mothur →
1.40.5-2 →
armhf → 2018-09-16 07:47:57
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| mothur 1.40.5-2 (armhf) Sun, 16 Sep 2018 07:05:09 +0000 |
+==============================================================================+
Package: mothur
Version: 1.40.5-2
Source Version: 1.40.5-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-53a22d36-6c17-4590-89cc-6a5a1ed1b2eb' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.8 MB in 11s (2128 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 1843 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main mothur 1.40.5-2 (dsc) [2084 B]
Get:2 http://172.17.0.1/private buster-staging/main mothur 1.40.5-2 (tar) [1821 kB]
Get:3 http://172.17.0.1/private buster-staging/main mothur 1.40.5-2 (diff) [19.9 kB]
Fetched 1843 kB in 1s (1835 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/mothur-jSE4IJ/mothur-1.40.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mothur-jSE4IJ' 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-O6QuNY/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-O6QuNY/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-O6QuNY/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (11.3 kB/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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 71 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-O6QuNY/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 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 (>= 11), gfortran, libboost-iostreams-dev, libopenmpi-dev, libreadline-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 11), gfortran, libboost-iostreams-dev, libopenmpi-dev, libreadline-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-mothur-dummy' in '/<<BUILDDIR>>/resolver-O6QuNY/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-O6QuNY/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Sources [530 B]
Get:5 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ Packages [608 B]
Fetched 2471 B in 0s (13.1 kB/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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8 gcc-8-base
gettext gettext-base gfortran gfortran-8 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0
groff-base ibverbs-providers icu-devtools intltool-debian
libarchive-zip-perl libasan5 libatomic1 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libcc1-0 libcroco3 libedit2
libelf1 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libfreetype6 libgcc-8-dev libgcc1
libgfortran-8-dev libgfortran5 libgirepository-1.0-1 libglib2.0-0
libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgomp1
libgraphite2-3 libgraphite2-dev libgssapi-krb5-2 libharfbuzz-dev
libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhwloc-dev
libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu-dev
libicu-le-hb-dev libicu-le-hb0 libicu60 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpdec2
libncurses-dev libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi3
libpciaccess0 libpcre16-3 libpcre3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpmix2 libpython3-stdlib libpython3.6-minimal
libpython3.6-stdlib libreadline-dev libsigsegv2 libssl1.0.2 libstdc++-8-dev
libstdc++6 libtimedate-perl libtool libubsan1 libxml2 m4 man-db mime-support
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.6 python3.6-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation gcc-8-locales dh-make gcc-8-doc libstdc++6-8-dbg libgcc1-dbg
libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg
libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
libasprintf-dev libgettextpo-dev gfortran-doc gfortran-8-doc
libgfortran5-dbg libcoarrays-dev groff libboost1.62-doc
libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev
libboost-coroutine1.62-dev libboost-date-time1.62-dev
libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-serialization1.62-dev
libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev
libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev
libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev
libglib2.0-doc libgraphite2-utils krb5-doc krb5-user
libhwloc-contrib-plugins icu-doc libtool-doc ncurses-doc openmpi-doc
pciutils readline-doc libstdc++-8-doc gcj-jdk m4-doc apparmor less
www-browser opencl-icd keychain libpam-ssh monkeysphere ssh-askpass
libmail-box-perl python3-doc python3-tk python3-venv python3.6-venv
python3.6-doc binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl shared-mime-info xdg-user-dirs
krb5-locales libcoarrays-dev open-coarrays-bin xauth libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran
gfortran-8 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base ibverbs-providers
icu-devtools intltool-debian libarchive-zip-perl libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libcroco3 libedit2 libelf1
libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
libfile-stripnondeterminism-perl libfreetype6 libgfortran-8-dev libgfortran5
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev
libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0
libharfbuzz0b libhwloc-dev libhwloc-plugins libhwloc5 libibverbs-dev
libibverbs1 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libltdl-dev libltdl7 libmagic-mgc
libmagic1 libmpdec2 libncurses-dev libnl-3-200 libnl-route-3-200
libopenmpi-dev libopenmpi3 libpciaccess0 libpcre16-3 libpcre3-dev
libpcre32-3 libpcrecpp0v5 libpipeline1 libpmix2 libpython3-stdlib
libpython3.6-minimal libpython3.6-stdlib libreadline-dev libsigsegv2
libssl1.0.2 libtimedate-perl libtool libxml2 m4 man-db mime-support
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.6 python3.6-minimal sbuild-build-depends-mothur-dummy zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libpcre3 libstdc++-8-dev libstdc++6 libubsan1
14 upgraded, 107 newly installed, 0 to remove and 57 not upgraded.
Need to get 88.8 MB/90.1 MB of archives.
After this operation, 334 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-O6QuNY/apt_archive ./ sbuild-build-depends-mothur-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-6+rpi1 [30.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-6+rpi1 [187 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-6+rpi1 [36.5 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-6+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-6+rpi1 [8104 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-6+rpi1 [317 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-6+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-6+rpi1 [5939 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-6+rpi1 [1562 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-6+rpi1 [595 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-6+rpi1 [5841 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-6+rpi1 [5474 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-6+rpi1 [325 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6-1 [565 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6-1 [1383 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1638 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6-1 [234 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpcre3 armhf 2:8.39-11+rpi1 [313 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20180525-1 [70.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.3 [12.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.8p1-1 [673 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.8-2+rpi1 [860 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-6+rpi1 [206 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-6+rpi1 [248 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-6+rpi1 [5813 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.1.0-1+rpi1 [1424 B]
Get:67 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.8.8-2+rpi1 [648 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.8.8-2+rpi1 [655 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 20.0-1 [43.2 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 20.0-1 [19.9 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-8 [7003 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-8 [233 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.8.8-2+rpi1 [641 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.6-1 [144 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.12-1 [22.6 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.8.8-2+rpi1 [930 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-8 [327 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-8 [49.3 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-8 [58.8 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:98 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2.1 [386 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.10-3+rpi1 [86.2 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2.1 [158 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.10-3+rpi1 [141 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.10-3+rpi1 [15.6 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 20.0-1 [108 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180714-1 [279 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 3.0.1-2 [345 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.1.2-1+rpi1 [2071 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.1.2-1+rpi1 [162 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.1.2-1+rpi1 [194 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.1.2-1+rpi1 [953 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 88.8 MB in 34s (2628 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 15689 files and directories currently installed.)
Preparing to unpack .../libbsd0_0.9.1-1_armhf.deb ...
Unpacking libbsd0:armhf (0.9.1-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Preparing to unpack .../libcc1-0_8.2.0-6+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../gcc-8-base_8.2.0-6+rpi1_armhf.deb ...
Unpacking gcc-8-base:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Setting up gcc-8-base:armhf (8.2.0-6+rpi1) ...
(Reading database ... 15814 files and directories currently installed.)
Preparing to unpack .../libgcc1_1%3a8.2.0-6+rpi1_armhf.deb ...
Unpacking libgcc1:armhf (1:8.2.0-6+rpi1) over (1:8.1.0-12+rpi1) ...
Setting up libgcc1:armhf (1:8.2.0-6+rpi1) ...
(Reading database ... 15814 files and directories currently installed.)
Preparing to unpack .../0-libgomp1_8.2.0-6+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../1-libatomic1_8.2.0-6+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../2-libasan5_8.2.0-6+rpi1_armhf.deb ...
Unpacking libasan5:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../3-libubsan1_8.2.0-6+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../4-g++-8_8.2.0-6+rpi1_armhf.deb ...
Unpacking g++-8 (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../5-libstdc++-8-dev_8.2.0-6+rpi1_armhf.deb ...
Unpacking libstdc++-8-dev:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../6-libgcc-8-dev_8.2.0-6+rpi1_armhf.deb ...
Unpacking libgcc-8-dev:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../7-gcc-8_8.2.0-6+rpi1_armhf.deb ...
Unpacking gcc-8 (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../8-cpp-8_8.2.0-6+rpi1_armhf.deb ...
Unpacking cpp-8 (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Preparing to unpack .../9-libstdc++6_8.2.0-6+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (8.2.0-6+rpi1) over (8.1.0-12+rpi1) ...
Setting up libstdc++6:armhf (8.2.0-6+rpi1) ...
Selecting previously unselected package groff-base.
(Reading database ... 15814 files and directories currently installed.)
Preparing to unpack .../00-groff-base_1.22.3-10_armhf.deb ...
Unpacking groff-base (1.22.3-10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../01-libpipeline1_1.5.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.0-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../02-man-db_2.8.4-2_armhf.deb ...
Unpacking man-db (2.8.4-2) ...
Selecting previously unselected package libpython3.6-minimal:armhf.
Preparing to unpack .../03-libpython3.6-minimal_3.6.6-1_armhf.deb ...
Unpacking libpython3.6-minimal:armhf (3.6.6-1) ...
Selecting previously unselected package python3.6-minimal.
Preparing to unpack .../04-python3.6-minimal_3.6.6-1_armhf.deb ...
Unpacking python3.6-minimal (3.6.6-1) ...
Selecting previously unselected package python3-minimal.
Preparing to unpack .../05-python3-minimal_3.6.5-3_armhf.deb ...
Unpacking python3-minimal (3.6.5-3) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../06-mime-support_3.61_all.deb ...
Unpacking mime-support (3.61) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../07-libmpdec2_2.4.2-2_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.2-2) ...
Selecting previously unselected package libpython3.6-stdlib:armhf.
Preparing to unpack .../08-libpython3.6-stdlib_3.6.6-1_armhf.deb ...
Unpacking libpython3.6-stdlib:armhf (3.6.6-1) ...
Selecting previously unselected package python3.6.
Preparing to unpack .../09-python3.6_3.6.6-1_armhf.deb ...
Unpacking python3.6 (3.6.6-1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../10-libpython3-stdlib_3.6.5-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.6.5-3) ...
Setting up libpython3.6-minimal:armhf (3.6.6-1) ...
Setting up python3.6-minimal (3.6.6-1) ...
Setting up python3-minimal (3.6.5-3) ...
Selecting previously unselected package python3.
(Reading database ... 16964 files and directories currently installed.)
Preparing to unpack .../python3_3.6.5-3_armhf.deb ...
Unpacking python3 (3.6.5-3) ...
Preparing to unpack .../libpcre3_2%3a8.39-11+rpi1_armhf.deb ...
Unpacking libpcre3:armhf (2:8.39-11+rpi1) over (2:8.39-10) ...
Setting up libpcre3:armhf (2:8.39-11+rpi1) ...
Selecting previously unselected package libssl1.0.2:armhf.
(Reading database ... 16982 files and directories currently installed.)
Preparing to unpack .../00-libssl1.0.2_1.0.2o-1_armhf.deb ...
Unpacking libssl1.0.2:armhf (1.0.2o-1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.34-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.34-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.34-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.34-2) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.34-2_armhf.deb ...
Unpacking file (1:5.34-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.19.8.1-7_armhf.deb ...
Unpacking gettext-base (0.19.8.1-7) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../05-libedit2_3.1-20180525-1_armhf.deb ...
Unpacking libedit2:armhf (3.1-20180525-1) ...
Selecting previously unselected package libevent-2.1-6:armhf.
Preparing to unpack .../06-libevent-2.1-6_2.1.8-stable-4_armhf.deb ...
Unpacking libevent-2.1-6:armhf (2.1.8-stable-4) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../07-libkeyutils1_1.5.9-9.3_armhf.deb ...
Unpacking libkeyutils1:armhf (1.5.9-9.3) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../08-libkrb5support0_1.16-2_armhf.deb ...
Unpacking libkrb5support0:armhf (1.16-2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../09-libk5crypto3_1.16-2_armhf.deb ...
Unpacking libk5crypto3:armhf (1.16-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../10-libkrb5-3_1.16-2_armhf.deb ...
Unpacking libkrb5-3:armhf (1.16-2) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../11-libgssapi-krb5-2_1.16-2_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.16-2) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../12-openssh-client_1%3a7.8p1-1_armhf.deb ...
Unpacking openssh-client (1:7.8p1-1) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../13-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../14-m4_1.4.18-1_armhf.deb ...
Unpacking m4 (1.4.18-1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../15-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../16-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../17-automake_1%3a1.16.1-1.1_all.deb ...
Unpacking automake (1:1.16.1-1.1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../18-autopoint_0.19.8.1-7_all.deb ...
Unpacking autopoint (0.19.8.1-7) ...
Selecting previously unselected package libtool.
Preparing to unpack .../19-libtool_2.4.6-4_all.deb ...
Unpacking libtool (2.4.6-4) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../20-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../21-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../22-libfile-stripnondeterminism-perl_0.042-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.042-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../23-libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../24-dh-strip-nondeterminism_0.042-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.042-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../25-libelf1_0.170-0.5_armhf.deb ...
Unpacking libelf1:armhf (0.170-0.5) ...
Selecting previously unselected package dwz.
Preparing to unpack .../26-dwz_0.12-2_armhf.deb ...
Unpacking dwz (0.12-2) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../27-libglib2.0-0_2.56.1-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.56.1-2) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../28-libfreetype6_2.8.1-2_armhf.deb ...
Unpacking libfreetype6:armhf (2.8.1-2) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../29-libgraphite2-3_1.3.12-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.12-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../30-libharfbuzz0b_1.8.8-2+rpi1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (1.8.8-2+rpi1) ...
Selecting previously unselected package libicu-le-hb0:armhf.
Preparing to unpack .../31-libicu-le-hb0_1.0.3+git161113-5_armhf.deb ...
Unpacking libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Selecting previously unselected package libicu60:armhf.
Preparing to unpack .../32-libicu60_60.2-6_armhf.deb ...
Unpacking libicu60:armhf (60.2-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../33-libxml2_2.9.4+dfsg1-7_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-7) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../34-libcroco3_0.6.12-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.12-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../35-gettext_0.19.8.1-7_armhf.deb ...
Unpacking gettext (0.19.8.1-7) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../36-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../37-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../38-debhelper_11.3.5_all.deb ...
Unpacking debhelper (11.3.5) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../39-libgfortran5_8.2.0-6+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (8.2.0-6+rpi1) ...
Selecting previously unselected package libgfortran-8-dev:armhf.
Preparing to unpack .../40-libgfortran-8-dev_8.2.0-6+rpi1_armhf.deb ...
Unpacking libgfortran-8-dev:armhf (8.2.0-6+rpi1) ...
Selecting previously unselected package gfortran-8.
Preparing to unpack .../41-gfortran-8_8.2.0-6+rpi1_armhf.deb ...
Unpacking gfortran-8 (8.2.0-6+rpi1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../42-gfortran_4%3a8.1.0-1+rpi1_armhf.deb ...
Unpacking gfortran (4:8.1.0-1+rpi1) ...
Selecting previously unselected package libgirepository-1.0-1:armhf.
Preparing to unpack .../43-libgirepository-1.0-1_1.56.1-1_armhf.deb ...
Unpacking libgirepository-1.0-1:armhf (1.56.1-1) ...
Selecting previously unselected package gir1.2-glib-2.0:armhf.
Preparing to unpack .../44-gir1.2-glib-2.0_1.56.1-1_armhf.deb ...
Unpacking gir1.2-glib-2.0:armhf (1.56.1-1) ...
Selecting previously unselected package libharfbuzz-gobject0:armhf.
Preparing to unpack .../45-libharfbuzz-gobject0_1.8.8-2+rpi1_armhf.deb ...
Unpacking libharfbuzz-gobject0:armhf (1.8.8-2+rpi1) ...
Selecting previously unselected package gir1.2-harfbuzz-0.0:armhf.
Preparing to unpack .../46-gir1.2-harfbuzz-0.0_1.8.8-2+rpi1_armhf.deb ...
Unpacking gir1.2-harfbuzz-0.0:armhf (1.8.8-2+rpi1) ...
Selecting previously unselected package libnl-3-200:armhf.
Preparing to unpack .../47-libnl-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-200:armhf.
Preparing to unpack .../48-libnl-route-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs1:armhf.
Preparing to unpack .../49-libibverbs1_20.0-1_armhf.deb ...
Unpacking libibverbs1:armhf (20.0-1) ...
Selecting previously unselected package ibverbs-providers:armhf.
Preparing to unpack .../50-ibverbs-providers_20.0-1_armhf.deb ...
Unpacking ibverbs-providers:armhf (20.0-1) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../51-icu-devtools_60.2-6_armhf.deb ...
Unpacking icu-devtools (60.2-6) ...
Selecting previously unselected package libboost1.62-dev:armhf.
Preparing to unpack .../52-libboost1.62-dev_1.62.0+dfsg-8_armhf.deb ...
Unpacking libboost1.62-dev:armhf (1.62.0+dfsg-8) ...
Selecting previously unselected package libboost-regex1.62.0:armhf.
Preparing to unpack .../53-libboost-regex1.62.0_1.62.0+dfsg-8_armhf.deb ...
Unpacking libboost-regex1.62.0:armhf (1.62.0+dfsg-8) ...
Selecting previously unselected package libharfbuzz-icu0:armhf.
Preparing to unpack .../54-libharfbuzz-icu0_1.8.8-2+rpi1_armhf.deb ...
Unpacking libharfbuzz-icu0:armhf (1.8.8-2+rpi1) ...
Selecting previously unselected package libglib2.0-data.
Preparing to unpack .../55-libglib2.0-data_2.56.1-2_all.deb ...
Unpacking libglib2.0-data (2.56.1-2) ...
Selecting previously unselected package libglib2.0-bin.
Preparing to unpack .../56-libglib2.0-bin_2.56.1-2_armhf.deb ...
Unpacking libglib2.0-bin (2.56.1-2) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../57-python3-lib2to3_3.6.6-1_all.deb ...
Unpacking python3-lib2to3 (3.6.6-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../58-python3-distutils_3.6.6-1_all.deb ...
Unpacking python3-distutils (3.6.6-1) ...
Selecting previously unselected package libglib2.0-dev-bin.
Preparing to unpack .../59-libglib2.0-dev-bin_2.56.1-2_armhf.deb ...
Unpacking libglib2.0-dev-bin (2.56.1-2) ...
Selecting previously unselected package libpcre16-3:armhf.
Preparing to unpack .../60-libpcre16-3_2%3a8.39-11+rpi1_armhf.deb ...
Unpacking libpcre16-3:armhf (2:8.39-11+rpi1) ...
Selecting previously unselected package libpcre32-3:armhf.
Preparing to unpack .../61-libpcre32-3_2%3a8.39-11+rpi1_armhf.deb ...
Unpacking libpcre32-3:armhf (2:8.39-11+rpi1) ...
Selecting previously unselected package libpcrecpp0v5:armhf.
Preparing to unpack .../62-libpcrecpp0v5_2%3a8.39-11+rpi1_armhf.deb ...
Unpacking libpcrecpp0v5:armhf (2:8.39-11+rpi1) ...
Selecting previously unselected package libpcre3-dev:armhf.
Preparing to unpack .../63-libpcre3-dev_2%3a8.39-11+rpi1_armhf.deb ...
Unpacking libpcre3-dev:armhf (2:8.39-11+rpi1) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../64-pkg-config_0.29-4_armhf.deb ...
Unpacking pkg-config (0.29-4) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../65-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package libglib2.0-dev:armhf.
Preparing to unpack .../66-libglib2.0-dev_2.56.1-2_armhf.deb ...
Unpacking libglib2.0-dev:armhf (2.56.1-2) ...
Selecting previously unselected package libgraphite2-dev:armhf.
Preparing to unpack .../67-libgraphite2-dev_1.3.12-1_armhf.deb ...
Unpacking libgraphite2-dev:armhf (1.3.12-1) ...
Selecting previously unselected package libharfbuzz-dev:armhf.
Preparing to unpack .../68-libharfbuzz-dev_1.8.8-2+rpi1_armhf.deb ...
Unpacking libharfbuzz-dev:armhf (1.8.8-2+rpi1) ...
Selecting previously unselected package libicu-le-hb-dev:armhf.
Preparing to unpack .../69-libicu-le-hb-dev_1.0.3+git161113-5_armhf.deb ...
Unpacking libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Selecting previously unselected package libicu-dev.
Preparing to unpack .../70-libicu-dev_60.2-6_armhf.deb ...
Unpacking libicu-dev (60.2-6) ...
Selecting previously unselected package libboost-regex1.62-dev:armhf.
Preparing to unpack .../71-libboost-regex1.62-dev_1.62.0+dfsg-8_armhf.deb ...
Unpacking libboost-regex1.62-dev:armhf (1.62.0+dfsg-8) ...
Selecting previously unselected package libboost-iostreams1.62.0:armhf.
Preparing to unpack .../72-libboost-iostreams1.62.0_1.62.0+dfsg-8_armhf.deb ...
Unpacking libboost-iostreams1.62.0:armhf (1.62.0+dfsg-8) ...
Selecting previously unselected package libboost-iostreams1.62-dev:armhf.
Preparing to unpack .../73-libboost-iostreams1.62-dev_1.62.0+dfsg-8_armhf.deb ...
Unpacking libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-8) ...
Selecting previously unselected package libboost-iostreams-dev:armhf.
Preparing to unpack .../74-libboost-iostreams-dev_1.62.0.1+b8_armhf.deb ...
Unpacking libboost-iostreams-dev:armhf (1.62.0.1+b8) ...
Selecting previously unselected package libevent-core-2.1-6:armhf.
Preparing to unpack .../75-libevent-core-2.1-6_2.1.8-stable-4_armhf.deb ...
Unpacking libevent-core-2.1-6:armhf (2.1.8-stable-4) ...
Selecting previously unselected package libevent-pthreads-2.1-6:armhf.
Preparing to unpack .../76-libevent-pthreads-2.1-6_2.1.8-stable-4_armhf.deb ...
Unpacking libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../77-libltdl7_2.4.6-2.1_armhf.deb ...
Unpacking libltdl7:armhf (2.4.6-2.1) ...
Selecting previously unselected package libhwloc5:armhf.
Preparing to unpack .../78-libhwloc5_1.11.10-3+rpi1_armhf.deb ...
Unpacking libhwloc5:armhf (1.11.10-3+rpi1) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../79-libltdl-dev_2.4.6-2.1_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.6-2.1) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../80-libhwloc-dev_1.11.10-3+rpi1_armhf.deb ...
Unpacking libhwloc-dev:armhf (1.11.10-3+rpi1) ...
Selecting previously unselected package libpciaccess0:armhf.
Preparing to unpack .../81-libpciaccess0_0.14-1_armhf.deb ...
Unpacking libpciaccess0:armhf (0.14-1) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../82-ocl-icd-libopencl1_2.2.12-1_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.2.12-1) ...
Selecting previously unselected package libhwloc-plugins:armhf.
Preparing to unpack .../83-libhwloc-plugins_1.11.10-3+rpi1_armhf.deb ...
Unpacking libhwloc-plugins:armhf (1.11.10-3+rpi1) ...
Selecting previously unselected package libibverbs-dev:armhf.
Preparing to unpack .../84-libibverbs-dev_20.0-1_armhf.deb ...
Unpacking libibverbs-dev:armhf (20.0-1) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../85-libncurses-dev_6.1+20180714-1_armhf.deb ...
Unpacking libncurses-dev:armhf (6.1+20180714-1) ...
Selecting previously unselected package libpmix2:armhf.
Preparing to unpack .../86-libpmix2_3.0.1-2_armhf.deb ...
Unpacking libpmix2:armhf (3.0.1-2) ...
Selecting previously unselected package libopenmpi3:armhf.
Preparing to unpack .../87-libopenmpi3_3.1.2-1+rpi1_armhf.deb ...
Unpacking libopenmpi3:armhf (3.1.2-1+rpi1) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../88-openmpi-common_3.1.2-1+rpi1_all.deb ...
Unpacking openmpi-common (3.1.2-1+rpi1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../89-openmpi-bin_3.1.2-1+rpi1_armhf.deb ...
Unpacking openmpi-bin (3.1.2-1+rpi1) ...
Selecting previously unselected package libopenmpi-dev:armhf.
Preparing to unpack .../90-libopenmpi-dev_3.1.2-1+rpi1_armhf.deb ...
Unpacking libopenmpi-dev:armhf (3.1.2-1+rpi1) ...
Selecting previously unselected package libreadline-dev:armhf.
Preparing to unpack .../91-libreadline-dev_7.0-5_armhf.deb ...
Unpacking libreadline-dev:armhf (7.0-5) ...
Selecting previously unselected package sbuild-build-depends-mothur-dummy.
Preparing to unpack .../92-sbuild-build-depends-mothur-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-mothur-dummy (0.invalid.0) ...
Setting up cpp-8 (8.2.0-6+rpi1) ...
Setting up libgomp1:armhf (8.2.0-6+rpi1) ...
Setting up libatomic1:armhf (8.2.0-6+rpi1) ...
Setting up libcc1-0:armhf (8.2.0-6+rpi1) ...
Setting up libevent-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libevent-core-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-7) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libgirepository-1.0-1:armhf (1.56.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libgraphite2-3:armhf (1.3.12-1) ...
Setting up libboost-iostreams1.62.0:armhf (1.62.0+dfsg-8) ...
Setting up libssl1.0.2:armhf (1.0.2o-1) ...
Setting up pkg-config (0.29-4) ...
Setting up gir1.2-glib-2.0:armhf (1.56.1-1) ...
Setting up libglib2.0-data (2.56.1-2) ...
Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Setting up openmpi-common (3.1.2-1+rpi1) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libltdl7:armhf (2.4.6-2.1) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up libpcrecpp0v5:armhf (2:8.39-11+rpi1) ...
Setting up libpcre32-3:armhf (2:8.39-11+rpi1) ...
Setting up libpcre16-3:armhf (2:8.39-11+rpi1) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-1) ...
Setting up libkeyutils1:armhf (1.5.9-9.3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up libncurses-dev:armhf (6.1+20180714-1) ...
Setting up libglib2.0-bin (2.56.1-2) ...
Setting up libasan5:armhf (8.2.0-6+rpi1) ...
Setting up libgfortran5:armhf (8.2.0-6+rpi1) ...
Setting up libgraphite2-dev:armhf (1.3.12-1) ...
Setting up autopoint (0.19.8.1-7) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libubsan1:armhf (8.2.0-6+rpi1) ...
Setting up libedit2:armhf (3.1-20180525-1) ...
Setting up libpython3.6-stdlib:armhf (3.6.6-1) ...
Setting up libpcre3-dev:armhf (2:8.39-11+rpi1) ...
Setting up python3.6 (3.6.6-1) ...
Setting up libltdl-dev:armhf (2.4.6-2.1) ...
Setting up libharfbuzz0b:armhf (1.8.8-2+rpi1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up libhwloc5:armhf (1.11.10-3+rpi1) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up automake (1:1.16.1-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libreadline-dev:armhf (7.0-5) ...
Setting up man-db (2.8.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libgcc-8-dev:armhf (8.2.0-6+rpi1) ...
Setting up libgfortran-8-dev:armhf (8.2.0-6+rpi1) ...
Setting up libharfbuzz-gobject0:armhf (1.8.8-2+rpi1) ...
Setting up libtool (2.4.6-4) ...
Setting up libpython3-stdlib:armhf (3.6.5-3) ...
Setting up libibverbs1:armhf (20.0-1) ...
Setting up libstdc++-8-dev:armhf (8.2.0-6+rpi1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up python3 (3.6.5-3) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-8) ...
Setting up libhwloc-dev:armhf (1.11.10-3+rpi1) ...
Setting up gcc-8 (8.2.0-6+rpi1) ...
Setting up g++-8 (8.2.0-6+rpi1) ...
Setting up gir1.2-harfbuzz-0.0:armhf (1.8.8-2+rpi1) ...
Setting up ibverbs-providers:armhf (20.0-1) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up python3-lib2to3 (3.6.6-1) ...
Setting up libibverbs-dev:armhf (20.0-1) ...
Setting up python3-distutils (3.6.6-1) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up gfortran-8 (8.2.0-6+rpi1) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up openssh-client (1:7.8p1-1) ...
Setting up gfortran (4:8.1.0-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libharfbuzz-icu0:armhf (1.8.8-2+rpi1) ...
Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-8) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up libhwloc-plugins:armhf (1.11.10-3+rpi1) ...
Setting up icu-devtools (60.2-6) ...
Setting up gettext (0.19.8.1-7) ...
Setting up libpmix2:armhf (3.0.1-2) ...
Setting up libicu-dev (60.2-6) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libharfbuzz-dev:armhf (1.8.8-2+rpi1) ...
Setting up libopenmpi3:armhf (3.1.2-1+rpi1) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up po-debconf (1.0.20) ...
Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-8) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-8) ...
Setting up openmpi-bin (3.1.2-1+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: error: no alternatives for mpi
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b8) ...
Setting up debhelper (11.3.5) ...
Setting up dh-autoreconf (19) ...
Setting up libopenmpi-dev:armhf (3.1.2-1+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up sbuild-build-depends-mothur-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-6+rpi1 gcc-8_8.2.0-6+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.2.0-6+rpi1 libstdc++6_8.2.0-6+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-6+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.2.0-6+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-6+rpi1 gcc-8-base_8.2.0-6+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gfortran_4:8.1.0-1+rpi1 gfortran-8_8.2.0-6+rpi1 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.8.8-2+rpi1 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 ibverbs-providers_20.0-1 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-6+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-8 libboost-iostreams1.62.0_1.62.0+dfsg-8 libboost-regex1.62-dev_1.62.0+dfsg-8 libboost-regex1.62.0_1.62.0+dfsg-8 libboost1.62-dev_1.62.0+dfsg-8 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-6+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libedit2_3.1-20180525-1 libelf1_0.170-0.5 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-6+rpi1 libgcc1_1:8.2.0-6+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-8-dev_8.2.0-6+rpi1 libgfortran5_8.2.0-6+rpi1 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2 libglib2.0-bin_2.56.1-2 libglib2.0-data_2.56.1-2 libglib2.0-dev_2.56.1-2 libglib2.0-dev-bin_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-6+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libgraphite2-dev_1.3.12-1 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.8.8-2+rpi1 libharfbuzz-gobject0_1.8.8-2+rpi1 libharfbuzz-icu0_1.8.8-2+rpi1 libharfbuzz0b_1.8.8-2+rpi1 libhogweed4_3.4-1 libhwloc-dev_1.11.10-3+rpi1 libhwloc-plugins_1.11.10-3+rpi1 libhwloc5_1.11.10-3+rpi1 libibverbs-dev_20.0-1 libibverbs1_20.0-1 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libltdl-dev_2.4.6-2.1 libltdl7_2.4.6-2.1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180714-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnl-3-200_3.4.0-1 libnl-route-3-200_3.4.0-1 libnpth0_1.6-1 libnss-systemd_239-7 libopenmpi-dev_3.1.2-1+rpi1 libopenmpi3_3.1.2-1+rpi1 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpciaccess0_0.14-1 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpmix2_3.0.1-2 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 libreadline-dev_7.0-5 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-6+rpi1 libstdc++6_8.2.0-6+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.2.0-6+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 ocl-icd-libopencl1_2.2.12-1 openmpi-bin_3.1.2-1+rpi1 openmpi-common_3.1.2-1+rpi1 openssh-client_1:7.8p1-1 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python3_3.6.5-3 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.5-3 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mothur-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Sep 14 09:35:49 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./mothur_1.40.5-2.dsc
dpkg-source: info: extracting mothur in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mothur_1.40.5.orig.tar.gz
dpkg-source: info: unpacking mothur_1.40.5-2.debian.tar.xz
dpkg-source: info: applying 0001-Add-hardening-flags.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-53a22d36-6c17-4590-89cc-6a5a1ed1b2eb
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package mothur
dpkg-buildpackage: info: source version 1.40.5-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build mothur-1.40.5
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f mothur
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 build-arch
dh build-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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/utils.o source/utils.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/myseqdist.o source/myseqdist.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/sensspeccalc.o source/sensspeccalc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/gotohoverlap.o source/gotohoverlap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/completelinkage.o source/completelinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In function 'double getDist(std::vector<int>&, std::vector<int>&, std::vector<std::vector<double> >&, MothurOut*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
source/utils.cpp: In member function 'int Utils::renameFile(std::__cxx11::string, std::__cxx11::string)':
source/utils.cpp:809:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'std::__cxx11::string Utils::sortFile(std::__cxx11::string, std::__cxx11::string)':
source/utils.cpp:1041:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
source/utils.cpp: In member function 'bool Utils::mkDir(std::__cxx11::string&)':
source/utils.cpp:1466:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(makeDirectoryCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/myseqdist.h:14,
from source/myseqdist.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'int correctDist::createProcess(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/opticluster.o source/opticluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/subsample.o source/subsample.cpp
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'double Utils::median(std::vector<double>)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<double> OptiCluster::getStats(long long int&, long long int&, long long int&, long long int&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long int> OptiCluster::getCloseFarCounts(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmap.o source/heatmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nast.o source/nast.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/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 unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getAverages(std::vector<std::vector<std::vector<seqDist> > >&, std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getAverages(std::vector<std::vector<std::vector<seqDist> > >&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<seqDist> > Utils::getStandardDeviation(std::vector<std::vector<std::vector<seqDist> > >&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/summary.o source/summary.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/averagelinkage.o source/averagelinkage.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::divideFile(std::__cxx11::string, int&, char)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::divideFile(std::__cxx11::string, int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::setFilePosFasta(std::__cxx11::string, long long int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::divideFilePerLine(std::__cxx11::string, int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/utils.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::setFilePosEachLine(std::__cxx11::string, long long int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::setFilePosEachLine(std::__cxx11::string, long long unsigned int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<long long unsigned int> Utils::setFilePosFasta(std::__cxx11::string, long long int&, char)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomnumber.o source/randomnumber.cpp
In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const float&>, std::tuple<>}; _Key = float; _Val = std::pair<const float, long long int>; _KeyOfValue = std::_Select1st<std::pair<const float, long long int> >; _Compare = std::less<float>; _Alloc = std::allocator<std::pair<const float, long long int> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, long long int>; _KeyOfValue = std::_Select1st<std::pair<const int, long long int> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, long long int> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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
In file included from /usr/include/c++/8/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++/8/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++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandfactory.o source/commandfactory.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getDefaults()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function '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++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getValues(std::map<float, long long int>&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
source/summary.cpp:189:1: 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
}
^
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<long long int> Summary::getValues(std::map<int, long long int>&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
source/summary.cpp:124:1: 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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarecalc.o source/rarecalc.cpp
In file included from /usr/include/c++/8/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++/8/bits/stl_map.h: In function 'void driverAlignSummarySummarize(seqSumData*)':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int Summary::summarizeContigsSummary(std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int Summary::summarizeFasta(std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothurout.o source/mothurout.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int Summary::summarizeAlignSummary(std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/summary.hpp:12,
from source/summary.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int Summary::summarizeFastaSummary(std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/progress.o source/progress.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/linearalgebra.o source/linearalgebra.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/rarefact.o source/rarefact.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trimoligos.o source/trimoligos.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validcalculator.o source/validcalculator.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::transpose(std::vector<std::vector<double> >)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LinearAlgebra::calculateEuclidianDistance(std::vector<std::vector<double> >&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/bits/vector.tcc: 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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/linearalgebra.h:13,
from source/linearalgebra.cpp:10:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/bits/stl_map.h: In member function 'double LinearAlgebra::calcKruskalWallis(std::vector<spearmanRank>&, double&)':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/optionparser.o source/optionparser.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/validcalculator.h:13,
from source/validcalculator.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/mothur.o source/mothur.cpp
source/mothur.cpp: In function 'int main(int, char**)':
source/mothur.cpp:45:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("clear");
~~~~~~^~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/engine.o source/engine.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/inputdata.o source/inputdata.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calcsparcc.o source/calcsparcc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clusterclassic.o source/clusterclassic.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/singlelinkage.o source/singlelinkage.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/seqnoise.o source/seqnoise.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/refchimeratest.o source/refchimeratest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/dlibshuff.o source/dlibshuff.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/refchimeratest.h:13,
from source/refchimeratest.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'double RefChimeraTest::alignQueryToReferences(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, double&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/currentfile.o source/currentfile.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/seqnoise.h:22,
from source/seqnoise.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'int seqNoise::countDiffs(std::vector<int>, std::vector<int>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/slibshuff.o source/slibshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/heatmapsim.o source/heatmapsim.cpp
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/fullmatrix.h:12,
from source/slibshuff.h:13,
from source/slibshuff.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'double SLibshuff::sCalculate(int, int)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/collect.o source/collect.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/trialSwap2.o source/trialSwap2.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<std::__cxx11::basic_string<char> > HeatMapSim::getPic(std::vector<SharedRAbundVector*>, std::vector<Calculator*>, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/trialswap2.h:13,
from source/trialSwap2.cpp:1:
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::__cxx11::string HeatMapSim::getPic(std::vector<std::vector<double> >, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
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/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
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/c++/8/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/raredisplay.o source/raredisplay.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void SharedCollectorsCurveData::notifyDisplays()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/consensus.o source/consensus.cpp
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/datastructures/datavector.hpp:4,
from source/datastructures/sabundvector.hpp:4,
from source/raredisplay.h:4,
from source/raredisplay.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'virtual void RareDisplay::close()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual void RareDisplay::inputTempFiles(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void RareDisplay::update(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void RareDisplay::update(std::vector<SharedRAbundVector*>, int, int, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commandoptionparser.o source/commandoptionparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/nastreport.o source/nastreport.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/fileoutput.o source/fileoutput.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/libshuff.o source/libshuff.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/cluster.o source/cluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/noalign.o source/noalign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/overlap.o source/overlap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/f1score.o source/calculators/f1score.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shen.o source/calculators/shen.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedSobsCS::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/canberra.o source/calculators/canberra.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'EstOutput Parsimony::createProcesses(Tree*, CountTable*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Shen::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/gower.o source/calculators/gower.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fdr.o source/calculators/fdr.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Canberra::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpson.o source/calculators/simpson.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Gower::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/spearman.o source/calculators/spearman.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Simpson::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/logsd.o source/calculators/logsd.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput MemPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Spearman::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fn.o source/calculators/fn.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput LogSD::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchord.o source/calculators/memchord.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput GoodsCoverage::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/solow.o source/calculators/solow.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput MemChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/geom.o source/calculators/geom.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Solow::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Manhattan::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Geom::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/prng.o source/calculators/prng.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/efron.o source/calculators/efron.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Bootstrap::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hamming.o source/calculators/hamming.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Jackknife::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Efron::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Hamming::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannon.o source/calculators/shannon.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput KSTest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/boneh.o source/calculators/boneh.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SorClass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Shannon::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Boneh::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput RangeShannon::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedchao1.o source/calculators/sharedchao1.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput NPShannon::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/weighted.o source/calculators/weighted.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput StructEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedChao1::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/chao1.o source/calculators/chao1.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput JAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/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++/8/bits/vector.tcc:413:7: 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++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Chao1::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/whittaker.o source/calculators/whittaker.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In function 'void driverWeighted(weightedData*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SimpsonEven::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'EstOutput Weighted::createProcesses(Tree*, CountTable*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput Weighted::getValues(Tree*, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tp.o source/calculators/tp.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput ThetaYC::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/specificity.o source/calculators/specificity.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchord.o source/calculators/structchord.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput StructChord::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bstick.o source/calculators/bstick.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput ShannonEven::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedAce::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/mcc.o source/calculators/mcc.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput BStick::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fpfn.o source/calculators/fpfn.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedJackknife::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/odum.o source/calculators/odum.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ppv.o source/calculators/ppv.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SorAbund::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/npv.o source/calculators/npv.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Odum::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/heip.o source/calculators/heip.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/ace.o source/calculators/ace.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput StructPearson::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/fp.o source/calculators/fp.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Heip::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Ace::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/uvest.o source/calculators/uvest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput JSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'EstOutput UVEst::getUVest(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput MemEuclidean::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/unweighted.o source/calculators/unweighted.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput MemChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput StructChi2::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SorEst::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/soergel.o source/calculators/soergel.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/bits/vector.tcc:413:7: 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++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SpeciesProfile::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'EstOutput Unweighted::createProcesses(Tree*, CountTable*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Soergel::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'EstOutput Unweighted::createProcesses(Tree*, std::vector<std::vector<int> >&, CountTable*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Jclass::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput KulczynskiCody::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp
source/venn.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > Venn::getPic(std::vector<SharedRAbundVector*>, std::vector<Calculator*>)':
source/venn.cpp:77:16: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
^~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedMarczewski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput StructKulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput RJSD::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput BrayCurtis::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Hellinger::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tn.o source/calculators/tn.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sensitivity.o source/calculators/sensitivity.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput ThetaN::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/coverage.o source/calculators/coverage.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Lennon::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Ochiai::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SmithWilson::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/tptn.o source/calculators/tptn.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Coverage::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput InvSimpson::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput MorHorn::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/qstat.o source/calculators/qstat.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Jest::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Kulczynski::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/pintail.o source/chimera/pintail.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput QStat::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput BergerParker::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/bellerophon.o source/chimera/bellerophon.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Anderberg::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/maligner.o source/chimera/maligner.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'double Perseus::modeledPairwiseAlignSeqs(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, std::vector<std::vector<double> >&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'double Perseus::basicPairwiseAlignSeqs(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string&, std::__cxx11::string&, pwModel)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<Sequence> Maligner::minCoverageFilter(std::vector<Sequence>)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int Bellerophon::driverChimeras(std::vector<int>)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::__cxx11::string Maligner::chimeraMaligner(int, DeCalculator)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/slayer.o source/chimera/slayer.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::__cxx11::string Maligner::getResults(Sequence, DeCalculator)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/ccode.o source/chimera/ccode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimerarealigner.o source/chimera/chimerarealigner.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<data_struct> Slayer::runBellerophon(Sequence, Sequence, Sequence, std::map<int, int>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/memory:62,
from /usr/include/boost/iostreams/filtering_stream.hpp:15,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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++/8/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
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/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
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<Sequence> ChimeraSlayer::getKmerSeqs(Sequence, std::vector<Sequence*>&, int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_vector.h: In member function 'std::vector<Sequence> ChimeraSlayer::getBlastSeqs(Sequence, std::vector<Sequence*>&, int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/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++/8/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
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/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
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1902:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
while (__comp(__first, __pivot))
~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1905:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
while (__comp(__pivot, __last))
~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::__cxx11::string Slayer::getResults(Sequence, std::vector<Sequence>)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/sequence.hpp:20,
from source/chimera/slayer.h:13,
from source/chimera/slayer.cpp:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<data_struct*, std::vector<data_struct> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/memory:62,
from /usr/include/boost/iostreams/filtering_stream.hpp:15,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/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++/8/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
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1847:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
if (__comp(__i, __first))
~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:222:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
if (__comp(__first + __secondChild,
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
__first + (__secondChild - 1)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/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
/usr/include/c++/8/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++/8/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
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/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
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/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
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1902:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
while (__comp(__first, __pivot))
~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1905:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
while (__comp(__pivot, __last))
~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual int ChimeraSlayer::getChimeras(Sequence*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/chimera/mothurchimera.h:14,
from source/chimera/chimeraslayer.h:14,
from source/chimera/chimeraslayer.cpp:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SeqCompare*, std::vector<SeqCompare> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/chimera/decalc.o source/chimera/decalc.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/classify.o source/classifier/classify.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/chimera/decalc.h:12,
from source/chimera/decalc.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<Sequence> DeCalculator::findClosest(Sequence, std::vector<Sequence*>&, std::vector<Sequence*>&, int, int)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/knn.o source/classifier/knn.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual std::__cxx11::string AlignTree::getTaxonomy(Sequence*, std::__cxx11::string&, bool&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual std::__cxx11::string KmerTree::getTaxonomy(Sequence*, std::__cxx11::string&, bool&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp
source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)':
source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp, "%ld\n", &dmat->ntaxa);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int CooccurrenceCommand::getCooccurrence(SharedRAbundVectors*&, std::ofstream&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp
source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
source/commands/distancecommand.cpp:325:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(("gzip -v " + outputFile).c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/matrixoutputcommand.o source/commands/matrixoutputcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/vector:64,
from source/mothur.h:40,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void DistanceCommand::createProcesses(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/distancecommand.h:13,
from source/commands/distancecommand.cpp:10:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/matrixoutputcommand.h:12,
from source/commands/matrixoutputcommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In function 'int driver(std::vector<SharedRAbundVector*>&, std::vector<std::vector<seqDist> >&, std::vector<Calculator*>, MothurOut*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp
/usr/include/c++/8/bits/stl_vector.h: In function 'int process(distSharedData*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int MatrixOutputCommand::createProcesses(SharedRAbundVectors*&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp
In file included from /usr/include/c++/8/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++/8/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++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/bits/stl_map.h: In member function 'int LibShuffCommand::printCoverageFile()':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/treegroupscommand.o source/commands/treegroupscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getotulabelscommand.o source/commands/getotulabelscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int ClusterFragmentsCommand::readFASTA()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/memory:62,
from /usr/include/boost/iostreams/filtering_stream.hpp:15,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/8/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++/8/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
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1847:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
if (__comp(__i, __first))
~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:222:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
if (__comp(__first + __secondChild,
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
__first + (__secondChild - 1)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/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++/8/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
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/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++/8/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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/8/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
std::__pop_heap(__first, __last, __last, __comp);
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clusterfragmentscommand.h:14,
from source/commands/clusterfragmentscommand.cpp:10:
/usr/include/c++/8/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
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/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
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1902:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
while (__comp(__first, __pivot))
~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1905:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
while (__comp(__pivot, __last))
~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'virtual int ClusterFragmentsCommand::execute()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqRNode*, std::vector<seqRNode> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/treegroupscommand.h:13,
from source/commands/treegroupscommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In function 'int driverTreeShared(std::vector<SharedRAbundVector*>&, std::vector<std::vector<seqDist> >&, std::vector<Calculator*>, MothurOut*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp
/usr/include/c++/8/bits/stl_vector.h: In function 'int process(treeSharedData*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int TreeGroupCommand::createProcesses(SharedRAbundVectors*&, CountTable&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp
source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::__cxx11::string)':
source/commands/makefilecommand.cpp:366:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(findCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, double>; _KeyOfValue = std::_Select1st<std::pair<const double, double> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int SummaryQualCommand::createProcessesCreateSummary(std::vector<int>&, std::vector<int>&, std::vector<std::vector<int> >&, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In function 'void driverWeightedRandom(weightedRandomData*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parselistscommand.o source/commands/parselistscommand.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int GetCoreMicroBiomeCommand::createTable(SharedRAbundFloatVectors*&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int UnifracWeightedCommand::getAverageSTDMatrices(std::vector<std::vector<double> >&, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracWeightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/unifracweightedcommand.h:13,
from source/commands/unifracweightedcommand.cpp:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual int UnifracWeightedCommand::execute()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
source/commands/clustercommand.cpp:624:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int HeatMapSimCommand::runCommandDist()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int DegapSeqsCommand::createProcesses(std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function '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++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'long long int AlignCommand::createProcesses(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::vector<long long int>&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'int UnifracUnweightedCommand::getAverageSTDMatrices(std::vector<std::vector<double> >&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
source/commands/aligncommand.cpp:587:1: 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/aligncommand.cpp:587:1: 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
/usr/include/c++/8/bits/vector.tcc: In member function 'void UnifracUnweightedCommand::printUnweightedFile(int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<Tree*> UnifracUnweightedCommand::buildTrees(std::vector<std::vector<double> >&, int, CountTable&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int UnifracUnweightedCommand::runRandomCalcs(Tree*, std::vector<double>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual int UnifracUnweightedCommand::execute()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int RareFactSharedCommand::subsampleLookup(SharedRAbundVectors*&, std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp
source/commands/trimflowscommand.cpp: In function 'int driverCreateTrim(trimFlowData*)':
source/commands/trimflowscommand.cpp:647:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/8/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 unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<long long unsigned int> TrimFlowsCommand::getFlowFileBreaks()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/venncommand.o source/commands/venncommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/trimflowscommand.h:13,
from source/commands/trimflowscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'int TrimFlowsCommand::createProcessesCreateTrim(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removeotulabelscommand.o source/commands/removeotulabelscommand.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual int GetSharedOTUCommand::execute()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp
In file included from /usr/include/c++/8/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++/8/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<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++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/8/bits/stl_map.h:518:8: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/bits/stl_map.h: In member function 'void ParsimonyCommand::printParsimonyFile()':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/screenseqscommand.h:12,
from source/commands/screenseqscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual int ParsimonyCommand::execute()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from source/mothur.h:42,
from source/commands/command.hpp:16,
from source/commands/parsimonycommand.h:12,
from source/commands/parsimonycommand.cpp:10:
/usr/include/c++/8/bits/stl_map.h:518:8: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:518:8: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/vector.tcc: In member function 'int ScreenSeqsCommand::createProcesses(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/memory:62,
from /usr/include/boost/iostreams/filtering_stream.hpp:15,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/8/bits/predefined_ops.h: In member function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Iterator2 = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = bool (*)(seqDist, seqDist)]':
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/8/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++/8/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
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > AnosimCommand::convertToRanks(std::vector<std::vector<double> >)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/anosimcommand.h:14,
from source/commands/anosimcommand.cpp:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/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::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function '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++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In function 'void driverGetCounts(primerCountsData*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/bits/vector.tcc:413:7: 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++/8/bits/vector.tcc: In member function 'std::set<int> PrimerDesignCommand::createProcesses(std::__cxx11::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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/catchallcommand.o source/commands/catchallcommand.cpp
source/commands/catchallcommand.cpp: In member function 'virtual int CatchAllCommand::execute()':
source/commands/catchallcommand.cpp:323:13: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
source/commands/catchallcommand.cpp:386:13: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
source/commands/catchallcommand.cpp:471:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(catchAllCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<double> MakeLookupCommand::convertSeqToFlow(std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int MakeLookupCommand::alignFlowGrams(std::vector<double>&, std::vector<double>&, double, std::vector<std::vector<double> >, std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual int MakeLookupCommand::execute()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In function 'void driverSummaryShared(summarySharedData*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int SummarySharedCommand::runCalcs(std::vector<SharedRAbundVector*>&, std::__cxx11::string, std::__cxx11::string, std::vector<std::vector<seqDist> >&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int NMDSCommand::normalizeConfiguration(std::vector<std::vector<double> >&, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int SummarySharedCommand::process(std::vector<SharedRAbundVector*>, std::__cxx11::string, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > NMDSCommand::readAxes(std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp
source/commands/chimeravsearchcommand.cpp: In member function 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)':
source/commands/chimeravsearchcommand.cpp:1186:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp
source/commands/trimseqscommand.cpp: In function 'int driverTrim(trimData*)':
source/commands/trimseqscommand.cpp:959:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from /usr/include/string.h:494,
from /usr/include/boost/range/detail/implementation_help.hpp:18,
from /usr/include/boost/range/end.hpp:24,
from /usr/include/boost/range/functions.hpp:19,
from /usr/include/boost/range/iterator_range_core.hpp:38,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/pipeline.hpp:18,
from /usr/include/boost/iostreams/detail/push.hpp:22,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/chimeravsearchcommand.h:12,
from source/commands/chimeravsearchcommand.cpp:9:
In function 'char* strncat(char*, const char*, size_t)',
inlined from 'int ChimeraVsearchCommand::driver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)' at source/commands/chimeravsearchcommand.cpp:1135:40:
/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=]
return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/trimseqscommand.h:13,
from source/commands/trimseqscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'int TrimSeqsCommand::setLines(std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > LefseCommand::getMeans(SharedRAbundFloatVectors*&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp
In file included from /usr/include/c++/8/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++/8/bits/stl_map.h: In member function 'std::map<int, double> LefseCommand::runWilcoxon(SharedRAbundFloatVectors*&, 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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'int LefseCommand::printResults(std::vector<std::vector<double> >, std::map<int, double>, std::map<int, double>, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/secondarystructurecommand.o source/commands/secondarystructurecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/mergesfffilecommand.h:12,
from source/commands/mergesfffilecommand.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const CommonHeader&}; _Tp = CommonHeader; _Alloc = std::allocator<CommonHeader>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<CommonHeader>::iterator' {aka '__gnu_cxx::__normal_iterator<CommonHeader*, std::vector<CommonHeader> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/mergesfffilecommand.h:12,
from source/commands/mergesfffilecommand.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'int MergeSfffilesCommand::mergeSffInfo(std::__cxx11::string, std::ofstream&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CommonHeader*, std::vector<CommonHeader> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/shhhercommand.h:13,
from source/commands/shhhercommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void ShhherCommand::getJointLookUp()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:478:5: 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
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int PCACommand::process(SharedRAbundFloatVectors*&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In function 'int driver(metastatsData*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'int MetaStatsCommand::process(SharedRAbundVectors*&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'bool ChopSeqsCommand::createProcesses(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<Sequence> SeqErrorCommand::getReferences(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/command.hpp:16,
from source/commands/preclustercommand.h:15,
from source/commands/preclustercommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void PreClusterCommand::createProcessesGroups(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp
source/commands/clusterfitcommand.cpp: In member function 'std::__cxx11::string ClusterFitCommand::calcDists(ListVector*)':
source/commands/clusterfitcommand.cpp:475:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void CollectDisplay::update(std::vector<SharedRAbundVector*>, int, int, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sharedcommand.o source/commands/sharedcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual EstOutput SharedNSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::driver(SharedRAbundVectors*&, std::vector<std::vector<seqDist> >&, Calculator*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<std::vector<double> > GetMetaCommunityCommand::generateDistanceMatrix(SharedRAbundVectors*&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/memory:62,
from /usr/include/boost/iostreams/filtering_stream.hpp:15,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/8/bits/predefined_ops.h: In member function 'bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Iterator2 = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = bool (*)(summaryData, summaryData)]':
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1847:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
if (__comp(__i, __first))
~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:222:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
if (__comp(__first + __secondChild,
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
__first + (__secondChild - 1)))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(summaryData, summaryData)>]':
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: 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++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1902:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
while (__comp(__first, __pivot))
~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/getmetacommunitycommand.h:12,
from source/commands/getmetacommunitycommand.cpp:9:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<summaryData*, std::vector<summaryData> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int GetMetaCommunityCommand::processDriver(SharedRAbundVectors*&, std::vector<int>&, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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 unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyrfsharedcommand.o source/commands/classifyrfsharedcommand.cpp
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/bits/vector.tcc:413:7: 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++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In function 'void driverContigsGroups(groupContigsData*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp
source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
source/commands/systemcommand.cpp:101:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int PcrSeqsCommand::createProcesses(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::set<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual int PcrSeqsCommand::execute()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/chimeraperseuscommand.h:16,
from source/commands/chimeraperseuscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'int ChimeraPerseusCommand::createProcessesGroups(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<int> CreateDatabaseCommand::readFasta(std::vector<Sequence>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'int OTUAssociationCommand::readMetadata()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
/usr/include/c++/8/bits/vector.tcc: In member function 'int OTUAssociationCommand::process(SharedRAbundFloatVectors*&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'int OTUAssociationCommand::process(SharedRAbundVectors*&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int SortSeqsCommand::readQual()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<QualityScores*, std::vector<QualityScores> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'int SortSeqsCommand::readFasta()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'long long int FilterSeqsCommand::createProcessesCreateFilter(Filters&, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'int FilterSeqsCommand::filterSequences()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'ClassifySvmSharedCommand::ClassifySvmSharedCommand(std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp
source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)':
source/commands/chimerauchimecommand.cpp:733:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp
In file included from /usr/include/string.h:494,
from /usr/include/boost/range/detail/implementation_help.hpp:18,
from /usr/include/boost/range/end.hpp:24,
from /usr/include/boost/range/functions.hpp:19,
from /usr/include/boost/range/iterator_range_core.hpp:38,
from /usr/include/boost/range/iterator_range.hpp:13,
from /usr/include/boost/iostreams/traits.hpp:38,
from /usr/include/boost/iostreams/pipeline.hpp:18,
from /usr/include/boost/iostreams/detail/push.hpp:22,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/chimerauchimecommand.h:14,
from source/commands/chimerauchimecommand.cpp:10:
In function 'char* strcpy(char*, const char*)',
inlined from 'int driver(uchimeData*)' at source/commands/chimerauchimecommand.cpp:704:19:
/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=]
return __builtin___strcpy_chk (__dest, __src, __bos (__dest));
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'int ChimeraUchimeCommand::createProcessesGroups(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double, clusterData*)':
source/commands/clustersplitcommand.cpp:1224:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(commandString.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/nocommands.o source/commands/nocommands.cpp
source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
source/commands/pairwiseseqscommand.cpp:277:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(("gzip -v " + outputFile).c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const double&>, std::tuple<>}; _Key = double; _Val = std::pair<const double, int>; _KeyOfValue = std::_Select1st<std::pair<const double, int> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, int> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::map<double, int> ClusterSplitCommand::completeListFile(std::vector<std::__cxx11::basic_string<char> >, std::__cxx11::string, std::set<std::__cxx11::basic_string<char> >&, ListVector*&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/commands/command.hpp:16,
from source/commands/clustersplitcommand.h:13,
from source/commands/clustersplitcommand.cpp:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/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++/8/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
__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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/bits/vector.tcc: In member function 'void PairwiseSeqsCommand::createProcesses(std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/commands/pairwiseseqscommand.h:13,
from source/commands/pairwiseseqscommand.cpp:10:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<linePair*, std::vector<linePair> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/pam.o source/communitytype/pam.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput Sobs::getValues(SAbundVector*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual EstOutput NSeqs::getValues(std::vector<SharedRAbundVector*>)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'double CommunityTypeFinder::rMedoid(std::vector<std::vector<double> >, std::vector<std::vector<double> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int CommunityTypeFinder::findkMeans()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual std::vector<double> CommunityTypeFinder::calcSilhouettes(std::vector<std::vector<double> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'virtual double Pam::calcCHIndex(std::vector<std::vector<double> >)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'int Pam::buildPhase()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'int SummaryCommand::process(SAbundVector*&, std::ofstream&, std::ofstream&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'void qFinderDMM::negativeLogDerivEvidenceLambdaPi(std::vector<double>&, std::vector<double>&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp
source/datastructures/blastalign.cpp: In member function 'virtual void BlastAlignment::align(std::__cxx11::string, std::__cxx11::string)':
source/datastructures/blastalign.cpp:64:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as
~~~~~~^~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function '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++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/sequence.hpp:20,
from source/datastructures/sequencedb.h:17,
from source/datastructures/sequencedb.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In constructor 'SequenceDB::SequenceDB(std::ifstream&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void SequenceDB::push_back(Sequence)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void DistanceDB::addSequence(Sequence)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/8/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++/8/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
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/datastructures/database.hpp:16,
from source/datastructures/distancedb.cpp:11:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'virtual std::vector<int> DistanceDB::findClosestSequences(Sequence*, int, std::vector<float>&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/sequenceparser.h:14,
from source/datastructures/sequenceparser.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Sequence}; _Tp = Sequence; _Alloc = std::allocator<Sequence>]':
/usr/include/c++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/sequenceparser.h:14,
from source/datastructures/sequenceparser.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In constructor 'SequenceParser::SequenceParser(std::__cxx11::string, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/utils.hpp:12,
from source/datastructures/sequenceparser.h:14,
from source/datastructures/sequenceparser.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In constructor 'SequenceParser::SequenceParser(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/tree.o source/datastructures/tree.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/sequencecountparser.h:12,
from source/datastructures/sequencecountparser.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/sequencecountparser.h:12,
from source/datastructures/sequencecountparser.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'int SequenceCountParser::readFasta(std::__cxx11::string, CountTable&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestSequences(Sequence*, int, std::vector<float>&)':
source/datastructures/blastdb.cpp:163:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual std::vector<int> BlastDB::findClosestMegaBlast(Sequence*, int, int)':
source/datastructures/blastdb.cpp:230:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(blastCommand.c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~~~~
source/datastructures/blastdb.cpp: In member function 'virtual void BlastDB::generateDB()':
source/datastructures/blastdb.cpp:301:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundfloatvectors.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/datastructures/alignmentdb.h:13,
from source/datastructures/alignmentdb.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In constructor 'AlignmentDB::AlignmentDB(std::__cxx11::string, std::__cxx11::string, int, float, float, float, float, int, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Sequence*, std::vector<Sequence> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp
In file included from /usr/include/c++/8/vector:69,
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++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'std::vector<double> MothurMetastats::permute_and_calc_ts(std::vector<std::vector<double> >&)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp
/usr/include/c++/8/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++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'int MothurMetastats::runMetastats(std::__cxx11::string, std::vector<std::vector<double> >&, int, std::vector<std::__cxx11::basic_string<char> >)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_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 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/randomforest/forest.o source/randomforest/forest.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/abstractdecisiontree.hpp:12,
from source/randomforest/abstractdecisiontree.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/abstractdecisiontree.hpp:12,
from source/randomforest/abstractdecisiontree.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual int AbstractDecisionTree::getBestSplitAndMinEntropy(std::vector<std::pair<int, int> >, std::vector<int>, double&, int&, double&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Distance = int; _Tp = std::pair<int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/decisiontree.hpp:12,
from source/randomforest/decisiontree.cpp:9:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readblast.o source/read/readblast.cpp
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/decisiontree.hpp:12,
from source/randomforest/decisiontree.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'int DecisionTree::findAndUpdateBestFeatureToSplitOn(RFTreeNode*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<int, double>&}; _Tp = std::pair<int, double>; _Alloc = std::allocator<std::pair<int, double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::pair<int, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<VariableRankDescendingSorterDouble>]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual int RandomForest::calcForrestVariableImportance(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<int, double>*, std::vector<std::pair<int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/mothurout.h:13,
from source/randomforest/macros.h:12,
from source/randomforest/randomforest.hpp:12,
from source/randomforest/randomforest.cpp:9:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual int RandomForest::populateDecisionTrees()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp
source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(NameAssignment*)':
source/read/formatcolumn.cpp:87:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
source/read/formatcolumn.cpp: In member function 'virtual int FormatColumnMatrix::read(CountTable*)':
source/read/formatcolumn.cpp:250:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/8/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++/8/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
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(seqDist, seqDist)>]':
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'int ReadBlast::read(NameAssignment*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/boost/iostreams/detail/adapter/range_adapter.hpp:15,
from /usr/include/boost/iostreams/detail/push.hpp:19,
from /usr/include/boost/iostreams/filtering_stream.hpp:19,
from source/mothur.h:21,
from source/read/readblast.h:12,
from source/read/readblast.cpp:10:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcolumn.o source/read/readcolumn.cpp
In file included from /usr/include/c++/8/vector:69,
from source/mothur.h:40,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from source/mothur.h:40,
from source/read/readphylipvector.h:14,
from source/read/readphylipvector.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<std::__cxx11::basic_string<char> > ReadPhylipVector::read(std::vector<seqDist>&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<seqDist*, std::vector<seqDist> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readcluster.o source/read/readcluster.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readtree.o source/read/readtree.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/formatphylip.o source/read/formatphylip.cpp
source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(NameAssignment*)':
source/read/formatphylip.cpp:108:12: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
source/read/formatphylip.cpp: In member function 'virtual int FormatPhylipMatrix::read(CountTable*)':
source/read/formatphylip.cpp:338:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(command.c_str());
~~~~~~^~~~~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/treereader.o source/read/treereader.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/read/readphylip.o source/read/readphylip.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -DVERSION="\"1.40.4\"" -DUSE_READLINE -DUSE_BOOST -I "\"Enter_your_boost_include_path_here\"" -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp
cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
+ CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit'
+ ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o'
+ rm -f '*.o' mk.stdout mk.stderr tmp.stderr
+ for CPPName in $CPPNames
+ echo addtargets2
addtargets2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 addtargets2.cpp -o addtargets2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alignchime
alignchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchime.cpp -o alignchime.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alignchimel
alignchimel
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alignchimel.cpp -o alignchimel.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alnparams
alnparams
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alnparams.cpp -o alnparams.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alpha
alpha
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha.cpp -o alpha.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo alpha2
alpha2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 alpha2.cpp -o alpha2.o
In file included from /usr/include/c++/8/vector:69,
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++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
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++/8/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++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo fractid
fractid
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 fractid.cpp -o fractid.o
In file included from /usr/include/c++/8/map:60,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2411:7: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo getparents
getparents
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 getparents.cpp -o getparents.o
In file included from /usr/include/c++/8/map:61,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/8/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++/8/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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
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++/8/bits/stl_vector.h: In member function 'SVM* SmoTrainer::train(KernelFunctionCache&, const LabeledObservationVector&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo globalalign2
globalalign2
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 globalalign2.cpp -o globalalign2.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo make3way
make3way
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 make3way.cpp -o make3way.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo mx
mx
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 mx.cpp -o mx.o
In file included from /usr/include/c++/8/map:60,
from source/svm/svm.hpp:18,
from source/svm/svm.cpp:17:
/usr/include/c++/8/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++/8/bits/stl_tree.h:2146:5: 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
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo myutils
myutils
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 myutils.cpp -o myutils.o
+ cat tmp.stderr
myutils.cpp: In function 'const char* SecsToHHMMSS(int)':
myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(Str, "%02d:%02d:%02d", HH, MM, SS);
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from myutils.cpp:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
myutils.cpp: In function 'const char* SecsToStr(double)':
myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(Str, "%02d:%02d:%02d", HH, MM, SS);
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from myutils.cpp:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
myutils.cpp: In function 'void Progress(const char*, ...)':
myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(Str, "%02d:%02d:%02d", HH, MM, SS);
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from myutils.cpp:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
myutils.cpp: In function 'void ProgressExit()':
myutils.cpp:729:16: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=]
sprintf(Str, "%02d:%02d:%02d", HH, MM, SS);
^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862,
from /usr/include/c++/8/cstdio:42,
from /usr/include/c++/8/ext/string_conversions.h:43,
from /usr/include/c++/8/bits/basic_string.h:6391,
from /usr/include/c++/8/string:52,
from myutils.cpp:7:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:34: note: '__builtin___sprintf_chk' output between 9 and 26 bytes into a destination of size 16
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo path
path
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 path.cpp -o path.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo searchchime
searchchime
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 searchchime.cpp -o searchchime.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo seqdb
seqdb
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 seqdb.cpp -o seqdb.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo setnucmx
setnucmx
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 setnucmx.cpp -o setnucmx.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo sfasta
sfasta
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 sfasta.cpp -o sfasta.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo tracebackbit
tracebackbit
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 tracebackbit.cpp -o tracebackbit.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo uchime_main
uchime_main
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 uchime_main.cpp -o uchime_main.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo usort
usort
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 usort.cpp -o usort.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo viterbifast
viterbifast
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 viterbifast.cpp -o viterbifast.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ for CPPName in $CPPNames
+ echo writechhit
writechhit
+ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 '-DVERSION="\"1.40.4\""' -DUSE_READLINE -DUSE_BOOST -I '"\"Enter_your_boost_include_path_here\""' -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 writechhit.cpp -o writechhit.o
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ LINK_OPTS=
+ g++ -g -o uchime addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -L '"\"Enter_your_boost_library_path_here\""' -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/
+ cat tmp.stderr
+ cat tmp.stderr
+ rm -f tmp.stderr
+ ls -lh uchime
-rwxrwxr-x 1 buildd buildd 3.7M Sep 16 07:45 uchime
+ sum uchime
17772 3702
g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -L "\"Enter_your_boost_library_path_here\"" -Lsource/ -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/metastats/ -Lsource/randomforest/ -Lsource/read/ -Lsource/svm/ -o mothur source/randomnumber.o source/gotohoverlap.o source/validparameter.o source/rarefact.o source/opticluster.o source/heatmap.o source/nast.o source/mothurout.o source/completelinkage.o source/averagelinkage.o source/collect.o source/seqnoise.o source/vsearchfileparser.o source/venn.o source/inputdata.o source/calcsparcc.o source/clusterclassic.o source/slibshuff.o source/trialSwap2.o source/consensus.o source/nastreport.o source/fileoutput.o source/cluster.o source/wilcox.o source/needlemanoverlap.o source/utils.o source/sensspeccalc.o source/refchimeratest.o source/myseqdist.o source/subsample.o source/commandfactory.o source/rarecalc.o source/weightedlinkage.o source/progress.o source/linearalgebra.o source/singlelinkage.o source/trimoligos.o source/validcalculator.o source/optionparser.o source/mothur.o source/engine.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/sharedjabund.o source/calculators/chao1.o source/calculators/sharedjclass.o source/calculators/efron.o source/calculators/sharedsobscollectsummary.o source/calculators/structchord.o source/calculators/mcc.o source/calculators/fpfn.o source/calculators/qstat.o source/calculators/tp.o source/calculators/prng.o source/calculators/ppv.o source/calculators/npv.o source/calculators/fp.o source/calculators/sharedjsd.o source/calculators/sharedthetan.o source/calculators/boneh.o source/calculators/uvest.o source/calculators/shannonrange.o source/calculators/sharedsorabund.o source/calculators/sharedbraycurtis.o source/calculators/hellinger.o source/calculators/accuracy.o source/calculators/sharedsobs.o source/calculators/sensitivity.o source/calculators/sharedkulczynski.o source/calculators/sharedsorclass.o source/calculators/sharedthetayc.o source/calculators/coverage.o source/calculators/tptn.o source/calculators/sharedace.o source/calculators/fn.o source/calculators/parsimony.o source/calculators/gower.o source/calculators/simpson.o source/calculators/mempearson.o source/calculators/manhattan.o source/calculators/whittaker.o source/calculators/shannon.o source/calculators/npshannon.o source/calculators/structeuclidean.o source/calculators/sharedochiai.o source/calculators/specificity.o source/calculators/sharedchao1.o source/calculators/weighted.o source/calculators/simpsoneven.o source/calculators/memchi2.o source/calculators/spearman.o source/calculators/shannoneven.o source/calculators/bstick.o source/calculators/solow.o source/calculators/sharedkulczynskicody.o source/calculators/sharedjest.o source/calculators/sharedanderbergs.o source/calculators/odum.o source/calculators/structpearson.o source/calculators/heip.o source/calculators/ace.o source/calculators/sharedlennon.o source/calculators/memeuclidean.o source/calculators/structchi2.o source/calculators/sharedsorest.o source/calculators/speciesprofile.o source/calculators/soergel.o source/calculators/sharedmarczewski.o source/calculators/structkulczynski.o source/calculators/sharedkstest.o source/calculators/f1score.o source/calculators/tn.o source/calculators/logsd.o source/calculators/sharedmorisitahorn.o source/calculators/fdr.o source/calculators/bergerparker.o source/calculators/smithwilson.o source/calculators/canberra.o source/calculators/hamming.o source/calculators/shen.o source/calculators/goodscoverage.o source/calculators/memchord.o source/calculators/geom.o source/calculators/bootstrap.o source/calculators/jackknife.o source/calculators/sharedrjsd.o source/calculators/invsimpson.o source/calculators/sharedjackknife.o source/calculators/unweighted.o source/chimera/pintail.o source/chimera/myPerseus.o source/chimera/bellerophon.o source/chimera/maligner.o source/chimera/chimeraslayer.o source/chimera/slayer.o source/chimera/ccode.o source/chimera/chimerarealigner.o source/chimera/chimeracheckrdp.o source/chimera/mothurchimera.o source/chimera/decalc.o source/classifier/classify.o source/classifier/phylosummary.o source/classifier/taxonomyequalizer.o source/classifier/kmernode.o source/classifier/phylotree.o source/classifier/aligntree.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/alignnode.o source/classifier/bayesian.o source/classifier/taxonomynode.o source/clearcut/distclearcut.o source/clearcut/cmdargs.o source/clearcut/clearcut.o source/clearcut/fasta.o source/clearcut/dmat.o source/clearcut/getopt_long.o source/commands/reversecommand.o source/commands/getcurrentcommand.o source/commands/collectcommand.o source/commands/cooccurrencecommand.o source/commands/clearcutcommand.o source/commands/listseqscommand.o source/commands/clusterdoturcommand.o source/commands/distancecommand.o source/commands/binsequencecommand.o source/commands/quitcommand.o source/commands/matrixoutputcommand.o source/commands/subsamplecommand.o source/commands/indicatorcommand.o source/commands/removegroupscommand.o source/commands/libshuffcommand.o source/commands/clusterfragmentscommand.o source/commands/treegroupscommand.o source/commands/kruskalwalliscommand.o source/commands/getotulabelscommand.o source/commands/removeseqscommand.o source/commands/mimarksattributescommand.o source/commands/renameseqscommand.o source/commands/makegroupcommand.o source/commands/removerarecommand.o source/commands/makefilecommand.o source/commands/getdistscommand.o source/commands/sensspeccommand.o source/commands/summaryqualcommand.o source/commands/unifracweightedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/splitgroupscommand.o source/commands/parselistscommand.o source/commands/normalizesharedcommand.o source/commands/countgroupscommand.o source/commands/heatmapsimcommand.o source/commands/clustercommand.o source/commands/degapseqscommand.o source/commands/summarytaxcommand.o source/commands/unifracunweightedcommand.o source/commands/rarefactsharedcommand.o source/commands/aligncommand.o source/commands/chimerabellerophoncommand.o source/commands/otuhierarchycommand.o source/commands/trimflowscommand.o source/commands/getrelabundcommand.o source/commands/removelineagecommand.o source/commands/venncommand.o source/commands/getsharedotucommand.o source/commands/classifyseqscommand.o source/commands/removeotulabelscommand.o source/commands/screenseqscommand.o source/commands/parsimonycommand.o source/commands/sracommand.o source/commands/mgclustercommand.o source/commands/anosimcommand.o source/commands/sffmultiplecommand.o source/commands/splitabundcommand.o source/commands/primerdesigncommand.o source/commands/getrabundcommand.o source/commands/catchallcommand.o source/commands/getgroupscommand.o source/commands/heatmapcommand.o source/commands/deconvolutecommand.o source/commands/mantelcommand.o source/commands/mergetaxsummarycommand.o source/commands/makelookupcommand.o source/commands/rarefactcommand.o source/commands/summarysharedcommand.o source/commands/getlineagecommand.o source/commands/nmdscommand.o source/commands/chimeravsearchcommand.o source/commands/trimseqscommand.o source/commands/listotulabelscommand.o source/commands/getsabundcommand.o source/commands/lefsecommand.o source/commands/phylodiversitycommand.o source/commands/makelefsecommand.o source/commands/filtersharedcommand.o source/commands/shhhercommand.o source/commands/mergesfffilecommand.o source/commands/secondarystructurecommand.o source/commands/pcacommand.o source/commands/seqsummarycommand.o source/commands/metastatscommand.o source/commands/chimeraslayercommand.o source/commands/chopseqscommand.o source/commands/sffinfocommand.o source/commands/makebiomcommand.o source/commands/seqerrorcommand.o source/commands/getlistcountcommand.o source/commands/getlabelcommand.o source/commands/consensusseqscommand.o source/commands/corraxescommand.o source/commands/preclustercommand.o source/commands/setdircommand.o source/commands/chimeraccodecommand.o source/commands/classifytreecommand.o source/commands/clusterfitcommand.o source/commands/getseqscommand.o source/commands/collectsharedcommand.o source/commands/deuniqueseqscommand.o source/commands/getmimarkspackagecommand.o source/commands/setcurrentcommand.o source/commands/getmetacommunitycommand.o source/commands/setseedcommand.o source/commands/sharedcommand.o source/commands/makecontigscommand.o source/commands/mergefilecommand.o source/commands/homovacommand.o source/commands/getcommandinfocommand.o source/commands/biominfocommand.o source/commands/classifyrfsharedcommand.o source/commands/helpcommand.o source/commands/mergegroupscommand.o source/commands/pcrseqscommand.o source/commands/systemcommand.o source/commands/chimeraperseuscommand.o source/commands/deuniquetreecommand.o source/commands/makefastqcommand.o source/commands/classifyotucommand.o source/commands/createdatabasecommand.o source/commands/chimerapintailcommand.o source/commands/sortseqscommand.o source/commands/otuassociationcommand.o source/commands/removedistscommand.o source/commands/parsefastaqcommand.o source/commands/amovacommand.o source/commands/filterseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/countseqscommand.o source/commands/chimerauchimecommand.o source/commands/renamefilecommand.o source/commands/getgroupcommand.o source/commands/chimeracheckcommand.o source/commands/clustersplitcommand.o source/commands/pairwiseseqscommand.o source/commands/nocommands.o source/commands/mergecountcommand.o source/commands/getoturepcommand.o source/commands/setlogfilecommand.o source/commands/sparcccommand.o source/commands/phylotypecommand.o source/commands/newcommandtemplate.o source/commands/pcoacommand.o source/commands/shhhseqscommand.o source/commands/summarycommand.o source/communitytype/communitytype.o source/communitytype/pam.o source/communitytype/kmeans.o source/communitytype/qFinderDMM.o source/datastructures/listvector.o source/datastructures/groupmap.o source/datastructures/fastamap.o source/datastructures/sharedlistvector.o source/datastructures/alignment.o source/datastructures/nameassignment.o source/datastructures/suffixtree.o source/datastructures/suffixnodes.o source/datastructures/tree.o source/datastructures/ordervector.o source/datastructures/kmeralign.o source/datastructures/blastalign.o source/datastructures/alignmentcell.o source/datastructures/sabundvector.o source/datastructures/rabundfloatvector.o source/datastructures/treenode.o source/datastructures/qualityscores.o source/datastructures/sparsedistancematrix.o source/datastructures/oligos.o source/datastructures/counttable.o source/datastructures/kmerdb.o source/datastructures/blastdb.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sequence.o source/datastructures/sequencedb.o source/datastructures/rabundvector.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/distancedb.o source/datastructures/sequenceparser.o source/datastructures/fastqread.o source/datastructures/kmer.o source/datastructures/flowdata.o source/datastructures/sparsematrix.o source/datastructures/fullmatrix.o source/datastructures/reportfile.o source/datastructures/sequencecountparser.o source/datastructures/treemap.o source/datastructures/alignmentdb.o source/datastructures/optimatrix.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/randomforest/regularizeddecisiontree.o source/randomforest/rftreenode.o source/randomforest/decisiontree.o source/randomforest/abstractdecisiontree.o source/randomforest/randomforest.o source/randomforest/forest.o source/read/readblast.o source/read/formatcolumn.o source/read/splitmatrix.o source/read/readphylipvector.o source/read/readcolumn.o source/read/readcluster.o source/read/readtree.o source/read/formatphylip.o source/read/treereader.o source/read/readphylip.o source/svm/svm.o -lreadline -lboost_iostreams -lz
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
true
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_installmenu -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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: 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: package could avoid a useless dependency if debian/mothur/usr/bin/mothur debian/mothur/usr/bin/uchime were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mothur/usr/bin/mothur was not linked against libz.so.1 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.40.5-2_armhf.deb'.
dpkg-deb: building package 'mothur' in '../mothur_1.40.5-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../mothur_1.40.5-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build mothur-1.40.5
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-09-16T07:47:40Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
mothur_1.40.5-2_armhf.changes:
------------------------------
Format: 1.8
Date: Fri, 14 Sep 2018 10:29:24 +0200
Source: mothur
Binary: mothur
Architecture: armhf
Version: 1.40.5-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
mothur - sequence analysis suite for research on microbiota
Closes: 908786
Changes:
mothur (1.40.5-2) unstable; urgency=medium
.
* Upstream dropped MPI support since it is slower and requires dual
maintenance (see README.Debian) Thus dropping MPI support from
Debian package
Closes: #908786
* Remove Tim Booth from Uploaders (Tim, thanks for your work on this
package)
* Drop unneeded get-orig-source target
* Standards-Version: 4.2.1
Checksums-Sha1:
f0c0c5951fba257ad9d686e544e51df1a71391f5 127560228 mothur-dbgsym_1.40.5-2_armhf.deb
916780ce7f2a02dcf3081d0b91fcea1b2d2adae3 7159 mothur_1.40.5-2_armhf.buildinfo
6b842cc6f2b2643051b0dbd207eac40f15290ab0 3529380 mothur_1.40.5-2_armhf.deb
Checksums-Sha256:
2410c006ef9226d1b848d22eba9cba4479447c597c0201fbc2f1b6160785c135 127560228 mothur-dbgsym_1.40.5-2_armhf.deb
90f255ecf5e130e745ad97cf45bb00971127f0189b7bfe3405a8023f0f233318 7159 mothur_1.40.5-2_armhf.buildinfo
36fe173c58aa60d10e3da1e0bb88b108546b65067f7cf0ad5c7bcce3abab444d 3529380 mothur_1.40.5-2_armhf.deb
Files:
fdfe3e7a9cc628e80f8c393fbbbad6b3 127560228 debug optional mothur-dbgsym_1.40.5-2_armhf.deb
357f499df48e9d97a2253a7f07f6ab57 7159 science optional mothur_1.40.5-2_armhf.buildinfo
3e51eb7a1b578064122bef5a2cc2b9c5 3529380 science optional mothur_1.40.5-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
mothur-dbgsym_1.40.5-2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 127560228 bytes: control archive=600 bytes.
412 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: mothur-dbgsym
Source: mothur
Version: 1.40.5-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 128940
Depends: mothur (= 1.40.5-2)
Section: debug
Priority: optional
Description: debug symbols for mothur
Build-Ids: 65e48098cf5dd86f8d58d66d01e35731483f68d3 b0e176aebafeb5b6f41c97d11ce40cba6a526e29
drwxr-xr-x root/root 0 2018-09-14 08:29 ./
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/lib/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/lib/debug/.build-id/65/
-rw-r--r-- root/root 130763840 2018-09-14 08:29 ./usr/lib/debug/.build-id/65/e48098cf5dd86f8d58d66d01e35731483f68d3.debug
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/lib/debug/.build-id/b0/
-rw-r--r-- root/root 1257744 2018-09-14 08:29 ./usr/lib/debug/.build-id/b0/e176aebafeb5b6f41c97d11ce40cba6a526e29.debug
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-09-14 08:29 ./usr/share/doc/mothur-dbgsym -> mothur
mothur_1.40.5-2_armhf.deb
-------------------------
new Debian package, version 2.0.
size 3529380 bytes: control archive=1356 bytes.
862 bytes, 18 lines control
762 bytes, 12 lines md5sums
192 bytes, 7 lines * postinst #!/bin/sh
167 bytes, 5 lines * postrm #!/bin/sh
Package: mothur
Version: 1.40.5-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12495
Depends: libboost-iostreams1.62.0, libc6 (>= 2.27), libgcc1 (>= 1:3.5), libreadline7 (>= 6.0), libstdc++6 (>= 6), zlib1g (>= 1:1.1.4)
Conflicts: uchime
Provides: uchime
Section: science
Priority: optional
Homepage: http://www.mothur.org
Description: sequence analysis suite for research on microbiota
Mothur seeks to develop a single piece of open-source, expandable
software to fill the bioinformatics needs of the microbial ecology
community. It has incorporated the functionality of dotur, sons,
treeclimber, s-libshuff, unifrac, and much more. In addition to improving
the flexibility of these algorithms, a number of other features including
calculators and visualization tools were added.
drwxr-xr-x root/root 0 2018-09-14 08:29 ./
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/bin/
-rwxr-xr-x root/root 12577136 2018-09-14 08:29 ./usr/bin/mothur
-rwxr-xr-x root/root 171432 2018-09-14 08:29 ./usr/bin/uchime
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/doc/mothur/
-rw-r--r-- root/root 12687 2018-09-14 08:29 ./usr/share/doc/mothur/HA.fasta.gz
-rw-r--r-- root/root 259 2018-09-14 08:29 ./usr/share/doc/mothur/README.Debian
-rw-r--r-- root/root 178 2018-09-14 08:29 ./usr/share/doc/mothur/README.test
-rw-r--r-- root/root 3523 2018-09-14 08:29 ./usr/share/doc/mothur/changelog.Debian.gz
-rw-r--r-- root/root 4544 2018-09-14 08:29 ./usr/share/doc/mothur/copyright
-rw-r--r-- root/root 280 2018-09-14 08:29 ./usr/share/doc/mothur/run-unit-test
-rw-r--r-- root/root 400 2018-09-14 08:29 ./usr/share/doc/mothur/test.batch
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/man/
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/man/man1/
-rw-r--r-- root/root 566 2018-09-14 08:29 ./usr/share/man/man1/mothur.1.gz
-rw-r--r-- root/root 3393 2018-09-14 08:29 ./usr/share/man/man1/uchime.1.gz
drwxr-xr-x root/root 0 2018-09-14 08:29 ./usr/share/menu/
-rw-r--r-- root/root 176 2018-09-14 08:29 ./usr/share/menu/mothur
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1622960
Build-Time: 1912
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 618
Job: mothur_1.40.5-2
Machine Architecture: armhf
Package: mothur
Package-Time: 2551
Source-Version: 1.40.5-2
Space: 1622960
Status: successful
Version: 1.40.5-2
--------------------------------------------------------------------------------
Finished at 2018-09-16T07:47:40Z
Build needed 00:42:31, 1622960k disk space