/calculators/solow.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Solow::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/spearman.h:15,
from source/calculators/spearman.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/spearman.h:15,
from source/calculators/spearman.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Spearman::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/speciesprofile.h:14,
from source/calculators/speciesprofile.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/speciesprofile.h:14,
from source/calculators/speciesprofile.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SpeciesProfile::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchord.o source/calculators/structchord.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structchi2.h:14,
from source/calculators/structchi2.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structchi2.h:14,
from source/calculators/structchi2.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput StructChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structchord.h:14,
from source/calculators/structchord.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structeuclidean.h:15,
from source/calculators/structeuclidean.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structchord.h:14,
from source/calculators/structchord.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput StructChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structeuclidean.h:15,
from source/calculators/structeuclidean.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput StructEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tn.o source/calculators/tn.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tp.o source/calculators/tp.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structkulczynski.h:14,
from source/calculators/structkulczynski.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structkulczynski.h:14,
from source/calculators/structkulczynski.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput StructKulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tptn.o source/calculators/tptn.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structpearson.h:15,
from source/calculators/structpearson.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/calculators/structpearson.h:15,
from source/calculators/structpearson.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput StructPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/unweighted.o source/calculators/unweighted.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/uvest.o source/calculators/uvest.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/weighted.o source/calculators/weighted.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/whittaker.o source/calculators/whittaker.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/bellerophon.o source/chimera/bellerophon.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/ccode.o source/chimera/ccode.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/set:60,
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++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'EstOutput Unweighted::createProcesses(Tree*, std::vector<std::vector<int> >&, CountTable*)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/11/bits/stl_map.h: In function 'void driverWeighted(weightedData*)':
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'EstOutput Weighted::createProcesses(Tree*, CountTable*)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'EstOutput Unweighted::createProcesses(Tree*, CountTable*)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/11/bits/stl_map.h: In member function 'virtual EstOutput Weighted::getValues(Tree*, std::string, std::string)':
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: 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' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/chimera/mothurchimera.h:14,
from source/chimera/bellerophon.h:14,
from source/chimera/bellerophon.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/chimera/mothurchimera.h:14,
from source/chimera/bellerophon.h:14,
from source/chimera/bellerophon.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int Bellerophon::driverChimeras(std::vector<int>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimerarealigner.o source/chimera/chimerarealigner.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp
In file included from /usr/include/c++/11/bits/stl_algobase.h:71,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/ios:40,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from source/mothur.h:29,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Iterator2 = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Compare = bool (*)(SeqCompare, SeqCompare)]':
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/chimera/decalc.h:12,
from source/chimera/maligner.h:12,
from source/chimera/maligner.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/chimera/decalc.h:12,
from source/chimera/maligner.h:12,
from source/chimera/maligner.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Sequence> Maligner::minCoverageFilter(std::vector<Sequence>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::string Maligner::chimeraMaligner(int, DeCalculator)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::string Maligner::getResults(Sequence, DeCalculator)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Sequence> DeCalculator::findClosest(Sequence, std::vector<Sequence*>&, std::vector<Sequence*>&, int, int)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SeqCompare&}; _Tp = SeqCompare; _Alloc = std::allocator<SeqCompare>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SeqCompare>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'double Perseus::basicPairwiseAlignSeqs(std::string, std::string, std::string&, std::string&, pwModel)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Sequence> ChimeraSlayer::getKmerSeqs(Sequence, std::vector<Sequence*>&, int)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence, std::vector<Sequence*>&, int)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'double Perseus::modeledPairwiseAlignSeqs(std::string, std::string, std::string&, std::string&, std::vector<std::vector<double> >&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:71,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/ios:40,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from source/mothur.h:29,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Iterator2 = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Compare = bool (*)(data_struct, data_struct)]':
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(SeqCompare, SeqCompare)>]':
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(SeqCompare, SeqCompare)>]':
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const data_struct&}; _Tp = data_struct; _Alloc = std::allocator<data_struct>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<data_struct>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Distance = int; _Tp = SeqCompare; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(SeqCompare, SeqCompare)>]':
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(SeqCompare, SeqCompare)>]':
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(SeqCompare, SeqCompare)>]':
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(SeqCompare, SeqCompare)>]':
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:84:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:86:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1884:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1884 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1887:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1887 | while (__comp(__pivot, __last))
| ~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1646 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual int ChimeraSlayer::getChimeras(Sequence*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<data_struct> Slayer::runBellerophon(Sequence, Sequence, Sequence, std::map<int, int>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(data_struct, data_struct)>]':
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(data_struct, data_struct)>]':
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Distance = int; _Tp = data_struct; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(data_struct, data_struct)>]':
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(data_struct, data_struct)>]':
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(data_struct, data_struct)>]':
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(data_struct, data_struct)>]':
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:84:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:86:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1884:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1884 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1887:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1887 | while (__comp(__pivot, __last))
| ~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1646 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::string Slayer::getResults(Sequence, std::vector<Sequence>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/alignnode.h:13,
from source/classifier/aligntree.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/alignnode.h:13,
from source/classifier/aligntree.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::string AlignTree::getTaxonomy(Sequence*, std::string&, bool&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/alignnode.h:13,
from source/classifier/aligntree.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/kmernode.h:14,
from source/classifier/kmertree.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/kmernode.h:14,
from source/classifier/kmertree.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::string KmerTree::getTaxonomy(Sequence*, std::string&, bool&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/kmernode.h:14,
from source/classifier/kmertree.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp
source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
456 | fscanf(fp, "%ld\n", &dmat->ntaxa);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncheckcommand.o source/commands/aligncheckcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp
In file included from /usr/include/c++/11/bits/stl_algobase.h:71,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/ios:40,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from source/mothur.h:29,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Iterator2 = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = bool (*)(seqDist, seqDist)]':
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/c++/11/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 = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/c++/11/bits/stl_vector.h: In constructor 'alignStruct::alignStruct(linePair, OutputWriter*, OutputWriter*, OutputWriter*, std::string, AlignmentDB*, std::string, float, float, float, float, float, bool, int, std::string)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int AlignCommand::createProcesses(std::string, std::string, std::string, std::string, std::vector<long long int>&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'virtual int AlignCommand::execute()':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1642 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:86:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > AnosimCommand::convertToRanks(std::vector<std::vector<double> >)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/chimeraperseuscommand.h:16,
from source/commands/chimeraperseuscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp
source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)':
source/commands/chimerauchimecommand.cpp:516:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
516 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp
source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)':
source/commands/chimeravsearchcommand.cpp:406:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
406 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int ChimeraPerseusCommand::createProcessesGroups(std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&, std::string, std::string, std::string, std::string, std::vector<std::__cxx11::basic_string<char> >, std::string, std::string, int&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'int ChimeraUchimeCommand::createProcessesGroups(std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&, std::string, std::string, std::string, std::string, std::vector<std::__cxx11::basic_string<char> >, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int ChimeraVsearchCommand::createProcessesGroups(std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&, std::string, std::string, std::string, std::string, std::string, std::vector<std::__cxx11::basic_string<char> >, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/chopseqscommand.h:14,
from source/commands/chopseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'bool ChopSeqsCommand::createProcesses(std::string, std::string, std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/classifyseqscommand.h:14,
from source/commands/classifyseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/classifysvmsharedcommand.h:14,
from source/commands/classifysvmsharedcommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int ClassifySeqsCommand::createProcesses(std::string, std::string, std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In constructor 'ClassifySvmSharedCommand::ClassifySvmSharedCommand(std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp
source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)':
source/commands/clustercommand.cpp:543:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
543 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp
In file included from /usr/include/c++/11/bits/stl_algobase.h:71,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/ios:40,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from source/mothur.h:29,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Iterator2 = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Compare = bool (*)(seqRNode, seqRNode)]':
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqRNode&}; _Tp = seqRNode; _Alloc = std::allocator<seqRNode>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqRNode>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int ClusterFragmentsCommand::readFASTA()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(seqRNode, seqRNode)>]':
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqRNode, seqRNode)>]':
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Distance = int; _Tp = seqRNode; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqRNode, seqRNode)>]':
/usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqRNode, seqRNode)>]':
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqRNode, seqRNode)>]':
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqRNode, seqRNode)>]':
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/stl_heap.h:424:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:84:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:86:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1884:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1884 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1887:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1887 | while (__comp(__pivot, __last))
| ~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1646:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1646 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In member function 'virtual int ClusterFragmentsCommand::execute()':
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp
source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::string, std::string, std::string, double, clusterData*)':
source/commands/clustersplitcommand.cpp:1053:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1053 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
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++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>&, int, bool, std::map<std::__cxx11::basic_string<char>, int>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In member function 'std::map<double, int> ClusterSplitCommand::completeListFile(std::vector<std::__cxx11::basic_string<char> >, std::string, std::set<std::__cxx11::basic_string<char> >&, ListVector*&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>&, int, bool, std::map<std::__cxx11::basic_string<char>, int>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int CooccurrenceCommand::getCooccurrence(SharedRAbundVectors*&, std::ofstream&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/createdatabasecommand.h:12,
from source/commands/createdatabasecommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/createdatabasecommand.h:12,
from source/commands/createdatabasecommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<int> CreateDatabaseCommand::readFasta(std::vector<Sequence>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/degapseqscommand.h:14,
from source/commands/degapseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int DegapSeqsCommand::createProcesses(std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp
source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
source/commands/distancecommand.cpp:323:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
323 | system(("gzip -v " + outputFile).c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const linePair&}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'int driver(std::vector<SharedRAbundVector*>&, std::vector<std::vector<seqDist> >&, std::vector<Calculator*>, MothurOut*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/diversityestimatorcommand.hpp:12,
from source/commands/diversityestimatorcommand.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mcmcSample&}; _Tp = mcmcSample; _Alloc = std::allocator<mcmcSample>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<mcmcSample>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function 'int process(distSharedData*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'void DistanceCommand::createProcesses(std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/diversityestimatorcommand.hpp:12,
from source/commands/diversityestimatorcommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int EstimatorSingleCommand::fillSampling(int, int, bool)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mcmcSample*, std::vector<mcmcSample> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/filterseqscommand.h:13,
from source/commands/filterseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int FilterSeqsCommand::createProcessesCreateFilter(Filters&, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int DistSharedCommand::createProcesses(SharedRAbundVectors*&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int EstimatorSingleCommand::processShared(SharedRAbundVectors*&, std::vector<std::basic_ofstream<char>*>&, std::string)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int FilterSeqsCommand::filterSequences()':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int GetCoreMicroBiomeCommand::createTable(SharedRAbundFloatVectors*&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::driver(SharedRAbundVectors*&, std::vector<std::vector<seqDist> >&, Calculator*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotuscommand.o source/commands/getotuscommand.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(SharedRAbundVectors*&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const summaryData&}; _Tp = summaryData; _Alloc = std::allocator<summaryData>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<summaryData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:71,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/ios:40,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from source/mothur.h:29,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/predefined_ops.h: In function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Iterator2 = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = bool (*)(summaryData, summaryData)]':
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/11/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1642 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:82:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
82 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:84:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
84 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:86:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
86 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:91:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
91 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:93:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
93 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::processDriver(SharedRAbundVectors*&, std::vector<int>&, std::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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getoturepcommand.h:14,
from source/commands/getoturepcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getoturepcommand.h:14,
from source/commands/getoturepcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::string GetOTURepCommand::findRep(std::vector<std::__cxx11::basic_string<char> >, std::map<std::__cxx11::basic_string<char>, long long int>&, std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
661 | }
| ^
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getsharedotucommand.h:13,
from source/commands/getsharedotucommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int HeatMapSimCommand::runCommandDist()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/getsharedotucommand.h:13,
from source/commands/getsharedotucommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual int GetSharedOTUCommand::execute()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp
In file included from /usr/include/c++/11/set:60,
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++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
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++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotuscommand.o source/commands/listotuscommand.cpp
In file included from /usr/include/c++/11/vector:72,
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++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runKruskalWallis(SharedRAbundFloatVectors*&, SharedCLRVectors*&, DesignMap&)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'int LefseCommand::normalize(SharedRAbundFloatVectors*&, SharedCLRVectors*&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LefseCommand::getMeans(SharedRAbundFloatVectors*&, SharedCLRVectors*&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/c++/11/bits/stl_map.h: In member function 'int LibShuffCommand::printCoverageFile()':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'void LefseCommand::printResults(std::vector<std::vector<double> >, std::map<int, double>, std::map<int, double>, std::string, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::string)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'void LefseCommand::printResultsAll(std::vector<std::vector<double> >, std::map<int, double>, std::map<int, double>, std::string, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::string)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'bool LefseCommand::testOTUWilcoxon(std::map<std::__cxx11::basic_string<char>, std::set<std::__cxx11::basic_string<char> > >&, std::vector<float>, 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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runWilcoxon(SharedRAbundFloatVectors*&, SharedCLRVectors*&, 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++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'std::map<int, double> LefseCommand::testLDA(SharedRAbundFloatVectors*&, SharedCLRVectors*&, 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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makeclrcommand.o source/commands/makeclrcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp
source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)':
source/commands/makefilecommand.cpp:353:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
353 | system(findCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int MakeContigsCommand::setLines(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<linePair>&, std::vector<linePair>&, char)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> MakeLookupCommand::convertSeqToFlow(std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int MakeLookupCommand::alignFlowGrams(std::vector<double>&, std::vector<double>&, double, std::vector<std::vector<double> >, std::string)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual int MakeLookupCommand::execute()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In function 'void driverContigsGroups(groupContigsData*)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'long long unsigned int MakeContigsCommand::createProcessesGroups(std::vector<std::vector<std::__cxx11::basic_string<char> > >, std::string, std::string, std::string, std::string, std::string, std::map<int, std::__cxx11::basic_string<char> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergeotuscommand.o source/commands/mergeotuscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'int driverShared(metastatsData*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In function 'int driverCLR(metastatsData*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int MetaStatsCommand::process(SharedRAbundVectors*&, DesignMap*&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/mgclustercommand.h:13,
from source/commands/mgclustercommand.cpp:10:
/usr/include/c++/11/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>, long long int>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int MetaStatsCommand::process(SharedCLRVectors*&, DesignMap*&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/mgclustercommand.h:13,
from source/commands/mgclustercommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h: In member function 'int MGClusterCommand::runOptiCluster()':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::readAxes(std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/otuassociationcommand.h:14,
from source/commands/otuassociationcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OTUAssociationCommand::readMetadata()':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
source/commands/pairwiseseqscommand.cpp:351:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
351 | system(("gzip -v " + outputFile).c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OTUAssociationCommand::process(SharedRAbundVectors*&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void OTUAssociationCommand::process(SharedRAbundFloatVectors*&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/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 = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const linePair&}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h: In member function 'void ParsimonyCommand::printParsimonyFile()':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int PCACommand::process(SharedRAbundFloatVectors*&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_tree.h:2161:5: 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' changed in GCC 7.1
2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'void PairwiseSeqsCommand::createProcesses(std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In member function 'virtual int ParsimonyCommand::execute()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/pcrseqscommand.h:13,
from source/commands/pcrseqscommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int PcrSeqsCommand::createProcesses(std::string, std::string, std::string, std::set<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/preclustercommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/11/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 = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In function 'void driverGetCounts(primerCountsData*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'std::set<int> PrimerDesignCommand::createProcesses(std::string, std::vector<double>&, std::vector<double>&, std::set<std::__cxx11::basic_string<char> >&, std::vector<Sequence>&, int, std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<Sequence> PrimerDesignCommand::createProcessesConSeqs(std::map<std::__cxx11::basic_string<char>, int>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void PreClusterCommand::createProcessesGroups(std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char> >, std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'int RareFactSharedCommand::subsampleLookup(SharedRAbundVectors*&, std::string)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotuscommand.o source/commands/removeotuscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/screenseqscommand.h:12,
from source/commands/screenseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/seqerrorcommand.h:13,
from source/commands/seqerrorcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/seqerrorcommand.h:13,
from source/commands/seqerrorcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Sequence> SeqErrorCommand::getReferences(std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int ScreenSeqsCommand::createProcesses(std::string, std::string, std::string, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/sffmultiplecommand.h:12,
from source/commands/sffmultiplecommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/shhhseqscommand.h:13,
from source/commands/shhhseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'void ShhherCommand::getJointLookUp()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/shhhseqscommand.h:13,
from source/commands/shhhseqscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'void driverShhSeqsGroups(shhhseqsData*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int SffMultipleCommand::createProcesses(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::string, std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const QualityScores&}; _Tp = QualityScores; _Alloc = std::allocator<QualityScores>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<QualityScores>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int SortSeqsCommand::readFasta()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int SortSeqsCommand::readQual()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<QualityScores*, std::vector<QualityScores> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FastqRead&}; _Tp = FastqRead; _Alloc = std::allocator<FastqRead>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<FastqRead>::iterator' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/srainfocommand.o source/commands/srainfocommand.cpp
source/commands/srainfocommand.cpp: In member function 'void SRAInfoCommand::runSystemCommand(std::string)':
source/commands/srainfocommand.cpp:489:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
489 | system(inputString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'int driverSplitFastq(splitGroupsStruct*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastqRead*, std::vector<FastqRead> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'virtual int SplitGroupCommand::execute()':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summaryqualcommand.h:14,
from source/commands/summaryqualcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int SummaryQualCommand::createProcessesCreateSummary(std::vector<int>&, std::vector<int>&, std::vector<std::vector<int> >&, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int SummaryCommand::process(SAbundVector*&, std::ofstream&, std::ofstream&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
source/commands/systemcommand.cpp:97:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
97 | system(command.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'void driverSummaryShared(summarySharedData*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int SummarySharedCommand::runCalcs(SharedRAbundVectors*&, std::string, std::string, std::vector<std::vector<seqDist> >&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'int SummarySharedCommand::process(SharedRAbundVectors*, std::string, std::string, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'int driverTreeShared(std::vector<SharedRAbundVector*>&, std::vector<std::vector<seqDist> >&, std::vector<Calculator*>, MothurOut*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<std::vector<double> > TreeSharedCommand::makeSimsDist(SparseDistanceMatrix*, int)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'int process(treeSharedData*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<double> TrimFlowsCommand::getFlowFileBreaks()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int TreeSharedCommand::createProcesses(SharedRAbundVectors*&, CountTable&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In member function 'int TrimSeqsCommand::setLines(std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'int TrimFlowsCommand::createProcessesCreateTrim(std::string, std::string, std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'int UnifracUnweightedCommand::getAverageSTDMatrices(std::vector<std::vector<double> >&, int)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void UnifracUnweightedCommand::printUnweightedFile(int)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracUnweightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual int UnifracUnweightedCommand::execute()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
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++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp
In file included from /usr/include/c++/11/vector:72,
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++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In function 'void driverWeightedRandom(weightedRandomData*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h: In member function 'void UnifracWeightedCommand::calculateFreqsCumuls(std::set<double>&, std::vector<std::vector<double> >, std::vector<std::map<double, double> >&, std::vector<std::map<double, double> >&)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> UnifracWeightedCommand::createProcesses(Tree*, CountTable*, std::vector<std::vector<std::__cxx11::basic_string<char> > >, std::vector<std::vector<int> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int CommunityTypeFinder::findkMeans()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In member function 'int UnifracWeightedCommand::getAverageSTDMatrices(std::vector<std::vector<double> >&, int)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracWeightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/pam.h:12,
from source/communitytype/pam.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/pam.h:12,
from source/communitytype/pam.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual double Pam::calcCHIndex(std::vector<std::vector<double> >)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int UnifracWeightedCommand::runRandomCalcs(Tree*, CountTable*, std::vector<double>, int, std::vector<double>&, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int Pam::buildPhase()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual int UnifracWeightedCommand::execute()':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
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++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
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++/11/bits/stl_vector.h: In member function 'void qFinderDMM::negativeLogDerivEvidenceLambdaPi(std::vector<double>&, std::vector<double>&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/aminoacid.o source/datastructures/aminoacid.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biom.o source/datastructures/biom.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biomhdf5.o source/datastructures/biomhdf5.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/biomsimple.o source/datastructures/biomsimple.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In constructor 'AlignmentDB::AlignmentDB(std::string, std::string, int, float, float, float, float, int, bool)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/biom.hpp:12,
from source/datastructures/biom.cpp:9:
/usr/include/c++/11/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Taxonomy*, std::vector<Taxonomy> >; _ForwardIterator = Taxonomy*; bool _TrivialValueTypes = false]':
/usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
85 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Taxonomy; _Alloc = std::allocator<Taxonomy>]':
/usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
148 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
151 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp
source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::string, std::string, bool)':
source/datastructures/blastalign.cpp:65:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
65 | system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/biom.hpp:12,
from source/datastructures/biomsimple.hpp:14,
from source/datastructures/biomsimple.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Taxonomy&}; _Tp = Taxonomy; _Alloc = std::allocator<Taxonomy>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Taxonomy>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int, std::vector<float>&) const':
source/datastructures/blastdb.cpp:164:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
164 | system(blastCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int, int)':
source/datastructures/blastdb.cpp:227:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
227 | system(blastCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual void BlastDB::generateDB()':
source/datastructures/blastdb.cpp:294:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
294 | system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/contigsreport.o source/datastructures/contigsreport.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/biom.hpp:12,
from source/datastructures/biomsimple.hpp:14,
from source/datastructures/biomsimple.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void BiomSimple::read(std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/searchdatabase.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/datastructures/searchdatabase.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void DistanceDB::addSequence(Sequence)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/searchdatabase.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/searchdatabase.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/11/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++/11/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/searchdatabase.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1642 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In member function 'virtual std::vector<int> DistanceDB::findClosestSequences(Sequence*, int, std::vector<float>&) const':
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optidata.o source/datastructures/optidata.cpp
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optiblastmatrix.hpp:12,
from source/datastructures/optiblastmatrix.cpp:9:
/usr/include/c++/11/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>, long long int>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optiblastmatrix.hpp:12,
from source/datastructures/optiblastmatrix.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiBlastMatrix::readBlastNames(std::map<std::__cxx11::basic_string<char>, long long int>&)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optidb.o source/datastructures/optidb.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiBlastMatrix::readBlast()':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optimatrix.h:12,
from source/datastructures/optimatrix.cpp:9:
/usr/include/c++/11/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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optirefmatrix.o source/datastructures/optirefmatrix.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
/usr/include/c++/11/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 = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optimatrix.h:12,
from source/datastructures/optimatrix.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiMatrix::readPhylip()':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/optidb.hpp:12,
from source/datastructures/optidb.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/optidb.hpp:12,
from source/datastructures/optidb.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void OptiDB::addSequence(Sequence)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiMatrix::readColumn()':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/picrust.o source/datastructures/picrust.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/protein.o source/datastructures/protein.cpp
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/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<long long int&&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/proteindb.o source/datastructures/proteindb.cpp
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/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 = long long int; _Tp = long long int; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<long long int> OptiRefMatrix::getFitSeqs()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual std::vector<long long int> OptiRefMatrix::getRefSeqs()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'virtual OptiData* OptiRefMatrix::extractRefMatrix()':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'virtual OptiData* OptiRefMatrix::extractMatrixSubset(std::set<long long int>&)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/protein.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AminoAcid&}; _Tp = AminoAcid; _Alloc = std::allocator<AminoAcid>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AminoAcid>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/protein.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<AminoAcid> Protein::getProtein(std::ifstream&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AminoAcid*, std::vector<AminoAcid> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/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>, long long int>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/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 = long long int; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> >]':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'void Protein::setUnaligned(std::vector<AminoAcid>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AminoAcid*, std::vector<AminoAcid> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'virtual std::vector<long long int> OptiRefMatrix::getTranslatedBins(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<std::vector<long long int> >&)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/proteindb.hpp:12,
from source/datastructures/proteindb.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Protein&}; _Tp = Protein; _Alloc = std::allocator<Protein>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Protein>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
source/datastructures/optirefmatrix.cpp:286:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
286 | }
| ^
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/proteindb.hpp:12,
from source/datastructures/proteindb.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void ProteinDB::push_back(Protein)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Protein*, std::vector<Protein> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optirefmatrix.hpp:12,
from source/datastructures/optirefmatrix.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'std::map<long long int, long long int> OptiRefMatrix::readPhylipSingletons(std::vector<bool>&, std::string, long long int&, std::map<std::__cxx11::basic_string<char>, long long int>&)':
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor 'ProteinDB::ProteinDB(std::ifstream&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Protein*, std::vector<Protein> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/proteindb.hpp:12,
from source/datastructures/proteindb.cpp:9:
/usr/include/c++/11/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const AminoAcid*, std::vector<AminoAcid> >; _ForwardIterator = AminoAcid*; bool _TrivialValueTypes = false]':
/usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const AminoAcid*, std::vector<AminoAcid> >' changed in GCC 7.1
85 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:85:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const AminoAcid*, std::vector<AminoAcid> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h: In function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = AminoAcid; _Alloc = std::allocator<AminoAcid>]':
/usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const AminoAcid*, std::vector<AminoAcid> >' changed in GCC 7.1
148 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
151 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiRefMatrix::readPhylip(std::string, bool, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, long long int>&, std::map<long long int, long long int>&)':
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/proteindb.hpp:12,
from source/datastructures/proteindb.cpp:9:
/usr/include/c++/11/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 = Protein; _Alloc = std::allocator<Protein>]':
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<Protein>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiRefMatrix::readFiles(std::string, std::string, std::string, std::string, std::set<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/protein.hpp:12,
from source/datastructures/proteindb.hpp:12,
from source/datastructures/proteindb.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In constructor 'ProteinDB::ProteinDB(int)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Protein*, std::vector<Protein> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiRefMatrix::readFiles(std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string, std::string)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/report.o source/datastructures/report.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/storagedatabase.hpp:12,
from source/datastructures/sequencedb.h:16,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/11/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 = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sffheader.o source/datastructures/sffheader.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/storagedatabase.hpp:12,
from source/datastructures/sequencedb.h:16,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(int)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/storagedatabase.hpp:12,
from source/datastructures/sequencedb.h:16,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Sequence&}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/storagedatabase.hpp:12,
from source/datastructures/sequencedb.h:16,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void SequenceDB::push_back(Sequence)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(std::ifstream&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(const SequenceDB&, std::set<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(const SequenceDB&, std::set<std::__cxx11::basic_string<char> >, int, std::vector<std::vector<int> >&, std::vector<int>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(std::ifstream&, int, std::vector<std::vector<int> >&, std::vector<int>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sffread.o source/datastructures/sffread.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedclrvector.o source/datastructures/sharedclrvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedclrvectors.o source/datastructures/sharedclrvectors.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundfloatvectors.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/taxonomy.o source/datastructures/taxonomy.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engines/batchengine.o source/engines/batchengine.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engines/interactengine.o source/engines/interactengine.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engines/scriptengine.o source/engines/scriptengine.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permute_and_calc_ts(std::vector<std::vector<double> >&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_heap.h:134:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
134 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _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++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1642 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1642:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1917:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1917 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int ReadBlast::read(NameAssignment*)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'int MothurMetastats::runMetastats(std::string, std::vector<std::vector<double> >&, int, std::vector<std::__cxx11::basic_string<char> >, bool)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::__cxx11::basic_string<char> > ReadPhylipVector::read(std::vector<seqDist>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/alignreport.o source/alignreport.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/svm/svm.hpp:23,
from source/svm/svm.cpp:17:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:60,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/11/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++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function 'void SmoTrainer::assignNumericLabels(std::vector<double>&, const LabeledObservationVector&, NumericClassToLabel&)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/svm/svm.hpp:23,
from source/svm/svm.cpp:17:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'SVM* SmoTrainer::train(KernelFunctionCache&, const LabeledObservationVector&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandfactory.o source/commandfactory.cpp
In file included from /usr/include/c++/11/map:60,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/11/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 = std::vector<std::__cxx11::basic_string<char> >; _Val = std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary>; _KeyOfValue = std::_Select1st<std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary> >; _Compare = std::less<std::vector<std::__cxx11::basic_string<char> > >; _Alloc = std::allocator<std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary> >]':
/usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type 'std::_Rb_tree<std::vector<std::__cxx11::basic_string<char> >, std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary>, std::_Select1st<std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary> >, std::less<std::vector<std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary> > >::const_iterator' changed in GCC 7.1
2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/11/bits/stl_map.h: In constructor 'ParameterSetBuilder::ParameterSetBuilder(const ParameterRangeMap&)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/completelinkage.o source/completelinkage.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/consensus.o source/consensus.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/currentfile.o source/currentfile.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/dlibshuff.o source/dlibshuff.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/gotohoverlap.o source/gotohoverlap.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void SharedOneColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void OneColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void ThreeColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void SharedThreeColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmap.o source/heatmap.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmapsim.o source/heatmapsim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/heatmapsim.h:12,
from source/heatmapsim.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<std::__cxx11::basic_string<char> > HeatMapSim::getPic(SharedRAbundVectors*&, std::vector<Calculator*>, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::string HeatMapSim::getPic(std::vector<std::vector<double> >, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothurout.o source/mothurout.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::transpose(std::vector<std::vector<double> >)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&, int)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'int LinearAlgebra::svd(std::vector<std::vector<double> >&, std::vector<double>&, std::vector<std::vector<double> >&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In function 'double getDist(std::vector<int>&, std::vector<int>&, std::vector<std::vector<double> >&, MothurOut*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const linePair&}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int correctDist::createProcess(std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optifitcluster.o source/optifitcluster.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/11/bits/stl_map.h: In member function 'double LinearAlgebra::calcKruskalWallis(std::vector<spearmanRank>&, double&)':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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<long long int&&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function '_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val<const long long int>]':
/usr/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
813 | __remove_if(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<double> OptiCluster::getStats(double&, double&, double&, double&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, std::__cxx11::basic_string<char> >; _KeyOfValue = std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
/usr/include/c++/11/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<long long int&&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const long long int, long long int> >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiCluster::initialize(double&, bool, std::string)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> OptiCluster::getCloseFarCounts(long long int, long long int)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'virtual bool OptiCluster::update(double&)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_algo.h:860:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
860 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
861 | __gnu_cxx::__ops::__iter_equals_val(__value));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<double> OptiFitCluster::getStats(double&, double&, double&, double&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<double> OptiFitCluster::getFitStats(double&, double&, double&, double&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function '_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val<const int>]':
/usr/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
813 | __remove_if(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:813:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In member function 'virtual void RareDisplay::close()':
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void RareDisplay::update(SAbundVector&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'ListVector* OptiFitCluster::getFittedList(std::string, bool)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual void RareDisplay::update(std::vector<SharedRAbundVector*>, int)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/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 = long long int; _Val = std::pair<const long long int, std::__cxx11::basic_string<char> >; _KeyOfValue = std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > >]':
/usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::__cxx11::basic_string<char> >, std::_Select1st<std::pair<const long long int, std::__cxx11::basic_string<char> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::__cxx11::basic_string<char> > > >::const_iterator' changed in GCC 7.1
2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'int OptiFitCluster::initialize(double&, bool, std::vector<std::vector<std::__cxx11::basic_string<char> > >, std::vector<std::__cxx11::basic_string<char> >, std::string, bool)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/sensspeccalc.o source/sensspeccalc.cpp
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual bool OptiFitCluster::update(double&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_algo.h:860:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
860 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
861 | __gnu_cxx::__ops::__iter_equals_val(__value));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, long long int>, std::_Select1st<std::pair<const long long int, long long int> >, std::less<long long int>, std::allocator<std::pair<const long long int, long long int> > >::const_iterator' changed in GCC 7.1
520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
521 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
522 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'double RefChimeraTest::alignQueryToReferences(std::string, std::string, std::string&, std::string&, double&)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/subsample.o source/subsample.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/summary.o source/summary.cpp
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In member function 'double SLibshuff::sCalculate(int, int)':
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'int seqNoise::countDiffs(std::vector<int>, std::vector<int>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/subsample.h:12,
from source/subsample.cpp:9:
/usr/include/c++/11/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 long long int&>, std::tuple<>}; _Key = long long int; _Val = std::pair<const long long int, std::set<long long int> >; _KeyOfValue = std::_Select1st<std::pair<const long long int, std::set<long long int> > >; _Compare = std::less<long long int>; _Alloc = std::allocator<std::pair<const long long int, std::set<long long int> > >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::set<long long int> >, std::_Select1st<std::pair<const long long int, std::set<long long int> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::set<long long int> > > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/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 float&>, std::tuple<>}; _Key = float; _Val = std::pair<const float, long long int>; _KeyOfValue = std::_Select1st<std::pair<const float, long long int> >; _Compare = std::less<float>; _Alloc = std::allocator<std::pair<const float, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<float, std::pair<const float, long long int>, std::_Select1st<std::pair<const float, long long int> >, std::less<float>, std::allocator<std::pair<const float, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<float, std::pair<const float, long long int>, std::_Select1st<std::pair<const float, long long int> >, std::less<float>, std::allocator<std::pair<const float, long long int> > >::const_iterator' changed in GCC 7.1
/usr/include/c++/11/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, 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++/11/bits/stl_tree.h:2426:7: 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' changed in GCC 7.1
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/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 = int; _Tp = long long int; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, long long int> >]':
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getDefaults()':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/subsample.h:12,
from source/subsample.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'std::set<long long int> SubSample::getWeightedSample(std::map<long long int, long long int>&, long long int)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::set<long long int> >, std::_Select1st<std::pair<const long long int, std::set<long long int> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::set<long long int> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::set<long long int> >, std::_Select1st<std::pair<const long long int, std::set<long long int> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::set<long long int> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long int, std::pair<const long long int, std::set<long long int> >, std::_Select1st<std::pair<const long long int, std::set<long long int> > >, std::less<long long int>, std::allocator<std::pair<const long long int, std::set<long long int> > > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In function 'void driverAlignSummarySummarize(seqSumData*)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<float, std::pair<const float, long long int>, std::_Select1st<std::pair<const float, long long int> >, std::less<float>, std::allocator<std::pair<const float, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<float, std::pair<const float, long long int>, std::_Select1st<std::pair<const float, long long int> >, std::less<float>, std::allocator<std::pair<const float, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::string, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >)':
source/utils.cpp:781:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
781 | system(versionTestCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)':
source/utils.cpp:1349:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1349 | system(command.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {linePair}; _Tp = linePair; _Alloc = std::allocator<linePair>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int Summary::summarizeFasta(std::string, std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int Summary::summarizeAlignSummary(std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<float, std::pair<const float, long long int>, std::_Select1st<std::pair<const float, long long int> >, std::less<float>, std::allocator<std::pair<const float, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<float, std::pair<const float, long long int>, std::_Select1st<std::pair<const float, long long int> >, std::less<float>, std::allocator<std::pair<const float, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int Summary::summarizeFastaSummary(std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'long long int Summary::summarizeContigsSummary(std::string)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp
/usr/include/c++/11/bits/stl_algo.h: In member function 'double Utils::median(std::vector<double>)':
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const seqDist&}; _Tp = seqDist; _Alloc = std::allocator<seqDist>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getAverages(std::vector<std::vector<std::vector<seqDist> > >&, std::string)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getAverages(std::vector<std::vector<std::vector<seqDist> > >&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getStandardDeviation(std::vector<std::vector<std::vector<seqDist> > >&, std::vector<std::vector<seqDist> >&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getStandardDeviation(std::vector<std::vector<std::vector<seqDist> > >&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/venn.h:13,
from source/venn.cpp:10:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/venn.h:13,
from source/venn.cpp:10:
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::shuffle(_RAIter, _RAIter, _UGenerator&&) [with _RAIter = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _UGenerator = std::mersenne_twister_engine<long long unsigned int, 64, 312, 156, 31, 13043109905998158313, 29, 6148914691236517205, 17, 8202884508482404352, 37, 18444473444759240704, 43, 6364136223846793005>&]':
/usr/include/c++/11/bits/stl_algo.h:3729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
3729 | shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~
/usr/include/c++/11/bits/stl_algo.h:3729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:3729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
source/utils.cpp: In member function 'void Utils::mothurRandomShuffle(std::vector<long long int>&)':
source/utils.cpp:138:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
138 | shuffle (randomize.begin(), randomize.end(), mersenne_twister_engine);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from source/mothur.h:51,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function 'void std::shuffle(_RAIter, _RAIter, _UGenerator&&) [with _RAIter = __gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >; _UGenerator = std::mersenne_twister_engine<long long unsigned int, 64, 312, 156, 31, 13043109905998158313, 29, 6148914691236517205, 17, 8202884508482404352, 37, 18444473444759240704, 43, 6364136223846793005>&]':
/usr/include/c++/11/bits/stl_algo.h:3729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >' changed in GCC 7.1
3729 | shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~
/usr/include/c++/11/bits/stl_algo.h:3729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:3729:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >' changed in GCC 7.1
source/utils.cpp: In member function 'void Utils::mothurRandomShuffle(std::vector<weightedSeq>&)':
source/utils.cpp:127:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >' changed in GCC 7.1
127 | shuffle (randomize.begin(), randomize.end(), mersenne_twister_engine);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd ..
make[3]: Entering directory '/<<PKGBUILDDIR>>/source/uchime_src'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/source/uchime_src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/source/uchime_src'
make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o addtargets2.o addtargets2.cpp
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchime.o alignchime.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosEachLine(std::string, long long int&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::getAverages(std::vector<std::vector<double> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::getStandardDeviation(std::vector<std::vector<double> >&, std::vector<double>&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::getStandardDeviation(std::vector<std::vector<double> >&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosFasta(std::string, long long int&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::divideFilePerLine(std::string, int&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/calculators/calculator.h:5,
from source/venn.h:13,
from source/venn.cpp:10:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::divideFile(std::string, int&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosFasta(std::string, long long int&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::divideFile(std::string, int&, char)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosEachLine(std::string, long long unsigned int&)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchimel.o alignchimel.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnparams.o alnparams.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alpha.o alpha.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alpha2.o alpha2.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o fractid.o fractid.cpp
In file included from /usr/include/c++/11/set:60,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/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>, long long int>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> >]':
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from source/mothur.h:43,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_map.h: In member function 'void Utils::readNames(std::string, std::map<std::__cxx11::basic_string<char>, long long int>&)':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o getparents.o getparents.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o globalalign2.o globalalign2.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o make3way.o make3way.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mx.o mx.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o myutils.o myutils.cpp
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<std::__cxx11::basic_string<char> > Venn::getPic(std::vector<SharedRAbundVector*>, std::vector<Calculator*>, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Taxonomy&}; _Tp = Taxonomy; _Alloc = std::allocator<Taxonomy>]':
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Taxonomy>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function 'void Utils::readConsTax(std::string, std::vector<Taxonomy>&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function 'std::vector<Taxonomy> Utils::readConsTax(std::string, PhyloTree&)':
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o path.o path.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o searchchime.o searchchime.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqdb.o seqdb.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o setnucmx.o setnucmx.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sfasta.o sfasta.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tracebackbit.o tracebackbit.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o uchime_main.o uchime_main.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o usort.o usort.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o viterbifast.o viterbifast.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o writechhit.o writechhit.cpp
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/source/uchime_src'
g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/engines/ -Lsource/metastats/ -Lsource/read/ -Lsource/svm/ -o mothur source/calculators/accuracy.o source/calculators/ace.o source/calculators/bergerparker.o source/calculators/boneh.o source/calculators/bootstrap.o source/calculators/bstick.o source/calculators/calculator.o source/calculators/canberra.o source/calculators/chao1.o source/calculators/coverage.o source/calculators/diversityutils.o source/calculators/eachgapdist.o source/calculators/eachgapignore.o source/calculators/efron.o source/calculators/erarefaction.o source/calculators/f1score.o source/calculators/fdr.o source/calculators/fn.o source/calculators/fp.o source/calculators/fpfn.o source/calculators/geom.o source/calculators/goodscoverage.o source/calculators/gower.o source/calculators/hamming.o source/calculators/heip.o source/calculators/hellinger.o source/calculators/igabundance.o source/calculators/ignoregaps.o source/calculators/igrarefaction.o source/calculators/invsimpson.o source/calculators/jackknife.o source/calculators/kimura.o source/calculators/kmerdist.o source/calculators/lnabundance.o source/calculators/lnrarefaction.o source/calculators/lnshift.o source/calculators/logsd.o source/calculators/lsabundance.o source/calculators/lsrarefaction.o source/calculators/manhattan.o source/calculators/mcc.o source/calculators/memchi2.o source/calculators/memchord.o source/calculators/memeuclidean.o source/calculators/mempearson.o source/calculators/metroig.o source/calculators/metrolognormal.o source/calculators/metrologstudent.o source/calculators/metrosichel.o source/calculators/npshannon.o source/calculators/npv.o source/calculators/odum.o source/calculators/onegapdist.o source/calculators/onegapignore.o source/calculators/parsimony.o source/calculators/ppv.o source/calculators/prng.o source/calculators/qstat.o source/calculators/sensitivity.o source/calculators/shannon.o source/calculators/shannoneven.o source/calculators/shannonrange.o source/calculators/sharedace.o source/calculators/sharedanderbergs.o source/calculators/sharedbraycurtis.o source/calculators/sharedchao1.o source/calculators/sharedjabund.o source/calculators/sharedjackknife.o source/calculators/sharedjclass.o source/calculators/sharedjest.o source/calculators/sharedjsd.o source/calculators/sharedkstest.o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynskicody.o source/calculators/sharedlennon.o source/calculators/sharedmarczewski.o source/calculators/sharedmorisitahorn.o source/calculators/sharedochiai.o source/calculators/sharedrjsd.o source/calculators/sharedsobs.o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsorabund.o source/calculators/sharedsorclass.o source/calculators/sharedsorest.o source/calculators/sharedthetan.o source/calculators/sharedthetayc.o source/calculators/shen.o source/calculators/siabundance.o source/calculators/simpson.o source/calculators/simpsoneven.o source/calculators/sirarefaction.o source/calculators/sishift.o source/calculators/smithwilson.o source/calculators/soergel.o source/calculators/solow.o source/calculators/spearman.o source/calculators/speciesprofile.o source/calculators/specificity.o source/calculators/structchi2.o source/calculators/structchord.o source/calculators/structeuclidean.o source/calculators/structkulczynski.o source/calculators/structpearson.o source/calculators/tn.o source/calculators/tp.o source/calculators/tptn.o source/calculators/unweighted.o source/calculators/uvest.o source/calculators/weighted.o source/calculators/whittaker.o source/chimera/bellerophon.o source/chimera/ccode.o source/chimera/chimeracheckrdp.o source/chimera/chimerarealigner.o source/chimera/chimeraslayer.o source/chimera/decalc.o source/chimera/maligner.o source/chimera/mothurchimera.o source/chimera/myPerseus.o source/chimera/pintail.o source/chimera/slayer.o source/classifier/alignnode.o source/classifier/aligntree.o source/classifier/bayesian.o source/classifier/classify.o source/classifier/kmernode.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/phylosummary.o source/classifier/phylotree.o source/classifier/taxonomyequalizer.o source/classifier/taxonomynode.o source/clearcut/clearcut.o source/clearcut/cmdargs.o source/clearcut/distclearcut.o source/clearcut/dmat.o source/clearcut/fasta.o source/clearcut/getopt_long.o source/commands/aligncheckcommand.o source/commands/aligncommand.o source/commands/amovacommand.o source/commands/anosimcommand.o source/commands/binsequencecommand.o source/commands/biominfocommand.o source/commands/chimerabellerophoncommand.o source/commands/chimeraccodecommand.o source/commands/chimeracheckcommand.o source/commands/chimeraperseuscommand.o source/commands/chimerapintailcommand.o source/commands/chimeraslayercommand.o source/commands/chimerauchimecommand.o source/commands/chimeravsearchcommand.o source/commands/chopseqscommand.o source/commands/classifyotucommand.o source/commands/classifyseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/classifytreecommand.o source/commands/clearcutcommand.o source/commands/clustercommand.o source/commands/clusterdoturcommand.o source/commands/clusterfitcommand.o source/commands/clusterfragmentscommand.o source/commands/clustersplitcommand.o source/commands/collectcommand.o source/commands/collectsharedcommand.o source/commands/consensusseqscommand.o source/commands/cooccurrencecommand.o source/commands/corraxescommand.o source/commands/countgroupscommand.o source/commands/countseqscommand.o source/commands/createdatabasecommand.o source/commands/deconvolutecommand.o source/commands/degapseqscommand.o source/commands/deuniqueseqscommand.o source/commands/deuniquetreecommand.o source/commands/distancecommand.o source/commands/distsharedcommand.o source/commands/diversityestimatorcommand.o source/commands/filterseqscommand.o source/commands/filtersharedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/getcurrentcommand.o source/commands/getdistscommand.o source/commands/getgroupcommand.o source/commands/getgroupscommand.o source/commands/getlabelcommand.o source/commands/getlineagecommand.o source/commands/getlistcountcommand.o source/commands/getmetacommunitycommand.o source/commands/getmimarkspackagecommand.o source/commands/getoturepcommand.o source/commands/getotuscommand.o source/commands/getrabundcommand.o source/commands/getrelabundcommand.o source/commands/getsabundcommand.o source/commands/getseqscommand.o source/commands/getsharedotucommand.o source/commands/heatmapcommand.o source/commands/heatmapsimcommand.o source/commands/helpcommand.o source/commands/homovacommand.o source/commands/indicatorcommand.o source/commands/kruskalwalliscommand.o source/commands/lefsecommand.o source/commands/libshuffcommand.o source/commands/listotuscommand.o source/commands/listseqscommand.o source/commands/makebiomcommand.o source/commands/makeclrcommand.o source/commands/makecontigscommand.o source/commands/makefastqcommand.o source/commands/makefilecommand.o source/commands/makegroupcommand.o source/commands/makelefsecommand.o source/commands/makelookupcommand.o source/commands/makesharedcommand.o source/commands/mantelcommand.o source/commands/mergecountcommand.o source/commands/mergefilecommand.o source/commands/mergegroupscommand.o source/commands/mergeotuscommand.o source/commands/mergesfffilecommand.o source/commands/mergetaxsummarycommand.o source/commands/metastatscommand.o source/commands/mgclustercommand.o source/commands/mimarksattributescommand.o source/commands/newcommandtemplate.o source/commands/nmdscommand.o source/commands/nocommands.o source/commands/normalizesharedcommand.o source/commands/otuassociationcommand.o source/commands/otuhierarchycommand.o source/commands/pairwiseseqscommand.o source/commands/parsefastaqcommand.o source/commands/parsimonycommand.o source/commands/pcacommand.o source/commands/pcoacommand.o source/commands/pcrseqscommand.o source/commands/phylodiversitycommand.o source/commands/phylotypecommand.o source/commands/preclustercommand.o source/commands/primerdesigncommand.o source/commands/quitcommand.o source/commands/rarefactcommand.o source/commands/rarefactsharedcommand.o source/commands/removedistscommand.o source/commands/removegroupscommand.o source/commands/removelineagecommand.o source/commands/removeotuscommand.o source/commands/removerarecommand.o source/commands/removeseqscommand.o source/commands/renamefilecommand.o source/commands/renameseqscommand.o source/commands/reversecommand.o source/commands/screenseqscommand.o source/commands/sensspeccommand.o source/commands/seqerrorcommand.o source/commands/seqsummarycommand.o source/commands/setcurrentcommand.o source/commands/setdircommand.o source/commands/setlogfilecommand.o source/commands/setseedcommand.o source/commands/sffinfocommand.o source/commands/sffmultiplecommand.o source/commands/shhhercommand.o source/commands/shhhseqscommand.o source/commands/sortseqscommand.o source/commands/sparcccommand.o source/commands/splitabundcommand.o source/commands/splitgroupscommand.o source/commands/sracommand.o source/commands/srainfocommand.o source/commands/subsamplecommand.o source/commands/summarycommand.o source/commands/summaryqualcommand.o source/commands/summarysharedcommand.o source/commands/summarytaxcommand.o source/commands/systemcommand.o source/commands/treesharedcommand.o source/commands/trimflowscommand.o source/commands/trimseqscommand.o source/commands/unifracunweightedcommand.o source/commands/unifracweightedcommand.o source/commands/venncommand.o source/communitytype/communitytype.o source/communitytype/kmeans.o source/communitytype/pam.o source/communitytype/qFinderDMM.o source/datastructures/alignment.o source/datastructures/alignmentcell.o source/datastructures/alignmentdb.o source/datastructures/aminoacid.o source/datastructures/biom.o source/datastructures/biomhdf5.o source/datastructures/biomsimple.o source/datastructures/blastalign.o source/datastructures/blastdb.o source/datastructures/contigsreport.o source/datastructures/counttable.o source/datastructures/designmap.o source/datastructures/distancedb.o source/datastructures/fastamap.o source/datastructures/fastqread.o source/datastructures/filefile.o source/datastructures/flowdata.o source/datastructures/fullmatrix.o source/datastructures/groupmap.o source/datastructures/kmer.o source/datastructures/kmeralign.o source/datastructures/kmerdb.o source/datastructures/listvector.o source/datastructures/nameassignment.o source/datastructures/oligos.o source/datastructures/optiblastmatrix.o source/datastructures/optidata.o source/datastructures/optidb.o source/datastructures/optimatrix.o source/datastructures/optirefmatrix.o source/datastructures/ordervector.o source/datastructures/picrust.o source/datastructures/protein.o source/datastructures/proteindb.o source/datastructures/qualityscores.o source/datastructures/rabundfloatvector.o source/datastructures/rabundvector.o source/datastructures/report.o source/datastructures/sabundvector.o source/datastructures/sequence.o source/datastructures/sequencecountparser.o source/datastructures/sequencedb.o source/datastructures/sequenceparser.o source/datastructures/sffheader.o source/datastructures/sffread.o source/datastructures/sharedclrvector.o source/datastructures/sharedclrvectors.o source/datastructures/sharedlistvector.o source/datastructures/sharedordervector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvectors.o source/datastructures/sparsedistancematrix.o source/datastructures/sparsematrix.o source/datastructures/suffixdb.o source/datastructures/suffixnodes.o source/datastructures/suffixtree.o source/datastructures/taxonomy.o source/datastructures/tree.o source/datastructures/treemap.o source/datastructures/treenode.o source/engines/batchengine.o source/engines/interactengine.o source/engines/scriptengine.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/read/readblast.o source/read/readcluster.o source/read/readcolumn.o source/read/readphylip.o source/read/readphylipvector.o source/read/readtree.o source/read/splitmatrix.o source/read/treereader.o source/svm/svm.o source/alignreport.o source/averagelinkage.o source/calcsparcc.o source/cluster.o source/clusterclassic.o source/collect.o source/commandfactory.o source/commandoptionparser.o source/completelinkage.o source/consensus.o source/currentfile.o source/dlibshuff.o source/fileoutput.o source/gotohoverlap.o source/heatmap.o source/heatmapsim.o source/inputdata.o source/libshuff.o source/linearalgebra.o source/mothur.o source/mothurout.o source/myseqdist.o source/nast.o source/needlemanoverlap.o source/noalign.o source/opticluster.o source/optifitcluster.o source/optionparser.o source/overlap.o source/raredisplay.o source/rarefact.o source/refchimeratest.o source/sensspeccalc.o source/seqnoise.o source/singlelinkage.o source/slibshuff.o source/subsample.o source/summary.o source/trialSwap2.o source/trimoligos.o source/utils.o source/validcalculator.o source/validparameter.o source/venn.o source/vsearchfileparser.o source/weightedlinkage.o source/wilcox.o -lreadline
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# source/uchime_src/mk vanished from upstream source so this should probably not be called any more)
# (cd source/uchime_src && CXX=g++ ./mk && mv uchime ../..)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
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_missing -a
debian/rules override_dh_dwz
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo Do not run dh_dwz due to:
Do not run dh_dwz due to:
echo " dwz: Too few files for multifile optimization"
dwz: Too few files for multifile optimization
echo " objcopy: 'debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug': No such file"
objcopy: 'debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug': No such file
echo " dh_dwz: objcopy --compress-debug-sections debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug returned exit code 1"
dh_dwz: objcopy --compress-debug-sections debian/mothur/usr/lib/debug/.dwz/x86_64-linux-gnu/mothur.debug returned exit code 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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/mothur was not linked against ld-linux-armhf.so.3 (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' in '../mothur_1.46.1-1_armhf.deb'.
dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.46.1-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mothur_1.46.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-11-11T09:56:09Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mothur_1.46.1-1_armhf.changes:
------------------------------
Format: 1.8
Date: Mon, 08 Nov 2021 18:08:09 +0100
Source: mothur
Binary: mothur mothur-dbgsym
Architecture: armhf
Version: 1.46.1-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mothur - sequence analysis suite for research on microbiota
Closes: 984243
Changes:
mothur (1.46.1-1) unstable; urgency=medium
.
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.6.0 (routine-update)
* Fix build with gcc-11
Closes: #984243
* Follow parts of the hints by Aaron M. Ucko
* Fix linking
.
[ Hamid Nassiby ]
* Fix linking
Checksums-Sha1:
70f31d2cdd148b7a8053370cbba7fcdaa0f662bd 161598724 mothur-dbgsym_1.46.1-1_armhf.deb
4b69f6ea78d83dda201c3f9d22c5799aa478b0fb 5656 mothur_1.46.1-1_armhf.buildinfo
b6b3fb1839d7afe3970d5121546152966dae320e 3950480 mothur_1.46.1-1_armhf.deb
Checksums-Sha256:
4b18c49e6650f2d1d39afe381f51fded56fcde49f1f6661233270ebf5645442f 161598724 mothur-dbgsym_1.46.1-1_armhf.deb
7646df5a5ad5c65f76b4348cd8b13073d52d54f7efcf95f7116ac1ac221905bf 5656 mothur_1.46.1-1_armhf.buildinfo
839f35de77e74fb9a17492ef4c15f3e424e1e950e08e55e2bc53ad41d3962935 3950480 mothur_1.46.1-1_armhf.deb
Files:
2d02fff14b184783bb3ccc1081debe78 161598724 debug optional mothur-dbgsym_1.46.1-1_armhf.deb
e5786c8a553103af90c3154d2461fd3e 5656 science optional mothur_1.46.1-1_armhf.buildinfo
c334e2103e1c7cf1ba42f99927075666 3950480 science optional mothur_1.46.1-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mothur-dbgsym_1.46.1-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 161598724 bytes: control archive=596 bytes.
412 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: mothur-dbgsym
Source: mothur
Version: 1.46.1-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 162395
Depends: mothur (= 1.46.1-1)
Section: debug
Priority: optional
Description: debug symbols for mothur
Build-Ids: 43092ee69368c47f9924bee88f303fe790f66a85 7da5be485f625f1537287e5cf0b37be72678c50c
drwxr-xr-x root/root 0 2021-11-08 17:08 ./
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/lib/debug/.build-id/43/
-rw-r--r-- root/root 47316 2021-11-08 17:08 ./usr/lib/debug/.build-id/43/092ee69368c47f9924bee88f303fe790f66a85.debug
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 166232456 2021-11-08 17:08 ./usr/lib/debug/.build-id/7d/a5be485f625f1537287e5cf0b37be72678c50c.debug
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-11-08 17:08 ./usr/share/doc/mothur-dbgsym -> mothur
mothur_1.46.1-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 3950480 bytes: control archive=1324 bytes.
817 bytes, 18 lines control
762 bytes, 12 lines md5sums
185 bytes, 7 lines * postinst #!/bin/sh
160 bytes, 5 lines * postrm #!/bin/sh
Package: mothur
Version: 1.46.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14652
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libreadline8 (>= 6.0), libstdc++6 (>= 11)
Conflicts: uchime
Provides: uchime
Section: science
Priority: optional
Homepage: https://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 2021-11-08 17:08 ./
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/bin/
-rwxr-xr-x root/root 14780464 2021-11-08 17:08 ./usr/bin/mothur
-rwxr-xr-x root/root 175936 2021-11-08 17:08 ./usr/bin/uchime
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/doc/mothur/
-rw-r--r-- root/root 12687 2021-11-08 17:08 ./usr/share/doc/mothur/HA.fasta.gz
-rw-r--r-- root/root 259 2021-11-08 17:08 ./usr/share/doc/mothur/README.Debian
-rw-r--r-- root/root 178 2021-11-08 17:08 ./usr/share/doc/mothur/README.test
-rw-r--r-- root/root 4111 2021-11-08 17:08 ./usr/share/doc/mothur/changelog.Debian.gz
-rw-r--r-- root/root 4544 2021-11-08 17:08 ./usr/share/doc/mothur/copyright
-rw-r--r-- root/root 316 2021-11-08 17:08 ./usr/share/doc/mothur/run-unit-test
-rw-r--r-- root/root 400 2021-11-08 17:08 ./usr/share/doc/mothur/test.batch
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/man/
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/man/man1/
-rw-r--r-- root/root 566 2021-11-08 17:08 ./usr/share/man/man1/mothur.1.gz
-rw-r--r-- root/root 3393 2021-11-08 17:08 ./usr/share/man/man1/uchime.1.gz
drwxr-xr-x root/root 0 2021-11-08 17:08 ./usr/share/menu/
-rw-r--r-- root/root 176 2021-11-08 17:08 ./usr/share/menu/mothur
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1675544
Build-Time: 7559
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 602
Job: mothur_1.46.1-1
Machine Architecture: armhf
Package: mothur
Package-Time: 8232
Source-Version: 1.46.1-1
Space: 1675544
Status: successful
Version: 1.46.1-1
--------------------------------------------------------------------------------
Finished at 2021-11-11T09:56:09Z
Build needed 02:17:12, 1675544k disc space