mothur →
1.44.2-1 →
armhf → 2020-07-24 19:20:24
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| mothur 1.44.2-1 (armhf) Fri, 24 Jul 2020 17:03:46 +0000 |
+==============================================================================+
Package: mothur
Version: 1.44.2-1
Source Version: 1.44.2-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-5e0ee444-42f7-4e49-9b42-eb14be1fa949' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 25s (1006 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 1628 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main mothur 1.44.2-1 (dsc) [2071 B]
Get:2 http://172.17.0.1/private bullseye-staging/main mothur 1.44.2-1 (tar) [1606 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main mothur 1.44.2-1 (diff) [20.3 kB]
Fetched 1628 kB in 0s (6908 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mothur-SCYaYi/mothur-1.44.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mothur-SCYaYi' 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-TNLDvE/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-TNLDvE/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-TNLDvE/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-TNLDvE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2627 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 packages were automatically installed and are no longer required:
bsdextrautils libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 24 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12348 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-TNLDvE/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-TNLDvE/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Sources [527 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ Packages [605 B]
Fetched 2465 B in 1s (3283 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 packages were automatically installed and are no longer required:
dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1 libjson-c4 libpam-cap
libssl1.1 netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-9
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0
libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgfortran-9-dev
libgfortran5 libglib2.0-0 libicu-dev libicu67 libmagic-mgc libmagic1
libmount1 libncurses-dev libncurses6 libpipeline1 libreadline-dev
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-9-doc libcoarrays-dev
groff libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev
libboost-container1.71-dev libboost-context1.71-dev
libboost-contract1.71-dev libboost-coroutine1.71-dev
libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-locale1.71-dev libboost-log1.71-dev
libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev
libboost-numpy1.71-dev libboost-program-options1.71-dev
libboost-python1.71-dev libboost-random1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev icu-doc ncurses-doc
readline-doc libtool-doc gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-9
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.71-dev libboost-iostreams1.71.0
libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgfortran-9-dev
libgfortran5 libglib2.0-0 libicu-dev libicu67 libmagic-mgc libmagic1
libncurses-dev libncurses6 libpipeline1 libreadline-dev libsigsegv2
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:
libmount1
1 upgraded, 49 newly installed, 0 to remove and 23 not upgraded.
Need to get 47.9 MB of archives.
After this operation, 290 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TNLDvE/apt_archive ./ sbuild-build-depends-mothur-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmount1 armhf 2.35.2-7 [190 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-14+rpi1 [278 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-14+rpi1 [8112 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-3 [170 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71.0 armhf 1.71.0-6+b1 [435 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-3 [9213 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71-dev armhf 1.71.0-6+b1 [571 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.71.0 armhf 1.71.0-6+b1 [256 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.71-dev armhf 1.71.0-6+b1 [271 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.71.0.3+b2 [4388 B]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2-1 [284 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-4 [116 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libmount1:armhf (2.35.2-7) ...
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Setting up libicu67:armhf (67.1-3) ...
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Setting up libsigsegv2:armhf (2.12-2) ...
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Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
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Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
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Setting up libtool (2.4.6-14) ...
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Setting up m4 (1.4.18-4) ...
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Setting up libboost-regex1.71-dev:armhf (1.71.0-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
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Setting up intltool-debian (0.35.0+20060710.5) ...
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Processing triggers for libc-bin (2.30-8+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_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-14+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-3 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.2-6 libboost-iostreams-dev_1.71.0.3+b2 libboost-iostreams1.71-dev_1.71.0-6+b1 libboost-iostreams1.71.0_1.71.0-6+b1 libboost-regex1.71-dev_1.71.0-6+b1 libboost-regex1.71.0_1.71.0-6+b1 libboost1.71-dev_1.71.0-6+b1 libbz2-1.0_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-14+rpi1 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libhogweed5_3.5.1+really3.5.1-2 libicu-dev_67.1-3 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libreadline-dev_8.0-4 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-6 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mothur-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-6 xz-utils_5.2.4-1 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 '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jul 22 10:01:58 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./mothur_1.44.2-1.dsc
dpkg-source: info: extracting mothur in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mothur_1.44.2.orig.tar.gz
dpkg-source: info: unpacking mothur_1.44.2-1.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 fix_makefile.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-5e0ee444-42f7-4e49-9b42-eb14be1fa949
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 1.44.2-1
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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/consensus.o source/consensus.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothurout.o source/mothurout.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/treenode.h:13,
from source/datastructures/tree.h:13,
from source/consensus.h:13,
from source/consensus.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/mothurout.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/commandoptionparser.hpp:4,
from source/engines/engine.hpp:13,
from source/engines/batchengine.hpp:12,
from source/mothur.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'double getDist(std::vector<int>&, std::vector<int>&, std::vector<std::vector<double> >&, MothurOut*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/subsample.o source/subsample.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/subsample.h:12,
from source/subsample.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int correctDist::createProcess(std::string)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/sensspeccalc.o source/sensspeccalc.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/sensspeccalc.hpp:12,
from source/sensspeccalc.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp
In file included from source/mothur.h:86,
from source/inputdata.h:4,
from source/inputdata.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calcsparcc.h:17,
from source/calcsparcc.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/subsample.h:12,
from source/subsample.cpp:9:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::set<long long int> > >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/subsample.h:12,
from source/subsample.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::set<long long int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::set<long long int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::set<long long int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::transpose(std::vector<std::vector<double> >)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/clusterclassic.h:5,
from source/clusterclassic.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/gotohoverlap.o source/gotohoverlap.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/alignmentcell.hpp:15,
from source/gotohoverlap.cpp:21:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/trimoligos.h:13,
from source/trimoligos.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/9/bits/stl_map.h: In member function 'double LinearAlgebra::calcKruskalWallis(std::vector<spearmanRank>&, double&)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/singlelinkage.cpp:2:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/currentfile.h:16,
from source/validparameter.h:13,
from source/validparameter.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
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:771:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
771 | system(versionTestCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)':
source/utils.cpp:1319:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
1319 | system(command.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'bool Utils::mkDir(std::string&)':
source/utils.cpp:1935:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
1935 | system(makeDirectoryCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'bool Utils::mothurInitialPrep(std::string&, std::string&, std::string&, std::string&, std::string&)':
source/utils.cpp:2054:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
2054 | system("clear");
| ~~~~~~^~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int seqNoise::countDiffs(std::vector<int>, std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optifitcluster.o source/optifitcluster.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'double RefChimeraTest::alignQueryToReferences(std::string, std::string, std::string&, std::string&, double&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Taxonomy>::iterator' {aka '__gnu_cxx::__normal_iterator<Taxonomy*, std::vector<Taxonomy> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function '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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<double> OptiFitCluster::getStats(double&, double&, double&, double&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<double> OptiFitCluster::getFitStats(double&, double&, double&, double&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getAverages(std::vector<std::vector<std::vector<seqDist> > >&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getStandardDeviation(std::vector<std::vector<std::vector<seqDist> > >&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_algo.h:3786:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
3786 | shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~
/usr/include/c++/9/bits/stl_algo.h:3786:5: 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++/9/bits/stl_algo.h:3786:5: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_algo.h:3786:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >' changed in GCC 7.1
3786 | shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~
/usr/include/c++/9/bits/stl_algo.h:3786:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<weightedSeq*, std::vector<weightedSeq> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:3786:5: 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);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual void RareDisplay::update(std::vector<SharedRAbundVector*>, int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::getAverages(std::vector<std::vector<double> >&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/stl_vector.h: In member function 'virtual void RareDisplay::update(SAbundVector&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::getStandardDeviation(std::vector<std::vector<double> >&, std::vector<double>&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/algorithm:62,
from source/mothur.h:50,
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++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::getStandardDeviation(std::vector<std::vector<double> >&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/stl_algo.h: In member function 'virtual void RareDisplay::close()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'ListVector* OptiFitCluster::getFittedList(std::string, bool)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmapsim.o source/heatmapsim.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/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++/9/bits/stl_tree.h:2187:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, std::__cxx11::basic_string<char> > >'} changed in GCC 7.1
2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val<const int>]':
/usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:112:5: 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++/9/vector:67,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual bool OptiFitCluster::update(double&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/optifitcluster.hpp:12,
from source/optifitcluster.cpp:9:
/usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
161 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
162 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Taxonomy> Utils::readConsTax(std::string, PhyloTree&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Taxonomy*, std::vector<Taxonomy> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/currentfile.o source/currentfile.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/currentfile.h:16,
from source/currentfile.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosFasta(std::string, long long int&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosFasta(std::string, long long int&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosEachLine(std::string, long long int&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::setFilePosEachLine(std::string, long long unsigned int&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::divideFile(std::string, int&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::divideFile(std::string, int&, char)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> Utils::divideFilePerLine(std::string, int&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<double> OptiCluster::getStats(double&, double&, double&, double&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'int OptiCluster::initialize(double&, bool, std::string)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
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++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
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++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> OptiCluster::getCloseFarCounts(long long int, long long int)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/bits/stl_algo.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __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++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:112:5: 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++/9/map:61,
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++/9/bits/stl_map.h: In member function 'virtual bool OptiCluster::update(double&)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/opticluster.h:12,
from source/opticluster.cpp:9:
/usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
161 | return __find_if(__first, __last, __pred,
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
162 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmap.o source/heatmap.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedrabundvectors.hpp:12,
from source/heatmap.h:12,
from source/heatmap.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/summary.o source/summary.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'double Utils::median(std::vector<double>)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getDefaults()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function '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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getValues(std::map<float, long long int>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
source/summary.cpp:168:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
168 | }
| ^
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getValues(std::map<int, long long int>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
source/summary.cpp:103:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
103 | }
| ^
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/averagelinkage.cpp:5:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/stl_map.h: In function 'void driverFastaSummarySummarize(seqSumData*)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const float, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandfactory.o source/commandfactory.cpp
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_map.h: In function 'void driverAlignSummarySummarize(seqSumData*)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const float, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const float, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commandfactory.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'long long int Summary::summarizeFasta(std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'long long int Summary::summarizeAlignSummary(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const float, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const float, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'long long int Summary::summarizeFastaSummary(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'long long int Summary::summarizeContigsSummary(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, long long int>, std::_Select1st<std::pair<const int, long long int> >, std::less<int>, std::allocator<std::pair<const int, long long int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp
In file included from source/mothur.h:86,
from source/commandoptionparser.hpp:4,
from source/commandoptionparser.cpp:11:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/dlibshuff.o source/dlibshuff.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/fullmatrix.h:12,
from source/dlibshuff.h:13,
from source/dlibshuff.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/completelinkage.o source/completelinkage.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void ColumnFile::updateOutput(std::vector<double>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/completelinkage.cpp:2:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void SharedOneColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void OneColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void ThreeColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void SharedThreeColumnFile::updateOutput(int, std::vector<double>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/fileoutput.h:4,
from source/fileoutput.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/vsearchfileparser.h:12,
from source/vsearchfileparser.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/alignmentcell.hpp:15,
from source/overlap.cpp:16:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/cluster.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp
In file included from source/mothur.h:86,
from source/datastructures/fullmatrix.h:12,
from source/libshuff.h:13,
from source/libshuff.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/optionparser.h:15,
from source/optionparser.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nastreport.o source/nastreport.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/nastreport.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp
In file included from source/mothur.h:86,
from source/rarefactioncurvedata.h:4,
from source/rarefact.h:4,
from source/rarefact.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/wilcox.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/cluster.hpp:4,
from source/weightedlinkage.cpp:4:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/alignment.hpp:16,
from source/noalign.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp
In file included from source/mothur.h:86,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/nast.cpp:18:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'double SLibshuff::sCalculate(int, int)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/collectorscurvedata.h:4,
from source/collect.h:4,
from source/collect.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/alignmentcell.hpp:15,
from source/needlemanoverlap.cpp:20:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/whittaker.o source/calculators/whittaker.cpp
In file included from source/mothur.h:86,
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/whittaker.h:11,
from source/calculators/whittaker.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Jackknife::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrologstudent.o source/calculators/metrologstudent.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/metrologstudent.hpp:12,
from source/calculators/metrologstudent.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrolognormal.o source/calculators/metrolognormal.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/metrolognormal.hpp:12,
from source/calculators/metrolognormal.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sirarefaction.o source/calculators/sirarefaction.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/sirarefaction.hpp:12,
from source/calculators/sirarefaction.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Hamming::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput KSTest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tn.o source/calculators/tn.cpp
In file included from source/mothur.h:86,
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/tn.hpp:12,
from source/calculators/tn.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Shen::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput InvSimpson::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput ThetaN::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/weighted.o source/calculators/weighted.cpp
In file included from source/mothur.h:86,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SorClass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tp.o source/calculators/tp.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/tp.hpp:12,
from source/calculators/tp.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Shannon::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Boneh::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput NPShannon::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnabundance.o source/calculators/lnabundance.cpp
In file included from /usr/include/c++/9/set:60,
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++/9/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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput RJSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In function 'void driverWeighted(weightedData*)':
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/map:61,
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++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'EstOutput Weighted::createProcesses(Tree*, CountTable*)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> LNAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedchao1.o source/calculators/sharedchao1.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Ochiai::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'virtual EstOutput Weighted::getValues(Tree*, std::string, std::string)':
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/weighted.h:14,
from source/calculators/weighted.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput StructChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/qstat.o source/calculators/qstat.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedChao1::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ignoregaps.o source/calculators/ignoregaps.cpp
In file included from source/mothur.h:86,
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/ignoregaps.h:12,
from source/calculators/ignoregaps.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Chao1::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput QStat::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnrarefaction.o source/calculators/lnrarefaction.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lnrarefaction.hpp:12,
from source/calculators/lnrarefaction.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
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/ignoregaps.h:12,
from source/calculators/ignoregaps.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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/ignoregaps.h:12,
from source/calculators/ignoregaps.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> ignoreGaps::calcDist(Sequence, classifierOTU, std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/specificity.o source/calculators/specificity.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Efron::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/specificity.hpp:12,
from source/calculators/specificity.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchord.o source/calculators/structchord.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Spearman::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput StructPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/uvest.o source/calculators/uvest.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput StructChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igabundance.o source/calculators/igabundance.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/calculators/uvest.h:16,
from source/calculators/uvest.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'EstOutput UVEst::getUVest(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput ShannonEven::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/diversityutils.o source/calculators/diversityutils.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/diversityutils.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> IGAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsabundance.o source/calculators/lsabundance.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput BStick::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metrosichel.o source/calculators/metrosichel.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/metrosichel.hpp:12,
from source/calculators/metrosichel.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedJackknife::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> LSAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fpfn.o source/calculators/fpfn.cpp
In file included from source/mothur.h:86,
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/fpfn.hpp:12,
from source/calculators/fpfn.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapignore.o source/calculators/eachgapignore.cpp
In file included from source/mothur.h:86,
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/eachgapignore.h:13,
from source/calculators/eachgapignore.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/eachgapdist.o source/calculators/eachgapdist.cpp
In file included from source/mothur.h:86,
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/eachgapdist.h:13,
from source/calculators/eachgapdist.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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/eachgapignore.h:13,
from source/calculators/eachgapignore.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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/eachgapignore.h:13,
from source/calculators/eachgapignore.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> eachGapIgnoreTermGapDist::calcDist(Sequence, classifierOTU, std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/siabundance.o source/calculators/siabundance.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Jest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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/eachgapdist.h:13,
from source/calculators/eachgapdist.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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/eachgapdist.h:13,
from source/calculators/eachgapdist.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> eachGapDist::calcDist(Sequence, classifierOTU, std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> SIAbundance::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Hellinger::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sishift.o source/calculators/sishift.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput GoodsCoverage::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npv.o source/calculators/npv.cpp
In file included from source/mothur.h:86,
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/npv.hpp:12,
from source/calculators/npv.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> SIShift::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapignore.o source/calculators/onegapignore.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Odum::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/onegapignore.h:13,
from source/calculators/onegapignore.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fp.o source/calculators/fp.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
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/fp.hpp:12,
from source/calculators/fp.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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/onegapignore.h:13,
from source/calculators/onegapignore.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Ace::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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/onegapignore.h:13,
from source/calculators/onegapignore.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> oneGapIgnoreTermGapDist::calcDist(Sequence, classifierOTU, std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput JSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput MemEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/erarefaction.o source/calculators/erarefaction.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput MemChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/unweighted.o source/calculators/unweighted.cpp
In file included from source/mothur.h:86,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput JAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mcc.o source/calculators/mcc.cpp
In file included from source/mothur.h:86,
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/mcc.hpp:12,
from source/calculators/mcc.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual void ERarefaction::getValues(SAbundVector*, std::vector<double>&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/coverage.o source/calculators/coverage.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Coverage::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/soergel.o source/calculators/soergel.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SorEst::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Soergel::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'EstOutput Unweighted::createProcesses(Tree*, CountTable*)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Heip::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'EstOutput Unweighted::createProcesses(Tree*, std::vector<std::vector<int> >&, CountTable*)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/unweighted.h:14,
from source/calculators/unweighted.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput RangeShannon::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedMarczewski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SimpsonEven::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SorAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/f1score.o source/calculators/f1score.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Solow::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/f1score.hpp:12,
from source/calculators/f1score.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/metroig.o source/calculators/metroig.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/metroig.hpp:12,
from source/calculators/metroig.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput BrayCurtis::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sensitivity.o source/calculators/sensitivity.cpp
In file included from source/mothur.h:86,
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/sensitivity.hpp:12,
from source/calculators/sensitivity.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Lennon::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp
In file included from source/mothur.h:86,
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/accuracy.hpp:12,
from source/calculators/accuracy.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Kulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/calculator.o source/calculators/calculator.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SmithWilson::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/calculator.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/prng.o source/calculators/prng.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput ThetaYC::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tptn.o source/calculators/tptn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lsrarefaction.o source/calculators/lsrarefaction.cpp
In file included from source/mothur.h:86,
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/tptn.hpp:12,
from source/calculators/tptn.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/lsrarefaction.hpp:12,
from source/calculators/lsrarefaction.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput MorHorn::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ppv.o source/calculators/ppv.cpp
In file included from source/mothur.h:86,
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/ppv.hpp:12,
from source/calculators/ppv.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedAce::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/lnshift.o source/calculators/lnshift.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput BergerParker::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/igrarefaction.o source/calculators/igrarefaction.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/calculators/diversitycalc.h:12,
from source/calculators/diversityutils.hpp:20,
from source/calculators/igrarefaction.hpp:12,
from source/calculators/igrarefaction.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> LNShift::getValues(int, std::vector<mcmcSample>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Anderberg::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fn.o source/calculators/fn.cpp
In file included from source/mothur.h:86,
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/fn.hpp:12,
from source/calculators/fn.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput SpeciesProfile::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp
In file included from source/mothur.h:86,
from source/calculators/treecalculator.h:13,
from source/calculators/parsimony.h:14,
from source/calculators/parsimony.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Jclass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Canberra::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput StructKulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fdr.o source/calculators/fdr.cpp
In file included from source/mothur.h:86,
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/fdr.hpp:12,
from source/calculators/fdr.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Gower::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/calculators/treecalculator.h:13,
from source/calculators/parsimony.h:14,
from source/calculators/parsimony.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'EstOutput Parsimony::createProcesses(Tree*, CountTable*)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput StructEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Simpson::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/onegapdist.o source/calculators/onegapdist.cpp
In file included from source/mothur.h:86,
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/onegapdist.h:12,
from source/calculators/onegapdist.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput MemPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput LogSD::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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/onegapdist.h:12,
from source/calculators/onegapdist.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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/onegapdist.h:12,
from source/calculators/onegapdist.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> oneGapDist::calcDist(Sequence, classifierOTU, std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput KulczynskiCody::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput MemChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/geom.o source/calculators/geom.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Manhattan::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Bootstrap::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/pintail.h:13,
from source/chimera/pintail.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual EstOutput Geom::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/bellerophon.o source/chimera/bellerophon.cpp
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/bellerophon.h:14,
from source/chimera/bellerophon.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/chimera/myPerseus.h:14,
from source/chimera/myPerseus.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'double Perseus::basicPairwiseAlignSeqs(std::string, std::string, std::string&, std::string&, pwModel)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp
In file included from source/mothur.h:86,
from source/chimera/decalc.h:12,
from source/chimera/maligner.h:12,
from source/chimera/maligner.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/chimera/mothurchimera.h:14,
from source/chimera/bellerophon.h:14,
from source/chimera/bellerophon.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/chimera/mothurchimera.h:14,
from source/chimera/bellerophon.h:14,
from source/chimera/bellerophon.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int Bellerophon::driverChimeras(std::vector<int>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/chimera/decalc.h:12,
from source/chimera/maligner.h:12,
from source/chimera/maligner.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/chimera/decalc.h:12,
from source/chimera/maligner.h:12,
from source/chimera/maligner.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Sequence> Maligner::minCoverageFilter(std::vector<Sequence>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::string Maligner::chimeraMaligner(int, DeCalculator)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::string Maligner::getResults(Sequence, DeCalculator)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/ccode.o source/chimera/ccode.cpp
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/ccode.h:13,
from source/chimera/ccode.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<data_struct>::iterator' {aka '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'std::vector<data_struct> Slayer::runBellerophon(Sequence, Sequence, Sequence, std::map<int, int>&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:71,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/ostream:38,
from /usr/include/c++/9/iostream:39,
from source/mothur.h:28,
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++/9/bits/predefined_ops.h: In member 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++/9/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
142 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/9/bits/predefined_ops.h:142:9: 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++/9/algorithm:62,
from source/mothur.h:50,
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++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SeqCompare>::iterator' {aka '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence, std::vector<Sequence*>&, int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Sequence> ChimeraSlayer::getKmerSeqs(Sequence, std::vector<Sequence*>&, int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:71,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/ostream:38,
from /usr/include/c++/9/iostream:39,
from source/mothur.h:28,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/predefined_ops.h: In member 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++/9/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
142 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/9/bits/predefined_ops.h:142:9: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: 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++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: 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++/9/bits/stl_heap.h:243:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
81 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
83 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
85 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
90 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
92 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1901:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1901 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1904:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1904 | while (__comp(__pivot, __last))
| ~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: 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++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'std::string Slayer::getResults(Sequence, std::vector<Sequence>)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
81 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
83 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
85 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
90 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
92 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1901:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1901 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1904:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1904 | while (__comp(__pivot, __last))
| ~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int ChimeraSlayer::getChimeras(Sequence*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimerarealigner.o source/chimera/chimerarealigner.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimerarealigner.h:13,
from source/chimera/chimerarealigner.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeracheckrdp.h:14,
from source/chimera/chimeracheckrdp.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp
In file included from source/mothur.h:86,
from source/chimera/mothurchimera.h:14,
from source/chimera/mothurchimera.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp
In file included from source/mothur.h:86,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp
In file included from source/mothur.h:86,
from source/classifier/classify.h:16,
from source/classifier/classify.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp
In file included from source/mothur.h:86,
from source/classifier/phylosummary.h:13,
from source/classifier/phylosummary.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/classifier/taxonomyequalizer.h:14,
from source/classifier/taxonomyequalizer.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Sequence> DeCalculator::findClosest(Sequence, std::vector<Sequence*>&, std::vector<Sequence*>&, int, int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/kmernode.h:14,
from source/classifier/kmernode.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/opticlassifier.o source/classifier/opticlassifier.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp
In file included from source/mothur.h:86,
from source/classifier/opticlassifier.hpp:12,
from source/classifier/opticlassifier.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/classifier/phylotree.h:14,
from source/classifier/phylotree.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::string AlignTree::getTaxonomy(Sequence*, std::string&, bool&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/alignnode.h:13,
from source/classifier/alignnode.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/classifier/knn.h:13,
from source/classifier/knn.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual std::string KmerTree::getTaxonomy(Sequence*, std::string&, bool&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp
In file included from source/mothur.h:86,
from source/classifier/bayesian.h:13,
from source/classifier/bayesian.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/classifier/taxonomynode.h:15,
from source/classifier/taxonomynode.cpp:12:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp
In file included from /usr/include/string.h:495,
from source/clearcut/distclearcut.cpp:54:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'DMAT* NJ_compute_dmat(NJ_ARGS*, NJ_alignment*)' at source/clearcut/distclearcut.cpp:155:12:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
source/clearcut/distclearcut.cpp: In function 'DMAT* NJ_compute_dmat(NJ_ARGS*, NJ_alignment*)':
source/clearcut/distclearcut.cpp:155:12: note: length computed here
155 | strncpy(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i]));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp
source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
456 | fscanf(fp, "%ld\n", &dmat->ntaxa);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/reversecommand.h:13,
from source/commands/reversecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotuscommand.o source/commands/listotuscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/listotuscommand.h:13,
from source/commands/listotuscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/commands/chimeraccodecommand.h:13,
from source/commands/chimeraccodecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectcommand.h:12,
from source/commands/collectcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/cooccurrencecommand.h:14,
from source/commands/cooccurrencecommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int CooccurrenceCommand::getCooccurrence(SharedRAbundVectors*&, std::ofstream&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
source/venn.cpp:77:16: note: variable tracking size limit exceeded with '-fvar-tracking-assignments', retrying without
77 | vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs, vector<string> thisOtuLabels) {
| ^~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncheckcommand.o source/commands/aligncheckcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/aligncheckcommand.h:13,
from source/commands/aligncheckcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotuscommand.o source/commands/getotuscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getotuscommand.h:13,
from source/commands/getotuscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makesharedcommand.h:12,
from source/commands/makesharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/listseqscommand.h:13,
from source/commands/listseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/clusterdoturcommand.h:13,
from source/commands/clusterdoturcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/setlogfilecommand.h:13,
from source/commands/setlogfilecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp
In file included from source/mothur.h:86,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
source/commands/distancecommand.cpp:332:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
332 | system(("gzip -v " + outputFile).c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/quitcommand.h:12,
from source/commands/quitcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/removegroupscommand.h:14,
from source/commands/removegroupscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/indicatorcommand.h:13,
from source/commands/indicatorcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void DistanceCommand::createProcesses(std::string)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getgroupscommand.h:14,
from source/commands/getgroupscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqRNode>::iterator' {aka '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int ClusterFragmentsCommand::readFASTA()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:71,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/ios:40,
from /usr/include/c++/9/ostream:38,
from /usr/include/c++/9/iostream:39,
from source/mothur.h:28,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/bits/predefined_ops.h: In member 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++/9/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
142 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/9/bits/predefined_ops.h:142:9: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
81 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
83 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
85 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
90 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
92 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1901:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1901 | while (__comp(__first, __pivot))
| ~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1904:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1904 | while (__comp(__pivot, __last))
| ~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'virtual int ClusterFragmentsCommand::execute()':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/kruskalwalliscommand.h:11,
from source/commands/kruskalwalliscommand.cpp:8:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp
In file included from source/mothur.h:86,
from source/commands/sensspeccommand.h:14,
from source/commands/sensspeccommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/removeseqscommand.h:13,
from source/commands/removeseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mimarksattributescommand.h:12,
from source/commands/mimarksattributescommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/renameseqscommand.h:12,
from source/commands/renameseqscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makegroupcommand.h:13,
from source/commands/makegroupcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/deuniqueseqscommand.h:12,
from source/commands/deuniqueseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/classifyseqscommand.h:14,
from source/commands/classifyseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makefilecommand.h:12,
from source/commands/makefilecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)':
source/commands/makefilecommand.cpp:353:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
353 | system(findCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getdistscommand.h:12,
from source/commands/getdistscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/classifyseqscommand.h:14,
from source/commands/classifyseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int ClassifySeqsCommand::createProcesses(std::string, std::string, std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/summaryqualcommand.h:14,
from source/commands/summaryqualcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summaryqualcommand.h:14,
from source/commands/summaryqualcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/diversityestimatorcommand.hpp:12,
from source/commands/diversityestimatorcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'void driverWeightedRandom(weightedRandomData*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracWeightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/diversityestimatorcommand.hpp:12,
from source/commands/diversityestimatorcommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getcoremicrobiomecommand.h:14,
from source/commands/getcoremicrobiomecommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int GetCoreMicroBiomeCommand::createTable(SharedRAbundFloatVectors*&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int UnifracWeightedCommand::getAverageSTDMatrices(std::vector<std::vector<double> >&, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<mcmcSample>::iterator' {aka '__gnu_cxx::__normal_iterator<mcmcSample*, std::vector<mcmcSample> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<FastqRead>::iterator' {aka '__gnu_cxx::__normal_iterator<FastqRead*, std::vector<FastqRead> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/sffmultiplecommand.h:12,
from source/commands/sffmultiplecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/diversityestimatorcommand.hpp:12,
from source/commands/diversityestimatorcommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int EstimatorSingleCommand::fillSampling(int, int, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<mcmcSample*, std::vector<mcmcSample> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, double>, std::_Select1st<std::pair<const double, double> >, std::less<double>, std::allocator<std::pair<const double, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int EstimatorSingleCommand::processShared(SharedRAbundVectors*&, std::vector<std::basic_ofstream<char>*>&, std::string)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int UnifracWeightedCommand::execute()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'int driverSplitFastq(splitGroupsStruct*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<FastqRead*, std::vector<FastqRead> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/removerarecommand.h:14,
from source/commands/removerarecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/sffmultiplecommand.h:12,
from source/commands/sffmultiplecommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/splitgroupscommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual int SplitGroupCommand::execute()':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/normalizesharedcommand.h:13,
from source/commands/normalizesharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/heatmapsimcommand.h:13,
from source/commands/heatmapsimcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int HeatMapSimCommand::runCommandDist()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/clustercommand.h:12,
from source/commands/clustercommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/degapseqscommand.h:14,
from source/commands/degapseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)':
source/commands/clustercommand.cpp:557:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
557 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/summarytaxcommand.h:13,
from source/commands/summarytaxcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/degapseqscommand.h:14,
from source/commands/degapseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'long long int DegapSeqsCommand::createProcesses(std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/systemcommand.h:13,
from source/commands/systemcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/seqerrorcommand.h:13,
from source/commands/seqerrorcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracUnweightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
source/commands/systemcommand.cpp:99:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
99 | system(command.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void UnifracUnweightedCommand::printUnweightedFile(int)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc: In member function 'int UnifracUnweightedCommand::getAverageSTDMatrices(std::vector<std::vector<double> >&, int)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/unifracunweightedcommand.h:13,
from source/commands/unifracunweightedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int UnifracUnweightedCommand::execute()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/otuhierarchycommand.h:12,
from source/commands/otuhierarchycommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/seqerrorcommand.h:13,
from source/commands/seqerrorcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/seqerrorcommand.h:13,
from source/commands/seqerrorcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<Sequence> SeqErrorCommand::getReferences(std::string)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/c++/9/bits/vector.tcc: In member function '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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/aligncommand.h:12,
from source/commands/aligncommand.cpp:17:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getrelabundcommand.h:13,
from source/commands/getrelabundcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual int AlignCommand::execute()':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/removelineagecommand.h:13,
from source/commands/removelineagecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp
In file included from source/mothur.h:86,
from source/commands/chimerabellerophoncommand.h:13,
from source/commands/chimerabellerophoncommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getsharedotucommand.h:13,
from source/commands/getsharedotucommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/venncommand.h:12,
from source/commands/venncommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getsharedotucommand.h:13,
from source/commands/getsharedotucommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/parsefastaqcommand.h:14,
from source/commands/parsefastaqcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/countgroupscommand.h:13,
from source/commands/countgroupscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergeotuscommand.o source/commands/mergeotuscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mergeotuscommand.hpp:12,
from source/commands/mergeotuscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getsharedotucommand.h:13,
from source/commands/getsharedotucommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int GetSharedOTUCommand::execute()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp
In file included from source/mothur.h:86,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/screenseqscommand.h:12,
from source/commands/screenseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/parsefastaqcommand.h:14,
from source/commands/parsefastaqcommand.cpp:10:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<double> TrimFlowsCommand::getFlowFileBreaks()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsefastaqcommand.h:14,
from source/commands/parsefastaqcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/setdircommand.h:13,
from source/commands/setdircommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int TrimFlowsCommand::createProcessesCreateTrim(std::string, std::string, std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/screenseqscommand.h:12,
from source/commands/screenseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/sracommand.h:12,
from source/commands/sracommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mgclustercommand.h:13,
from source/commands/mgclustercommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/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++/9/bits/stl_tree.h:2187:5: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void ParsimonyCommand::printParsimonyFile()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/splitabundcommand.h:20,
from source/commands/splitabundcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/mgclustercommand.h:13,
from source/commands/mgclustercommand.cpp:10:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'int MGClusterCommand::runOptiCluster()':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function '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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In function 'void driverGetCounts(primerCountsData*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getlistcountcommand.h:12,
from source/commands/getlistcountcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/primerdesigncommand.h:12,
from source/commands/primerdesigncommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/heatmapcommand.h:14,
from source/commands/heatmapcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/deconvolutecommand.h:12,
from source/commands/deconvolutecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mantelcommand.h:13,
from source/commands/mantelcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp
In file included from source/mothur.h:86,
from source/commands/mergetaxsummarycommand.h:12,
from source/commands/mergetaxsummarycommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makefastqcommand.h:14,
from source/commands/makefastqcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<double> MakeLookupCommand::convertSeqToFlow(std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactcommand.h:12,
from source/commands/rarefactcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getlineagecommand.h:13,
from source/commands/getlineagecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makelookupcommand.h:12,
from source/commands/makelookupcommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual int MakeLookupCommand::execute()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarysharedcommand.h:13,
from source/commands/summarysharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'void driverSummaryShared(summarySharedData*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int SummarySharedCommand::runCalcs(SharedRAbundVectors*&, std::string, std::string, std::vector<std::vector<seqDist> >&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/nmdscommand.h:13,
from source/commands/nmdscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int NMDSCommand::normalizeConfiguration(std::vector<std::vector<double> >&, int, int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::readAxes(std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getsabundcommand.h:14,
from source/commands/getsabundcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)':
source/commands/chimeravsearchcommand.cpp:480:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
480 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from source/mothur.h:45,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
In function 'char* strncat(char*, const char*, size_t)',
inlined from 'void driver(vsearchData*)' at source/commands/chimeravsearchcommand.cpp:430:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: 'void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int)' writing 11 bytes into a region of size 9 overflows the destination [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/collectsharedcommand.h:13,
from source/commands/collectsharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int TrimSeqsCommand::setLines(std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runKruskalWallis(SharedRAbundFloatVectors*&, SharedCLRVectors*&, DesignMap&)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotuscommand.o source/commands/removeotuscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/removeotuscommand.h:13,
from source/commands/removeotuscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'int LefseCommand::normalize(SharedRAbundFloatVectors*&, SharedCLRVectors*&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/phylodiversitycommand.h:13,
from source/commands/phylodiversitycommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/filtersharedcommand.h:12,
from source/commands/filtersharedcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/map:61,
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++/9/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runWilcoxon(SharedRAbundFloatVectors*&, SharedCLRVectors*&, DesignMap&, std::map<int, double>, std::map<std::__cxx11::basic_string<char>, std::set<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'int 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> >)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/lefsecommand.h:12,
from source/commands/lefsecommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/pcoacommand.h:13,
from source/commands/pcoacommand.cpp:11:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/filterseqscommand.h:13,
from source/commands/filterseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp
In file included from source/mothur.h:86,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mergesfffilecommand.h:12,
from source/commands/mergesfffilecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/filterseqscommand.h:13,
from source/commands/filterseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'long long int FilterSeqsCommand::createProcessesCreateFilter(Filters&, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void ShhherCommand::getJointLookUp()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int FilterSeqsCommand::filterSequences()':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/subsamplecommand.h:13,
from source/commands/subsamplecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcacommand.h:13,
from source/commands/pcacommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int PCACommand::process(SharedRAbundFloatVectors*&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'int driverShared(metastatsData*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'int driverCLR(metastatsData*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/metastatscommand.h:13,
from source/commands/metastatscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
In file included from source/mothur.h:86,
from source/commands/chimeraslayercommand.h:13,
from source/commands/chimeraslayercommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'int MetaStatsCommand::process(SharedRAbundVectors*&, DesignMap*&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc: In member function 'int MetaStatsCommand::process(SharedCLRVectors*&, DesignMap*&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/chopseqscommand.h:14,
from source/commands/chopseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp
In file included from source/mothur.h:86,
from source/commands/seqsummarycommand.h:13,
from source/commands/seqsummarycommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/chopseqscommand.h:14,
from source/commands/chopseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'bool ChopSeqsCommand::createProcesses(std::string, std::string, std::string, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makebiomcommand.h:13,
from source/commands/makebiomcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getlabelcommand.h:13,
from source/commands/getlabelcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/consensusseqscommand.h:14,
from source/commands/consensusseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/sffinfocommand.h:13,
from source/commands/sffinfocommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/distsharedcommand.h:12,
from source/commands/distsharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'int driver(std::vector<SharedRAbundVector*>&, std::vector<std::vector<seqDist> >&, std::vector<Calculator*>, MothurOut*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/preclustercommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'int process(distSharedData*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/classifytreecommand.h:12,
from source/commands/classifytreecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/corraxescommand.h:13,
from source/commands/corraxescommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int DistSharedCommand::createProcesses(SharedRAbundVectors*&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/clusterfitcommand.hpp:12,
from source/commands/clusterfitcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getseqscommand.h:13,
from source/commands/getseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/splitgroupscommand.h:17,
from source/commands/preclustercommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getmimarkspackagecommand.h:12,
from source/commands/getmimarkspackagecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/setcurrentcommand.h:14,
from source/commands/setcurrentcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/setseedcommand.h:12,
from source/commands/setseedcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::driver(SharedRAbundVectors*&, std::vector<std::vector<seqDist> >&, Calculator*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(SharedRAbundVectors*&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<summaryData>::iterator' {aka '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getcurrentcommand.h:13,
from source/commands/getcurrentcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/srainfocommand.o source/commands/srainfocommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/srainfocommand.hpp:12,
from source/commands/srainfocommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp
In file included from source/mothur.h:86,
from source/commands/mergefilecommand.h:13,
from source/commands/mergefilecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/biominfocommand.h:12,
from source/commands/biominfocommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getgroupcommand.h:13,
from source/commands/getgroupcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/helpcommand.h:14,
from source/commands/helpcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/pcrseqscommand.h:13,
from source/commands/pcrseqscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp
In file included from source/mothur.h:86,
from source/commands/chimeraperseuscommand.h:16,
from source/commands/chimeraperseuscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/makecontigscommand.h:12,
from source/commands/makecontigscommand.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In function 'void driverContigsGroups(groupContigsData*)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > AnosimCommand::convertToRanks(std::vector<std::vector<double> >)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/pcrseqscommand.h:13,
from source/commands/pcrseqscommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/chimeraperseuscommand.h:16,
from source/commands/chimeraperseuscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treesharedcommand.h:13,
from source/commands/treesharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'int driverTreeShared(std::vector<SharedRAbundVector*>&, std::vector<std::vector<seqDist> >&, std::vector<Calculator*>, MothurOut*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'int process(treeSharedData*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/deuniquetreecommand.h:14,
from source/commands/deuniquetreecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/binsequencecommand.h:14,
from source/commands/binsequencecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'int TreeSharedCommand::createProcesses(SharedRAbundVectors*&, CountTable&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/commands/makelefsecommand.h:12,
from source/commands/makelefsecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getrabundcommand.h:14,
from source/commands/getrabundcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/classifyotucommand.h:13,
from source/commands/classifyotucommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/createdatabasecommand.h:12,
from source/commands/createdatabasecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/createdatabasecommand.h:12,
from source/commands/createdatabasecommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/createdatabasecommand.h:12,
from source/commands/createdatabasecommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<int> CreateDatabaseCommand::readFasta(std::vector<Sequence>&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/otuassociationcommand.h:14,
from source/commands/otuassociationcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/otuassociationcommand.h:14,
from source/commands/otuassociationcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void OTUAssociationCommand::readMetadata()':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int SortSeqsCommand::readFasta()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/removedistscommand.h:12,
from source/commands/removedistscommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<QualityScores>::iterator' {aka '__gnu_cxx::__normal_iterator<QualityScores*, std::vector<QualityScores> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/sortseqscommand.h:15,
from source/commands/sortseqscommand.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int SortSeqsCommand::readQual()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<QualityScores*, std::vector<QualityScores> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void OTUAssociationCommand::process(SharedRAbundFloatVectors*&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc: In member function 'void OTUAssociationCommand::process(SharedRAbundVectors*&)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/amovacommand.h:13,
from source/commands/amovacommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/renamefilecommand.h:12,
from source/commands/renamefilecommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/homovacommand.h:14,
from source/commands/homovacommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/clearcutcommand.h:13,
from source/commands/clearcutcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/classifysvmsharedcommand.h:14,
from source/commands/classifysvmsharedcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/countseqscommand.h:13,
from source/commands/countseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/classifysvmsharedcommand.h:14,
from source/commands/classifysvmsharedcommand.cpp:9:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)':
source/commands/chimerauchimecommand.cpp:607:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
607 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In constructor 'ClassifySvmSharedCommand::ClassifySvmSharedCommand(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/set:60,
from source/mothur.h:41,
from source/commands/command.hpp:16,
from source/commands/libshuffcommand.h:13,
from source/commands/libshuffcommand.cpp:16:
/usr/include/c++/9/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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makeclrcommand.o source/commands/makeclrcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/makeclrcommand.hpp:12,
from source/commands/makeclrcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp
In file included from source/mothur.h:86,
from source/commands/chimerapintailcommand.h:13,
from source/commands/chimerapintailcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from source/mothur.h:45,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
In function 'char* strcpy(char*, const char*)',
inlined from 'int driver(uchimeData*)' at source/commands/chimerauchimecommand.cpp:578:19:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:90:33: warning: 'void* __builtin___memcpy_chk(void*, const void*, unsigned int, unsigned int)' writing 6 bytes into a region of size 5 overflows the destination [-Wstringop-overflow=]
90 | return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'int LibShuffCommand::printCoverageFile()':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, std::vector<int> >, std::_Select1st<std::pair<const double, std::vector<int> > >, std::less<double>, std::allocator<std::pair<const double, std::vector<int> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, std::vector<int> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
In file included from source/mothur.h:86,
from source/commands/chimeracheckcommand.h:13,
from source/commands/chimeracheckcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::string, std::string, std::string, double, clusterData*)':
source/commands/clustersplitcommand.cpp:1188:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
1188 | system(commandString.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
source/commands/pairwiseseqscommand.cpp:268:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
268 | system(("gzip -v " + outputFile).c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mergegroupscommand.h:13,
from source/commands/mergegroupscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/mergecountcommand.hpp:12,
from source/commands/mergecountcommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<linePair>::iterator' {aka '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void PairwiseSeqsCommand::createProcesses(std::string)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/getoturepcommand.h:14,
from source/commands/getoturepcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, int>, std::_Select1st<std::pair<const double, int> >, std::less<double>, std::allocator<std::pair<const double, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const double, int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/nocommands.h:14,
from source/commands/nocommands.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/sparcccommand.h:12,
from source/commands/sparcccommand.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
In file included from source/mothur.h:86,
from source/classifier/taxonomyequalizer.h:14,
from source/commands/phylotypecommand.h:14,
from source/commands/phylotypecommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getoturepcommand.h:14,
from source/commands/getoturepcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/getoturepcommand.h:14,
from source/commands/getoturepcommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} 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' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
source/commands/getoturepcommand.cpp:661:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/newcommandtemplate.h:25,
from source/commands/newcommandtemplate.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/rarefactsharedcommand.h:12,
from source/commands/rarefactsharedcommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/shhhseqscommand.h:13,
from source/commands/shhhseqscommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
In file included from source/mothur.h:86,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int RareFactSharedCommand::subsampleLookup(SharedRAbundVectors*&, std::string)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/shhhseqscommand.h:13,
from source/commands/shhhseqscommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/communitytype.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'double CommunityTypeFinder::rMedoid(std::vector<std::vector<double> >, std::vector<std::vector<double> >)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'int CommunityTypeFinder::findkMeans()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/shhhseqscommand.h:13,
from source/commands/shhhseqscommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In function 'void driverShhSeqsGroups(shhhseqsData*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<double> CommunityTypeFinder::calcSilhouettes(std::vector<std::vector<double> >)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/kmeans.h:12,
from source/communitytype/kmeans.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/summarycommand.h:12,
from source/commands/summarycommand.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int SummaryCommand::process(SAbundVector*&, std::ofstream&, std::ofstream&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'int Pam::buildPhase()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual double Pam::calcCHIndex(std::vector<std::vector<double> >)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/datastructures/listvector.cpp:11:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp
In file included from source/mothur.h:86,
from source/datastructures/fastqread.h:12,
from source/datastructures/fastqread.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/qFinderDMM.h:12,
from source/communitytype/qFinderDMM.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/communitytype/communitytype.h:15,
from source/communitytype/qFinderDMM.h:12,
from source/communitytype/qFinderDMM.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void qFinderDMM::negativeLogDerivEvidenceLambdaPi(std::vector<double>&, std::vector<double>&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedrabundfloatvector.hpp:12,
from source/datastructures/sharedrabundfloatvector.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedclrvectors.o source/datastructures/sharedclrvectors.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedclrvectors.hpp:12,
from source/datastructures/sharedclrvectors.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optirefmatrix.o source/datastructures/optirefmatrix.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
In file included from source/mothur.h:86,
from source/datastructures/qualityscores.h:16,
from source/datastructures/qualityscores.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual std::vector<long long int> OptiRefMatrix::getFitSeqs()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual std::vector<long long int> OptiRefMatrix::getRefSeqs()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/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++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/filefile.hpp:12,
from source/datastructures/filefile.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
source/datastructures/optirefmatrix.cpp:273:1: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1
273 | }
| ^
In file included from /usr/include/c++/9/map:61,
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++/9/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++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optidata.o source/datastructures/optidata.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optidata.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp
In file included from source/mothur.h:86,
from source/datastructures/alignment.hpp:16,
from source/datastructures/kmeralign.h:17,
from source/datastructures/kmeralign.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optidata.cpp:9:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/mothur.h:42,
from source/mothurout.h:13,
from source/datastructures/optidata.hpp:12,
from source/datastructures/optidata.cpp:9:
/usr/include/c++/9/bits/stl_map.h: In member function 'std::map<std::__cxx11::basic_string<char>, long long int> OptiData::getNameIndexMap()':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'virtual OptiData* OptiRefMatrix::extractRefMatrix()':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/ordervector.hpp:4,
from source/datastructures/ordervector.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequence.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
/usr/include/c++/9/bits/stl_map.h: In member function 'virtual OptiData* OptiRefMatrix::extractMatrixSubset(std::set<long long int>&)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
In file included from source/mothur.h:86,
from source/datastructures/suffixnodes.hpp:19,
from source/datastructures/suffixnodes.cpp:16:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/kmer.hpp:13,
from source/datastructures/kmer.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/rabundvector.hpp:4,
from source/datastructures/rabundvector.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/flowdata.h:13,
from source/datastructures/flowdata.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sffheader.o source/datastructures/sffheader.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sffheader.hpp:12,
from source/datastructures/sffheader.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/oligos.h:13,
from source/datastructures/oligos.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedordervector.h:18,
from source/datastructures/sharedordervector.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/fastamap.h:13,
from source/datastructures/fastamap.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_tree.h:2187:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'int OptiMatrix::readPhylip()':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'int OptiMatrix::readColumn()':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long int, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/suffixtree.cpp:25:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsematrix.hpp:4,
from source/datastructures/sparsematrix.cpp:2:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/datastructures/sharedlistvector.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sffread.o source/datastructures/sffread.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sffread.hpp:12,
from source/datastructures/sffread.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/database.hpp:16,
from source/datastructures/suffixdb.cpp:18:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void SequenceDB::push_back(Sequence)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(std::ifstream&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function '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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(int)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
In file included from source/mothur.h:86,
from source/datastructures/treenode.h:13,
from source/datastructures/treenode.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp
In file included from source/mothur.h:86,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optidb.o source/datastructures/optidb.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp
In file included from source/mothur.h:86,
from source/datastructures/groupmap.h:12,
from source/datastructures/groupmap.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void DistanceDB::addSequence(Sequence)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/9/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++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedclrvector.o source/datastructures/sharedclrvector.cpp
/usr/include/c++/9/bits/stl_algo.h: In member function 'virtual std::vector<int> DistanceDB::findClosestSequences(Sequence*, int, std::vector<float>&) const':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedclrvector.hpp:12,
from source/datastructures/sharedclrvector.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
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++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/sequenceparser.h:14,
from source/datastructures/sequenceparser.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
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++/9/bits/stl_vector.h: In member function 'virtual void OptiDB::addSequence(Sequence)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
/usr/include/c++/9/bits/stl_vector.h: In member function 'void OptiDB::calcIndicatorColumns()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from source/mothur.h:86,
from source/datastructures/treenode.h:13,
from source/datastructures/tree.h:13,
from source/datastructures/tree.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp
In file included from source/mothur.h:86,
from source/datastructures/reportfile.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/alignmentcell.hpp:15,
from source/datastructures/alignment.cpp:12:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
In file included from source/mothur.h:86,
from source/datastructures/sequencecountparser.h:12,
from source/datastructures/sequencecountparser.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp
In file included from source/mothur.h:86,
from source/datastructures/fullmatrix.h:12,
from source/datastructures/fullmatrix.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp
In file included from source/mothur.h:86,
from source/datastructures/alignment.hpp:16,
from source/datastructures/blastalign.cpp:15:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
In file included from source/mothur.h:86,
from source/datastructures/sparsedistancematrix.h:12,
from source/datastructures/sparsedistancematrix.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedrabundvector.hpp:12,
from source/datastructures/sharedrabundvector.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::string, std::string, bool)':
source/datastructures/blastalign.cpp:65:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
65 | system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedrabundvectors.hpp:12,
from source/datastructures/sharedrabundvectors.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/counttable.h:55,
from source/datastructures/counttable.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/alignmentcell.hpp:15,
from source/datastructures/alignmentcell.cpp:12:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/taxonomy.o source/datastructures/taxonomy.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/taxonomy.hpp:12,
from source/datastructures/taxonomy.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/rabundfloatvector.hpp:12,
from source/datastructures/rabundfloatvector.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
In file included from source/mothur.h:86,
from source/datastructures/nameassignment.hpp:4,
from source/datastructures/nameassignment.cpp:3:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/sequence.hpp:20,
from source/datastructures/kmerdb.cpp:25:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/designmap.h:12,
from source/datastructures/designmap.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp
In file included from source/mothur.h:86,
from source/datastructures/database.hpp:16,
from source/datastructures/blastdb.cpp:11:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp
In file included from source/mothur.h:86,
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/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int, std::vector<float>&) const':
source/datastructures/blastdb.cpp:164:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
164 | system(blastCommand.c_str());
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int, int)':
source/datastructures/blastdb.cpp:227:9: 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:294:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
294 | system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
from source/mothur.h:41,
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++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
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++/9/bits/stl_map.h: In member function 'int OptiBlastMatrix::readBlastNames(std::map<std::__cxx11::basic_string<char>, long long int>&)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'int OptiBlastMatrix::readBlast()':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long int> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
In file included from source/mothur.h:86,
from source/datastructures/treemap.h:12,
from source/datastructures/treemap.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/datastructures/sabundvector.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundfloatvectors.cpp
In file included from source/mothur.h:86,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sharedrabundfloatvectors.hpp:12,
from source/datastructures/sharedrabundfloatvectors.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engines/batchengine.o source/engines/batchengine.cpp
In file included from source/mothur.h:86,
from source/commandoptionparser.hpp:4,
from source/engines/engine.hpp:13,
from source/engines/batchengine.hpp:12,
from source/engines/batchengine.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Sequence>::iterator' {aka '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'AlignmentDB::AlignmentDB(std::string, std::string, int, float, float, float, float, int, bool)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engines/interactengine.o source/engines/interactengine.cpp
In file included from source/mothur.h:86,
from source/commandoptionparser.hpp:4,
from source/engines/engine.hpp:13,
from source/engines/interactengine.hpp:12,
from source/engines/interactengine.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engines/scriptengine.o source/engines/scriptengine.cpp
In file included from source/mothur.h:86,
from source/commandoptionparser.hpp:4,
from source/engines/engine.hpp:13,
from source/engines/scriptengine.hpp:12,
from source/engines/scriptengine.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/metastats/mothurfisher.h:14,
from source/metastats/mothurfisher.cpp:12:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp
In file included from source/mothur.h:86,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/read/splitmatrix.h:13,
from source/read/splitmatrix.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/metastats/mothurmetastats.h:14,
from source/metastats/mothurmetastats.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permute_and_calc_ts(std::vector<std::vector<double> >&)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp
In file included from source/mothur.h:86,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<std::__cxx11::basic_string<char> > ReadPhylipVector::read(std::vector<seqDist>&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp
In file included from source/mothur.h:86,
from source/read/readcluster.h:13,
from source/read/readcluster.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/read/treereader.h:12,
from source/read/treereader.cpp:9:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<seqDist>::iterator' {aka '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/9/bits/stl_vector.h: In member function 'int ReadBlast::read(NameAssignment*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from source/mothur.h:50,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp
In file included from source/mothur.h:86,
from source/read/readtree.h:12,
from source/read/readtree.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp
In file included from source/mothur.h:86,
from source/read/readmatrix.hpp:13,
from source/read/readcolumn.h:12,
from source/read/readcolumn.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
In file included from source/mothur.h:86,
from source/read/readmatrix.hpp:13,
from source/read/readphylip.h:12,
from source/read/readphylip.cpp:10:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.44.2\"" -DUSE_READLINE -Isource -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp
In file included from source/mothur.h:86,
from source/mothurout.h:13,
from source/svm/svm.hpp:23,
from source/svm/svm.cpp:17:
/usr/include/arm-linux-gnueabihf/sys/sysctl.h:21:2: warning: #warning "The <sys/sysctl.h> header is deprecated and will be removed." [-Wcpp]
21 | #warning "The <sys/sysctl.h> header is deprecated and will be removed."
| ^~~~~~~
cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd ..
make[3]: Entering directory '/<<PKGBUILDDIR>>/source/uchime_src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/source/uchime_src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/source/uchime_src'
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sfasta.o sfasta.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqdb.o seqdb.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o getparents.o getparents.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o fractid.o fractid.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alpha2.o alpha2.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alpha.o alpha.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o searchchime.o searchchime.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tracebackbit.o tracebackbit.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o setnucmx.o setnucmx.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o viterbifast.o viterbifast.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o writechhit.o writechhit.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchimel.o alignchimel.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnparams.o alnparams.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o addtargets2.o addtargets2.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alignchime.o alignchime.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o usort.o usort.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mx.o mx.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o path.o path.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o globalalign2.o globalalign2.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o myutils.o myutils.cpp
g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o make3way.o make3way.cpp
In file included from /usr/include/c++/9/vector:72,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/svm/svm.hpp:23,
from source/svm/svm.cpp:17:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/9/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++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'void SmoTrainer::assignNumericLabels(std::vector<double>&, const LabeledObservationVector&, NumericClassToLabel&)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/svm/svm.hpp:23,
from source/svm/svm.cpp:17:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'SVM* SmoTrainer::train(KernelFunctionCache&, const LabeledObservationVector&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/9/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++/9/bits/stl_tree.h:2187:5: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::vector<std::__cxx11::basic_string<char> >, SvmPerformanceSummary> >'} changed in GCC 7.1
2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -o uchime sfasta.o seqdb.o getparents.o fractid.o alpha2.o alpha.o searchchime.o tracebackbit.o setnucmx.o viterbifast.o writechhit.o uchime_main.o alignchimel.o alnparams.o addtargets2.o alignchime.o usort.o mx.o path.o globalalign2.o myutils.o make3way.o
In file included from /usr/include/c++/9/map:61,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/9/bits/stl_map.h: In constructor 'ParameterSetBuilder::ParameterSetBuilder(const ParameterRangeMap&)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
make[3]: Leaving directory '/<<PKGBUILDDIR>>/source/uchime_src'
g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/engines/ -Lsource/metastats/ -Lsource/read/ -Lsource/svm/ -o mothur source/gotohoverlap.o source/validparameter.o source/heatmap.o source/nast.o source/calcsparcc.o source/mothurout.o source/completelinkage.o source/averagelinkage.o source/collect.o source/venn.o source/inputdata.o source/clusterclassic.o source/utils.o source/slibshuff.o source/opticluster.o source/trialSwap2.o source/consensus.o source/fileoutput.o source/cluster.o source/refchimeratest.o source/nastreport.o source/needlemanoverlap.o source/optifitcluster.o source/sensspeccalc.o source/myseqdist.o source/subsample.o source/vsearchfileparser.o source/commandfactory.o source/rarefact.o source/weightedlinkage.o source/wilcox.o source/linearalgebra.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/mothur.o source/seqnoise.o source/dlibshuff.o source/heatmapsim.o source/currentfile.o source/summary.o source/raredisplay.o source/commandoptionparser.o source/libshuff.o source/noalign.o source/overlap.o source/calculators/sharedlennon.o source/calculators/memeuclidean.o source/calculators/sharedjabund.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/shen.o source/calculators/tn.o source/calculators/sirarefaction.o source/calculators/sensitivity.o source/calculators/sharedochiai.o source/calculators/fdr.o source/calculators/bergerparker.o source/calculators/lnshift.o source/calculators/canberra.o source/calculators/hamming.o source/calculators/onegapdist.o source/calculators/sharedkulczynskicody.o source/calculators/jackknife.o source/calculators/weighted.o source/calculators/invsimpson.o source/calculators/tp.o source/calculators/boneh.o source/calculators/gower.o source/calculators/igabundance.o source/calculators/unweighted.o source/calculators/sharedjackknife.o source/calculators/metrosichel.o source/calculators/hellinger.o source/calculators/mcc.o source/calculators/coverage.o source/calculators/structpearson.o source/calculators/accuracy.o source/calculators/structchord.o source/calculators/sharedthetayc.o source/calculators/tptn.o source/calculators/lnabundance.o source/calculators/igrarefaction.o source/calculators/sharedjclass.o source/calculators/sharedrjsd.o source/calculators/smithwilson.o source/calculators/simpson.o source/calculators/mempearson.o source/calculators/logsd.o source/calculators/manhattan.o source/calculators/whittaker.o source/calculators/sharedsobs.o source/calculators/sharedsorclass.o source/calculators/specificity.o source/calculators/sharedchao1.o source/calculators/qstat.o source/calculators/memchi2.o source/calculators/lnrarefaction.o source/calculators/spearman.o source/calculators/shannoneven.o source/calculators/lsrarefaction.o source/calculators/lsabundance.o source/calculators/erarefaction.o source/calculators/sharedjest.o source/calculators/eachgapdist.o source/calculators/sharedsobscollectsummary.o source/calculators/structchi2.o source/calculators/soergel.o source/calculators/sharedkstest.o source/calculators/f1score.o source/calculators/onegapignore.o source/calculators/sharedace.o source/calculators/sishift.o source/calculators/calculator.o source/calculators/memchord.o source/calculators/geom.o source/calculators/bootstrap.o source/calculators/metrologstudent.o source/calculators/prng.o source/calculators/shannonrange.o source/calculators/chao1.o source/calculators/sharedmorisitahorn.o source/calculators/diversityutils.o source/calculators/bstick.o source/calculators/fpfn.o source/calculators/eachgapignore.o source/calculators/uvest.o source/calculators/goodscoverage.o source/calculators/ppv.o source/calculators/npv.o source/calculators/fp.o source/calculators/sharedjsd.o source/calculators/sharedthetan.o source/calculators/sharedsorabund.o source/calculators/sharedbraycurtis.o source/calculators/metroig.o source/calculators/efron.o source/calculators/sharedkulczynski.o source/calculators/siabundance.o source/calculators/fn.o source/calculators/parsimony.o source/calculators/metrolognormal.o source/calculators/shannon.o source/calculators/npshannon.o source/calculators/structeuclidean.o source/calculators/simpsoneven.o source/calculators/ignoregaps.o source/calculators/solow.o source/calculators/sharedanderbergs.o source/calculators/odum.o source/calculators/heip.o source/calculators/ace.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimerarealigner.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/opticlassifier.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/clearcut/getopt_long.o source/clearcut/cmdargs.o source/commands/reversecommand.o source/commands/listotuscommand.o source/commands/collectcommand.o source/commands/cooccurrencecommand.o source/commands/chimeraccodecommand.o source/commands/aligncheckcommand.o source/commands/getotuscommand.o source/commands/makesharedcommand.o source/commands/listseqscommand.o source/commands/clusterdoturcommand.o source/commands/setlogfilecommand.o source/commands/distancecommand.o source/commands/quitcommand.o source/commands/removegroupscommand.o source/commands/indicatorcommand.o source/commands/clusterfragmentscommand.o source/commands/getgroupscommand.o source/commands/kruskalwalliscommand.o source/commands/sensspeccommand.o source/commands/removeseqscommand.o source/commands/mimarksattributescommand.o source/commands/renameseqscommand.o source/commands/makegroupcommand.o source/commands/deuniqueseqscommand.o source/commands/classifyseqscommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/summaryqualcommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/diversityestimatorcommand.o source/commands/splitgroupscommand.o source/commands/sffmultiplecommand.o source/commands/removerarecommand.o source/commands/normalizesharedcommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/systemcommand.o source/commands/seqerrorcommand.o source/commands/aligncommand.o source/commands/otuhierarchycommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/chimerabellerophoncommand.o source/commands/venncommand.o source/commands/getsharedotucommand.o source/commands/parsefastaqcommand.o source/commands/countgroupscommand.o source/commands/mergeotuscommand.o source/commands/trimflowscommand.o source/commands/screenseqscommand.o source/commands/setdircommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/mgclustercommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getlistcountcommand.o source/commands/heatmapcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/mergetaxsummarycommand.o source/commands/makefastqcommand.o source/commands/makelookupcommand.o source/commands/rarefactcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/trimseqscommand.o source/commands/collectsharedcommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/removeotuscommand.o source/commands/phylodiversitycommand.o source/commands/filtersharedcommand.o source/commands/pcoacommand.o source/commands/filterseqscommand.o source/commands/shhhercommand.o source/commands/mergesfffilecommand.o source/commands/pcacommand.o source/commands/metastatscommand.o source/commands/subsamplecommand.o source/commands/chimeraslayercommand.o source/commands/chopseqscommand.o source/commands/seqsummarycommand.o source/commands/makebiomcommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/sffinfocommand.o source/commands/corraxescommand.o source/commands/distsharedcommand.o source/commands/preclustercommand.o source/commands/classifytreecommand.o source/commands/clusterfitcommand.o source/commands/getseqscommand.o source/commands/getmimarkspackagecommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/setseedcommand.o source/commands/getcurrentcommand.o source/commands/srainfocommand.o source/commands/makecontigscommand.o source/commands/mergefilecommand.o source/commands/biominfocommand.o source/commands/getgroupcommand.o source/commands/helpcommand.o source/commands/pcrseqscommand.o source/commands/anosimcommand.o source/commands/chimeraperseuscommand.o source/commands/treesharedcommand.o source/commands/deuniquetreecommand.o source/commands/binsequencecommand.o source/commands/makelefsecommand.o source/commands/getrabundcommand.o source/commands/classifyotucommand.o source/commands/createdatabasecommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/removedistscommand.o source/commands/homovacommand.o source/commands/amovacommand.o source/commands/renamefilecommand.o source/commands/clearcutcommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/libshuffcommand.o source/commands/makeclrcommand.o source/commands/chimerapintailcommand.o source/commands/chimeracheckcommand.o source/commands/clustersplitcommand.o source/commands/pairwiseseqscommand.o source/commands/mergegroupscommand.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/nocommands.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/rarefactsharedcommand.o source/commands/newcommandtemplate.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/fastqread.o source/datastructures/ordervector.o source/datastructures/groupmap.o source/datastructures/optimatrix.o source/datastructures/fastamap.o source/datastructures/blastdb.o source/datastructures/sharedlistvector.o source/datastructures/alignmentcell.o source/datastructures/sffread.o source/datastructures/distancedb.o source/datastructures/nameassignment.o source/datastructures/rabundvector.o source/datastructures/suffixnodes.o source/datastructures/flowdata.o source/datastructures/tree.o source/datastructures/sharedclrvectors.o source/datastructures/sequenceparser.o source/datastructures/blastalign.o source/datastructures/sabundvector.o source/datastructures/rabundfloatvector.o source/datastructures/filefile.o source/datastructures/treenode.o source/datastructures/qualityscores.o source/datastructures/sparsedistancematrix.o source/datastructures/listvector.o source/datastructures/counttable.o source/datastructures/taxonomy.o source/datastructures/kmerdb.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/optidb.o source/datastructures/sharedrabundvector.o source/datastructures/designmap.o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundfloatvectors.o source/datastructures/suffixdb.o source/datastructures/sharedordervector.o source/datastructures/sharedclrvector.o source/datastructures/oligos.o source/datastructures/sparsematrix.o source/datastructures/fullmatrix.o source/datastructures/suffixtree.o source/datastructures/optirefmatrix.o source/datastructures/optiblastmatrix.o source/datastructures/sffheader.o source/datastructures/kmer.o source/datastructures/alignment.o source/datastructures/reportfile.o source/datastructures/sequencecountparser.o source/datastructures/treemap.o source/datastructures/alignmentdb.o source/datastructures/optidata.o source/datastructures/kmeralign.o source/engines/batchengine.o source/engines/interactengine.o source/engines/scriptengine.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readblast.o source/read/readcluster.o source/read/treereader.o source/read/readtree.o source/read/readcolumn.o source/read/readphylip.o source/svm/svm.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_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
true
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_installmenu -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_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 -a
dh_makeshlibs -a -a
dh_shlibdeps -a -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_1.44.2-1_armhf.deb'.
dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.44.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../mothur_1.44.2-1_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 2020-07-24T19:19:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mothur_1.44.2-1_armhf.changes:
------------------------------
Format: 1.8
Date: Wed, 22 Jul 2020 11:35:13 +0200
Source: mothur
Binary: mothur mothur-dbgsym
Architecture: armhf
Version: 1.44.2-1
Distribution: bullseye-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: 963288
Changes:
mothur (1.44.2-1) unstable; urgency=medium
.
* New upstream version
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit.
* Remove obsolete fields Contact, Name from debian/upstream/metadata (already
present in machine-readable debian/copyright).
* Fix include
Closes: #963288
* Fix makefile
* Do not build uchime explicitly in d/rules
Checksums-Sha1:
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ebc4e07151c703871eb972f9ca56b1e8fc14fc99 5133 mothur_1.44.2-1_armhf.buildinfo
0b37dc1f577dc663b1cbaf213eb77116d2d0a564 3787968 mothur_1.44.2-1_armhf.deb
Checksums-Sha256:
f0af644aa1ef2a4661debf5409374e87e908d966464d18d6b02990d64a8bd595 154835312 mothur-dbgsym_1.44.2-1_armhf.deb
549cd2b829471d8f5532e45e770821bd71893d369979050be6c42a216f67046e 5133 mothur_1.44.2-1_armhf.buildinfo
969e73e9a44c4bb17411272e7cee35773b931e4a010f7f32402b5a9a3bfd09a8 3787968 mothur_1.44.2-1_armhf.deb
Files:
bd08b38b28b03781f7b0b517a7fb28a5 154835312 debug optional mothur-dbgsym_1.44.2-1_armhf.deb
b64402a0c8dc0d2c1389b3c9c07cd6f7 5133 science optional mothur_1.44.2-1_armhf.buildinfo
5dd9c5ac53529f99df211f9d06e54b45 3787968 science optional mothur_1.44.2-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mothur-dbgsym_1.44.2-1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 154835312 bytes: control archive=596 bytes.
412 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: mothur-dbgsym
Source: mothur
Version: 1.44.2-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 156537
Depends: mothur (= 1.44.2-1)
Section: debug
Priority: optional
Description: debug symbols for mothur
Build-Ids: 0d6dcded40326d50029c010a410903a439399de7 e02e8645fb4961c9a28a2d859152c4fc4dade05d
drwxr-xr-x root/root 0 2020-07-22 09:35 ./
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/lib/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/lib/debug/.build-id/0d/
-rw-r--r-- root/root 160233112 2020-07-22 09:35 ./usr/lib/debug/.build-id/0d/6dcded40326d50029c010a410903a439399de7.debug
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/lib/debug/.build-id/e0/
-rw-r--r-- root/root 48312 2020-07-22 09:35 ./usr/lib/debug/.build-id/e0/2e8645fb4961c9a28a2d859152c4fc4dade05d.debug
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-07-22 09:35 ./usr/share/doc/mothur-dbgsym -> mothur
mothur_1.44.2-1_armhf.deb
-------------------------
new Debian package, version 2.0.
size 3787968 bytes: control archive=1328 bytes.
816 bytes, 18 lines control
762 bytes, 12 lines md5sums
190 bytes, 7 lines * postinst #!/bin/sh
165 bytes, 5 lines * postrm #!/bin/sh
Package: mothur
Version: 1.44.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 13395
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libreadline8 (>= 6.0), libstdc++6 (>= 9)
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 2020-07-22 09:35 ./
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/bin/
-rwxr-xr-x root/root 13506928 2020-07-22 09:35 ./usr/bin/mothur
-rwxr-xr-x root/root 163660 2020-07-22 09:35 ./usr/bin/uchime
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/doc/mothur/
-rw-r--r-- root/root 12687 2017-06-21 06:25 ./usr/share/doc/mothur/HA.fasta.gz
-rw-r--r-- root/root 259 2016-05-15 09:57 ./usr/share/doc/mothur/README.Debian
-rw-r--r-- root/root 178 2017-06-21 06:25 ./usr/share/doc/mothur/README.test
-rw-r--r-- root/root 3905 2020-07-22 09:35 ./usr/share/doc/mothur/changelog.Debian.gz
-rw-r--r-- root/root 4544 2020-06-09 14:15 ./usr/share/doc/mothur/copyright
-rw-r--r-- root/root 316 2020-06-09 14:14 ./usr/share/doc/mothur/run-unit-test
-rw-r--r-- root/root 400 2017-06-21 06:25 ./usr/share/doc/mothur/test.batch
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/man/
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/man/man1/
-rw-r--r-- root/root 566 2020-07-22 09:35 ./usr/share/man/man1/mothur.1.gz
-rw-r--r-- root/root 3393 2020-07-22 09:35 ./usr/share/man/man1/uchime.1.gz
drwxr-xr-x root/root 0 2020-07-22 09:35 ./usr/share/menu/
-rw-r--r-- root/root 176 2016-05-15 09:57 ./usr/share/menu/mothur
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 2030472
Build-Time: 7679
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 391
Job: mothur_1.44.2-1
Machine Architecture: armhf
Package: mothur
Package-Time: 8120
Source-Version: 1.44.2-1
Space: 2030472
Status: successful
Version: 1.44.2-1
--------------------------------------------------------------------------------
Finished at 2020-07-24T19:19:06Z
Build needed 02:15:20, 2030472k disc space