=> Building biology/mothur Started : Sunday, 7 JUL 2019 at 04:23:56 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/mothur XDG_CONFIG_HOME=/construction/biology/mothur HOME=/construction/biology/mothur TMPDIR="/tmp" PATH=/construction/biology/mothur/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/mothur XDG_CONFIG_HOME=/construction/biology/mothur HOME=/construction/biology/mothur TMPDIR="/tmp" PATH=/construction/biology/mothur/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-I/usr/local/include -isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/mothur/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/mothur" EXAMPLESDIR="share/examples/mothur" DATADIR="share/mothur" WWWDIR="www/mothur" ETCDIR="etc/mothur" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mothur DOCSDIR=/usr/local/share/doc/mothur EXAMPLESDIR=/usr/local/share/examples/mothur WWWDIR=/usr/local/www/mothur ETCDIR=/usr/local/etc/mothur -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> mothur-1.42.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> mothur-1.42.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mothur-1.42.2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by mothur-1.42.2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by mothur-1.42.2 for building => SHA256 Checksum OK for mothur-mothur-v.1.42.2_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by mothur-1.42.2 for building ===> Extracting for mothur-1.42.2 => SHA256 Checksum OK for mothur-mothur-v.1.42.2_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for mothur-1.42.2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> mothur-1.42.2 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.7.txz Installing bash-5.0.7... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done Extracting bash-5.0.7: .......... done ===> mothur-1.42.2 depends on executable: bash - found ===> Returning to build of mothur-1.42.2 ===> mothur-1.42.2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... Extracting gmake-4.2.1_3: .......... done ===> mothur-1.42.2 depends on executable: gmake - found ===> Returning to build of mothur-1.42.2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> mothur-1.42.2 depends on shared library: libreadline.so.8 - not found ===> Installing existing package /packages/All/readline-8.0.0.txz Installing readline-8.0.0... Extracting readline-8.0.0: .......... done ===> mothur-1.42.2 depends on shared library: libreadline.so.8 - found (/usr/local/lib/libreadline.so.8) ===> Returning to build of mothur-1.42.2 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for mothur-1.42.2 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for mothur-1.42.2 gmake[1]: Entering directory '/construction/biology/mothur/mothur-v.1.42.2' c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/overlap.o source/overlap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/noalign.o source/noalign.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/wilcox.o source/wilcox.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/nastreport.o source/nastreport.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/cluster.o source/cluster.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/libshuff.o source/libshuff.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/fileoutput.o source/fileoutput.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/myseqdist.o source/myseqdist.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commandoptionparser.o source/commandoptionparser.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/utils.o source/utils.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/consensus.o source/consensus.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/raredisplay.o source/raredisplay.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/trialSwap2.o source/trialSwap2.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/slibshuff.o source/slibshuff.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/currentfile.o source/currentfile.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/heatmapsim.o source/heatmapsim.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/dlibshuff.o source/dlibshuff.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/refchimeratest.o source/refchimeratest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/seqnoise.o source/seqnoise.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/singlelinkage.o source/singlelinkage.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clusterclassic.o source/clusterclassic.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calcsparcc.o source/calcsparcc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/inputdata.o source/inputdata.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/linearalgebra.o source/linearalgebra.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/venn.o source/venn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/engine.o source/engine.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/mothur.o source/mothur.cpp source/mothur.cpp: In function 'int main(int, char**)': source/mothur.cpp:194:38: warning: 'char* strncat(char*, const char*, size_t)' specified bound 15 equals source length [-Wstringop-overflow=] *temp = '\0'; strncat(temp, "#help();quit();", 15); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/optionparser.o source/optionparser.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/validcalculator.o source/validcalculator.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/trimoligos.o source/trimoligos.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/collect.o source/collect.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/weightedlinkage.o source/weightedlinkage.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/summary.o source/summary.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/rarefact.o source/rarefact.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/mothurout.o source/mothurout.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/validparameter.o source/validparameter.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commandfactory.o source/commandfactory.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomnumber.o source/randomnumber.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/averagelinkage.o source/averagelinkage.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/completelinkage.o source/completelinkage.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/nast.o source/nast.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/heatmap.o source/heatmap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/subsample.o source/subsample.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/opticluster.o source/opticluster.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/gotohoverlap.o source/gotohoverlap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/sensspeccalc.o source/sensspeccalc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/optifitcluster.o source/optifitcluster.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/npshannon.o source/calculators/npshannon.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/soergel.o source/calculators/soergel.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/speciesprofile.o source/calculators/speciesprofile.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedsorest.o source/calculators/sharedsorest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/uvest.o source/calculators/uvest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/boneh.o source/calculators/boneh.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/unweighted.o source/calculators/unweighted.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/erarefaction.o source/calculators/erarefaction.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedthetan.o source/calculators/sharedthetan.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/memchi2.o source/calculators/memchi2.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/memeuclidean.o source/calculators/memeuclidean.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedrjsd.o source/calculators/sharedrjsd.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedlennon.o source/calculators/sharedlennon.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/fpfn.o source/calculators/fpfn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/ace.o source/calculators/ace.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/heip.o source/calculators/heip.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/structpearson.o source/calculators/structpearson.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/npv.o source/calculators/npv.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/odum.o source/calculators/odum.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/mcc.o source/calculators/mcc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedanderbergs.o source/calculators/sharedanderbergs.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedsorabund.o source/calculators/sharedsorabund.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedjest.o source/calculators/sharedjest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedjsd.o source/calculators/sharedjsd.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/metrosichel.o source/calculators/metrosichel.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/diversityutils.o source/calculators/diversityutils.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/bstick.o source/calculators/bstick.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/igabundance.o source/calculators/igabundance.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/shannonrange.o source/calculators/shannonrange.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedjackknife.o source/calculators/sharedjackknife.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/shannoneven.o source/calculators/shannoneven.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/structchord.o source/calculators/structchord.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/specificity.o source/calculators/specificity.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/gower.o source/calculators/gower.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsobscollectsummary.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/ppv.o source/calculators/ppv.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/efron.o source/calculators/efron.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/whittaker.o source/calculators/whittaker.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/simpsoneven.o source/calculators/simpsoneven.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/chao1.o source/calculators/chao1.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedjabund.o source/calculators/sharedjabund.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/weighted.o source/calculators/weighted.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/fp.o source/calculators/fp.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedchao1.o source/calculators/sharedchao1.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/structeuclidean.o source/calculators/structeuclidean.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/shannon.o source/calculators/shannon.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/prng.o source/calculators/prng.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/tp.o source/calculators/tp.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedsorclass.o source/calculators/sharedsorclass.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedsobs.o source/calculators/sharedsobs.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/metrolognormal.o source/calculators/metrolognormal.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/metrologstudent.o source/calculators/metrologstudent.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/jackknife.o source/calculators/jackknife.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/bootstrap.o source/calculators/bootstrap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/geom.o source/calculators/geom.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/structchi2.o source/calculators/structchi2.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/memchord.o source/calculators/memchord.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/manhattan.o source/calculators/manhattan.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/goodscoverage.o source/calculators/goodscoverage.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/logsd.o source/calculators/logsd.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/mempearson.o source/calculators/mempearson.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/spearman.o source/calculators/spearman.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/hamming.o source/calculators/hamming.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedbraycurtis.o source/calculators/sharedbraycurtis.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/smithwilson.o source/calculators/smithwilson.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/metroig.o source/calculators/metroig.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/parsimony.o source/calculators/parsimony.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/canberra.o source/calculators/canberra.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedjclass.o source/calculators/sharedjclass.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/shen.o source/calculators/shen.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/igrarefaction.o source/calculators/igrarefaction.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/f1score.o source/calculators/f1score.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/bergerparker.o source/calculators/bergerparker.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/qstat.o source/calculators/qstat.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedace.o source/calculators/sharedace.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/lnabundance.o source/calculators/lnabundance.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/tptn.o source/calculators/tptn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedmorisitahorn.o source/calculators/sharedmorisitahorn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/invsimpson.o source/calculators/invsimpson.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/simpson.o source/calculators/simpson.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/coverage.o source/calculators/coverage.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedthetayc.o source/calculators/sharedthetayc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynski.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sensitivity.o source/calculators/sensitivity.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/fn.o source/calculators/fn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/tn.o source/calculators/tn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/fdr.o source/calculators/fdr.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedochiai.o source/calculators/sharedochiai.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/hellinger.o source/calculators/hellinger.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedkstest.o source/calculators/sharedkstest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/solow.o source/calculators/solow.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/structkulczynski.o source/calculators/structkulczynski.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedmarczewski.o source/calculators/sharedmarczewski.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calculators/sharedkulczynskicody.o source/calculators/sharedkulczynskicody.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/decalc.o source/chimera/decalc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/mothurchimera.o source/chimera/mothurchimera.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/chimeracheckrdp.o source/chimera/chimeracheckrdp.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/chimerarealigner.o source/chimera/chimerarealigner.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/ccode.o source/chimera/ccode.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/slayer.o source/chimera/slayer.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/chimeraslayer.o source/chimera/chimeraslayer.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/maligner.o source/chimera/maligner.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/bellerophon.o source/chimera/bellerophon.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/myPerseus.o source/chimera/myPerseus.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/chimera/pintail.o source/chimera/pintail.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/taxonomynode.o source/classifier/taxonomynode.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/bayesian.o source/classifier/bayesian.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/alignnode.o source/classifier/alignnode.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/knn.o source/classifier/knn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/kmertree.o source/classifier/kmertree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/aligntree.o source/classifier/aligntree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/phylotree.o source/classifier/phylotree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/kmernode.o source/classifier/kmernode.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/taxonomyequalizer.o source/classifier/taxonomyequalizer.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/phylosummary.o source/classifier/phylosummary.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/classifier/classify.o source/classifier/classify.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clearcut/clearcut.o source/clearcut/clearcut.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp source/clearcut/distclearcut.cpp: In function 'DMAT* NJ_compute_dmat(NJ_ARGS*, NJ_alignment*)': source/clearcut/distclearcut.cpp:155:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/deconvolutecommand.o source/commands/deconvolutecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getgroupscommand.o source/commands/getgroupscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mergeotuscommand.o source/commands/mergeotuscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getlistcountcommand.o source/commands/getlistcountcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/splitabundcommand.o source/commands/splitabundcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sracommand.o source/commands/sracommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/setdircommand.o source/commands/setdircommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/screenseqscommand.o source/commands/screenseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp source/commands/clearcutcommand.cpp: In member function 'virtual int ClearcutCommand::execute()': source/commands/clearcutcommand.cpp:278:41: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *clearcutParameters[0] = '\0'; strncat(clearcutParameters[0], "clearcut", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:281:111: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] if (phylipfile != "") { clearcutParameters[1] = new char[11]; *clearcutParameters[1] = '\0'; strncat(clearcutParameters[1], "--distance", 10); } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:284:103: warning: 'char* strncat(char*, const char*, size_t)' specified bound 11 equals source length [-Wstringop-overflow=] if (fastafile != "") { clearcutParameters[1] = new char[12]; *clearcutParameters[1] = '\0'; strncat(clearcutParameters[1], "--alignment", 11); } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:287:124: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] if (version) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--version", 9); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:288:124: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] if (verbose) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--verbose", 9); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:289:122: warning: 'char* strncat(char*, const char*, size_t)' specified bound 7 equals source length [-Wstringop-overflow=] if (quiet) { clearcutParameters[parameterCount] = new char[8]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--quiet", 7); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:296:125: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] if (norandom) { clearcutParameters[parameterCount] = new char[11]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--norandom", 10); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:297:124: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] if (shuffle) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--shuffle", 9); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:298:125: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] if (neighbor) { clearcutParameters[parameterCount] = new char[11]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--neighbor", 10); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:305:127: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] if (stdoutWanted) { clearcutParameters[parameterCount] = new char[9]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--stdout", 8); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:314:120: warning: 'char* strncat(char*, const char*, size_t)' specified bound 5 equals source length [-Wstringop-overflow=] if (DNA) { clearcutParameters[parameterCount] = new char[6]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--DNA", 5); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:315:124: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] if (protein) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--protein", 9); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:316:122: warning: 'char* strncat(char*, const char*, size_t)' specified bound 7 equals source length [-Wstringop-overflow=] if (jukes) { clearcutParameters[parameterCount] = new char[8]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--jukes", 7); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:317:122: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] if (kimura) { clearcutParameters[parameterCount] = new char[9]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--kimura", 8); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:334:123: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] if (expblen) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--expblen", 9); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clearcutcommand.cpp:335:123: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] if (expdist) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--expdist", 9); parameterCount++; } ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/parsefastaqcommand.o source/commands/parsefastaqcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getsharedotucommand.o source/commands/getsharedotucommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/removelineagecommand.o source/commands/removelineagecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getrelabundcommand.o source/commands/getrelabundcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/seqerrorcommand.o source/commands/seqerrorcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/removerarecommand.o source/commands/removerarecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -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:569:72: warning: 'char* strncat(char*, const char*, size_t)' specified bound 15 equals source length [-Wstringop-overflow=] char* maxaccepts = new char[16]; maxaccepts[0] = '\0'; strncat(maxaccepts, "--maxaccepts=16", 15); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustercommand.cpp:578:68: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] char* usersort = new char[11]; usersort[0] = '\0'; strncat(usersort, "--usersort", 10); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustercommand.cpp:591:76: warning: 'char* strncat(char*, const char*, size_t)' specified bound 17 equals source length [-Wstringop-overflow=] char* minseqlength = new char[18]; minseqlength[0] = '\0'; strncat(minseqlength, "--minseqlength=30", 17); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustercommand.cpp:595:72: warning: 'char* strncat(char*, const char*, size_t)' specified bound 14 equals source length [-Wstringop-overflow=] char* wordlength = new char[15]; wordlength[0] = '\0'; strncat(wordlength, "--wordlength=8", 14); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustercommand.cpp:609:72: warning: 'char* strncat(char*, const char*, size_t)' specified bound 15 equals source length [-Wstringop-overflow=] char* maxrejects = new char[16]; maxrejects[0] = '\0'; strncat(maxrejects, "--maxrejects=64", 15); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustercommand.cpp:613:64: warning: 'char* strncat(char*, const char*, size_t)' specified bound 13 equals source length [-Wstringop-overflow=] char* strand = new char[14]; strand[0] = '\0'; strncat(strand, "--strand=both", 13); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustercommand.cpp:623:74: warning: 'char* strncat(char*, const char*, size_t)' specified bound 11 equals source length [-Wstringop-overflow=] char* sizeorder = new char[12]; sizeorder[0] = '\0'; strncat(sizeorder, "--sizeorder", 11); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/heatmapsimcommand.o source/commands/heatmapsimcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/listseqscommand.o source/commands/listseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/normalizesharedcommand.o source/commands/normalizesharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/parselistscommand.o source/commands/parselistscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sffmultiplecommand.o source/commands/sffmultiplecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mimarksattributescommand.o source/commands/mimarksattributescommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/unifracweightedcommand.o source/commands/unifracweightedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getdistscommand.o source/commands/getdistscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/renameseqscommand.o source/commands/renameseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/venncommand.o source/commands/venncommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/removeseqscommand.o source/commands/removeseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getotulabelscommand.o source/commands/getotulabelscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/quitcommand.o source/commands/quitcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/kruskalwalliscommand.o source/commands/kruskalwalliscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/treegroupscommand.o source/commands/treegroupscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/seqsummarycommand.o source/commands/seqsummarycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mgclustercommand.o source/commands/mgclustercommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/indicatorcommand.o source/commands/indicatorcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/removegroupscommand.o source/commands/removegroupscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/matrixoutputcommand.o source/commands/matrixoutputcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/classifyrfsharedcommand.o source/commands/classifyrfsharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sensspeccommand.o source/commands/sensspeccommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mergetaxsummarycommand.o source/commands/mergetaxsummarycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/heatmapcommand.o source/commands/heatmapcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/collectcommand.o source/commands/collectcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/setlogfilecommand.o source/commands/setlogfilecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getsabundcommand.o source/commands/getsabundcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/reversecommand.o source/commands/reversecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/newcommandtemplate.o source/commands/newcommandtemplate.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/rarefactsharedcommand.o source/commands/rarefactsharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sparcccommand.o source/commands/sparcccommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/nocommands.o source/commands/nocommands.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getoturepcommand.o source/commands/getoturepcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mergegroupscommand.o source/commands/mergegroupscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double, clusterData*)': source/commands/clustersplitcommand.cpp:1158:72: warning: 'char* strncat(char*, const char*, size_t)' specified bound 15 equals source length [-Wstringop-overflow=] char* maxaccepts = new char[16]; maxaccepts[0] = '\0'; strncat(maxaccepts, "--maxaccepts=16", 15); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1162:66: warning: 'char* strncat(char*, const char*, size_t)' specified bound 11 equals source length [-Wstringop-overflow=] char* threads = new char[12]; threads[0] = '\0'; strncat(threads, "--threads=1", 11); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1166:68: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] char* usersort = new char[11]; usersort[0] = '\0'; strncat(usersort, "--usersort", 10); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1179:76: warning: 'char* strncat(char*, const char*, size_t)' specified bound 17 equals source length [-Wstringop-overflow=] char* minseqlength = new char[18]; minseqlength[0] = '\0'; strncat(minseqlength, "--minseqlength=30", 17); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1183:72: warning: 'char* strncat(char*, const char*, size_t)' specified bound 14 equals source length [-Wstringop-overflow=] char* wordlength = new char[15]; wordlength[0] = '\0'; strncat(wordlength, "--wordlength=8", 14); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1197:72: warning: 'char* strncat(char*, const char*, size_t)' specified bound 15 equals source length [-Wstringop-overflow=] char* maxrejects = new char[16]; maxrejects[0] = '\0'; strncat(maxrejects, "--maxrejects=64", 15); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1201:64: warning: 'char* strncat(char*, const char*, size_t)' specified bound 13 equals source length [-Wstringop-overflow=] char* strand = new char[14]; strand[0] = '\0'; strncat(strand, "--strand=both", 13); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/clustersplitcommand.cpp:1211:74: warning: 'char* strncat(char*, const char*, size_t)' specified bound 11 equals source length [-Wstringop-overflow=] char* sizeorder = new char[12]; sizeorder[0] = '\0'; strncat(sizeorder, "--sizeorder", 11); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/libshuffcommand.o source/commands/libshuffcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimerauchimecommand.o source/commands/chimerauchimecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:438:37: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempRef = '\0'; strncat(tempRef, "--db", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:447:32: warning: 'char* strncat(char*, const char*, size_t)' specified bound 7 equals source length [-Wstringop-overflow=] *tempIn = '\0'; strncat(tempIn, "--input", 7); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:456:31: warning: 'char* strncat(char*, const char*, size_t)' specified bound 11 equals source length [-Wstringop-overflow=] *tempO = '\0'; strncat(tempO, "--uchimeout", 11); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:466:35: warning: 'char* strncat(char*, const char*, size_t)' specified bound 12 equals source length [-Wstringop-overflow=] *tempA = '\0'; strncat(tempA, "--uchimealns", 12); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:477:35: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempA = '\0'; strncat(tempA, "--strand", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:486:38: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempskew = '\0'; strncat(tempskew, "--abskew", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:497:38: warning: 'char* strncat(char*, const char*, size_t)' specified bound 6 equals source length [-Wstringop-overflow=] *tempminh = '\0'; strncat(tempminh, "--minh", 6); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:508:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempmindiv = '\0'; strncat(tempmindiv, "--mindiv", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:520:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempxn = '\0'; strncat(tempxn, "--xn", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:531:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempdn = '\0'; strncat(tempdn, "--dn", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:542:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempxa = '\0'; strncat(tempxa, "--xa", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:553:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempchunks = '\0'; strncat(tempchunks, "--chunks", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:564:42: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] *tempminchunk = '\0'; strncat(tempminchunk, "--minchunk", 10); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:574:48: warning: 'char* strncat(char*, const char*, size_t)' specified bound 16 equals source length [-Wstringop-overflow=] *tempidsmoothwindow = '\0'; strncat(tempidsmoothwindow, "--idsmoothwindow", 16); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:586:38: warning: 'char* strncat(char*, const char*, size_t)' specified bound 6 equals source length [-Wstringop-overflow=] *tempmaxp = '\0'; strncat(tempmaxp, "--maxp", 6); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:597:42: warning: 'char* strncat(char*, const char*, size_t)' specified bound 12 equals source length [-Wstringop-overflow=] *tempskipgaps = '\0'; strncat(tempskipgaps, "--noskipgaps", 12); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:604:43: warning: 'char* strncat(char*, const char*, size_t)' specified bound 13 equals source length [-Wstringop-overflow=] *tempskipgaps2 = '\0'; strncat(tempskipgaps2, "--noskipgaps2", 13); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:610:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempminlen = '\0'; strncat(tempminlen, "--minlen", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:622:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempmaxlen = '\0'; strncat(tempmaxlen, "--maxlen", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimerauchimecommand.cpp:638:44: warning: 'char* strncat(char*, const char*, size_t)' specified bound 12 equals source length [-Wstringop-overflow=] *tempqueryfract = '\0'; strncat(tempqueryfract, "--queryfract", 12); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/renamefilecommand.o source/commands/renamefilecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/homovacommand.o source/commands/homovacommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/removedistscommand.o source/commands/removedistscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sortseqscommand.o source/commands/sortseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/anosimcommand.o source/commands/anosimcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/helpcommand.o source/commands/helpcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getgroupcommand.o source/commands/getgroupcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/shhhseqscommand.o source/commands/shhhseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mergefilecommand.o source/commands/mergefilecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sharedcommand.o source/commands/sharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/setseedcommand.o source/commands/setseedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getmetacommunitycommand.o source/commands/getmetacommunitycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/setcurrentcommand.o source/commands/setcurrentcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getmimarkspackagecommand.o source/commands/getmimarkspackagecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/deuniqueseqscommand.o source/commands/deuniqueseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getseqscommand.o source/commands/getseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getlabelcommand.o source/commands/getlabelcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makebiomcommand.o source/commands/makebiomcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/sffinfocommand.o source/commands/sffinfocommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getrabundcommand.o source/commands/getrabundcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/metastatscommand.o source/commands/metastatscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/secondarystructurecommand.o source/commands/secondarystructurecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/mergesfffilecommand.o source/commands/mergesfffilecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/shhhercommand.o source/commands/shhhercommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/removeotulabelscommand.o source/commands/removeotulabelscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/lefsecommand.o source/commands/lefsecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/listotulabelscommand.o source/commands/listotulabelscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getcommandinfocommand.o source/commands/getcommandinfocommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.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:1009:37: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempRef = '\0'; strncat(tempRef, "--db", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1017:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 12 equals source length [-Wstringop-overflow=] *tempIn = '\0'; strncat(tempIn, "--uchime_ref", 12); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1025:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 15 equals source length [-Wstringop-overflow=] *tempIn = '\0'; strncat(tempIn, "--uchime_denovo", 15); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1034:31: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] *tempO = '\0'; strncat(tempO, "--chimeras", 10); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1041:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 11 equals source length [-Wstringop-overflow=] *tempchimeraout = '\0'; strncat(tempchimeraout, "--uchimeout", 11); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1048:35: warning: 'char* strncat(char*, const char*, size_t)' specified bound 7 equals source length [-Wstringop-overflow=] *tempxsize = '\0'; strncat(tempxsize, "--xsize", 7); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1053:35: warning: 'char* strncat(char*, const char*, size_t)' specified bound 12 equals source length [-Wstringop-overflow=] *tempA = '\0'; strncat(tempA, "--uchimealns", 12); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1065:38: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempskew = '\0'; strncat(tempskew, "--abskew", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1076:38: warning: 'char* strncat(char*, const char*, size_t)' specified bound 6 equals source length [-Wstringop-overflow=] *tempminh = '\0'; strncat(tempminh, "--minh", 6); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1087:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 8 equals source length [-Wstringop-overflow=] *tempmindiv = '\0'; strncat(tempmindiv, "--mindiv", 8); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1098:40: warning: 'char* strncat(char*, const char*, size_t)' specified bound 10 equals source length [-Wstringop-overflow=] *tempmindiv = '\0'; strncat(tempmindiv, "--mindiffs", 10); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1108:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempxn = '\0'; strncat(tempxn, "--xn", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1119:36: warning: 'char* strncat(char*, const char*, size_t)' specified bound 4 equals source length [-Wstringop-overflow=] *tempdn = '\0'; strncat(tempdn, "--dn", 4); ~~~~~~~^~~~~~~~~~~~~~~~~~~ source/commands/chimeravsearchcommand.cpp:1128:66: warning: 'char* strncat(char*, const char*, size_t)' specified bound 9 equals source length [-Wstringop-overflow=] char* threads = new char[10]; threads[0] = '\0'; strncat(threads, "--threads", 9); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/nmdscommand.o source/commands/nmdscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/getlineagecommand.o source/commands/getlineagecommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/rarefactcommand.o source/commands/rarefactcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commands/makecontigscommand.o source/commands/makecontigscommand.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/communitytype/qFinderDMM.o source/communitytype/qFinderDMM.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/communitytype/kmeans.o source/communitytype/kmeans.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/communitytype/pam.o source/communitytype/pam.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/communitytype/communitytype.o source/communitytype/communitytype.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundfloatvectors.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/alignmentcell.o source/datastructures/alignmentcell.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/designmap.o source/datastructures/designmap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/blastdb.o source/datastructures/blastdb.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/fullmatrix.o source/datastructures/fullmatrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/alignment.o source/datastructures/alignment.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/reportfile.o source/datastructures/reportfile.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/tree.o source/datastructures/tree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp source/datastructures/tree.cpp: In member function 'int Tree::pruneNewTree(Tree*, std::vector >)': source/datastructures/tree.cpp:481:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/kmer.o source/datastructures/kmer.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/groupmap.o source/datastructures/groupmap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/distancedb.o source/datastructures/distancedb.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/kmeralign.o source/datastructures/kmeralign.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/alignmentdb.o source/datastructures/alignmentdb.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/fastamap.o source/datastructures/fastamap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/counttable.o source/datastructures/counttable.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp source/datastructures/counttable.cpp: In member function 'int CountTable::printGroupAbunds(std::ofstream&, int)': source/datastructures/counttable.cpp:1065:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optirefmatrix.o source/datastructures/optirefmatrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/flowdata.o source/datastructures/flowdata.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optidata.o source/datastructures/optidata.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/filefile.o source/datastructures/filefile.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/blastalign.o source/datastructures/blastalign.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/fastqread.o source/datastructures/fastqread.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/forest.o source/randomforest/forest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/randomforest.o source/randomforest/randomforest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/abstractdecisiontree.o source/randomforest/abstractdecisiontree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/decisiontree.o source/randomforest/decisiontree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/rftreenode.o source/randomforest/rftreenode.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/randomforest/regularizeddecisiontree.o source/randomforest/regularizeddecisiontree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readphylip.o source/read/readphylip.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/formatphylip.o source/read/formatphylip.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readtree.o source/read/readtree.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/treereader.o source/read/treereader.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readcluster.o source/read/readcluster.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readcolumn.o source/read/readcolumn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/formatcolumn.o source/read/formatcolumn.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readblast.o source/read/readblast.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.42.2\"" -DUSE_READLINE -I. -I source/ -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/metastats/ -I source/randomforest/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/svm/svm.o source/svm/svm.cpp cd source/uchime_src && ./mk && mv uchime ../../ && cd .. addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit -rwxr-xr-x 1 root wheel 447K Jul 8 04:38 uchime 52190 448 uchime c++ -L/usr/local/lib -std=c++11 -pthread -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/overlap.o source/noalign.o source/libshuff.o source/commandoptionparser.o source/raredisplay.o source/summary.o source/currentfile.o source/heatmapsim.o source/dlibshuff.o source/engine.o source/mothur.o source/optionparser.o source/validcalculator.o source/trimoligos.o source/linearalgebra.o source/weightedlinkage.o source/rarefact.o source/commandfactory.o source/subsample.o source/sensspeccalc.o source/myseqdist.o source/optifitcluster.o source/needlemanoverlap.o source/wilcox.o source/nastreport.o source/refchimeratest.o source/cluster.o source/fileoutput.o source/trialSwap2.o source/collect.o source/slibshuff.o source/utils.o source/singlelinkage.o source/vsearchfileparser.o source/clusterclassic.o source/inputdata.o source/venn.o source/seqnoise.o source/completelinkage.o source/mothurout.o source/randomnumber.o source/averagelinkage.o source/nast.o source/heatmap.o source/opticluster.o source/validparameter.o source/gotohoverlap.o source/calcsparcc.o source/consensus.o source/calculators/soergel.o source/calculators/structchi2.o source/calculators/structpearson.o source/calculators/sharedmarczewski.o source/calculators/sharedsobscollectsummary.o source/calculators/sharedjest.o source/calculators/erarefaction.o source/calculators/logsd.o source/calculators/bstick.o source/calculators/shannoneven.o source/calculators/spearman.o source/calculators/structkulczynski.o source/calculators/memchi2.o source/calculators/qstat.o source/calculators/sharedchao1.o source/calculators/specificity.o source/calculators/sharedsorclass.o source/calculators/sharedsobs.o source/calculators/whittaker.o source/calculators/manhattan.o source/calculators/mempearson.o source/calculators/simpson.o source/calculators/smithwilson.o source/calculators/igrarefaction.o source/calculators/sharedjackknife.o source/calculators/sharedace.o source/calculators/tptn.o source/calculators/coverage.o source/calculators/sharedthetayc.o source/calculators/accuracy.o source/calculators/boneh.o source/calculators/unweighted.o source/calculators/mcc.o source/calculators/hellinger.o source/calculators/metrosichel.o source/calculators/igabundance.o source/calculators/gower.o source/calculators/shen.o source/calculators/bergerparker.o source/calculators/tp.o source/calculators/invsimpson.o source/calculators/sharedrjsd.o source/calculators/efron.o source/calculators/jackknife.o source/calculators/sharedkulczynskicody.o source/calculators/hamming.o source/calculators/canberra.o source/calculators/sharedochiai.o source/calculators/sensitivity.o source/calculators/tn.o source/calculators/speciesprofile.o source/calculators/sharedsorest.o source/calculators/sharedjabund.o source/calculators/memeuclidean.o source/calculators/sharedlennon.o source/calculators/ace.o source/calculators/heip.o source/calculators/odum.o source/calculators/sharedanderbergs.o source/calculators/solow.o source/calculators/simpsoneven.o source/calculators/weighted.o source/calculators/structeuclidean.o source/calculators/npshannon.o source/calculators/shannon.o source/calculators/metrolognormal.o source/calculators/fdr.o source/calculators/parsimony.o source/calculators/fn.o source/calculators/geom.o source/calculators/sharedkulczynski.o source/calculators/metroig.o source/calculators/sharedbraycurtis.o source/calculators/sharedsorabund.o source/calculators/sharedthetan.o source/calculators/uvest.o source/calculators/sharedjsd.o source/calculators/fp.o source/calculators/npv.o source/calculators/ppv.o source/calculators/goodscoverage.o source/calculators/fpfn.o source/calculators/diversityutils.o source/calculators/sharedmorisitahorn.o source/calculators/structchord.o source/calculators/lnabundance.o source/calculators/sharedjclass.o source/calculators/chao1.o source/calculators/shannonrange.o source/calculators/prng.o source/calculators/metrologstudent.o source/calculators/memchord.o source/calculators/bootstrap.o source/calculators/f1score.o source/calculators/sharedkstest.o source/chimera/decalc.o source/chimera/mothurchimera.o source/chimera/chimeracheckrdp.o source/chimera/chimerarealigner.o source/chimera/ccode.o source/chimera/slayer.o source/chimera/chimeraslayer.o source/chimera/maligner.o source/chimera/bellerophon.o source/chimera/myPerseus.o source/chimera/pintail.o source/classifier/taxonomynode.o source/classifier/bayesian.o source/classifier/alignnode.o source/classifier/knn.o source/classifier/kmertree.o source/classifier/aligntree.o source/classifier/phylotree.o source/classifier/kmernode.o source/classifier/taxonomyequalizer.o source/classifier/phylosummary.o source/classifier/classify.o source/clearcut/dmat.o source/clearcut/fasta.o source/clearcut/clearcut.o source/clearcut/getopt_long.o source/clearcut/cmdargs.o source/clearcut/distclearcut.o source/commands/mantelcommand.o source/commands/deconvolutecommand.o source/commands/getgroupscommand.o source/commands/mergeotuscommand.o source/commands/getlistcountcommand.o source/commands/primerdesigncommand.o source/commands/splitabundcommand.o source/commands/chimerapintailcommand.o source/commands/trimseqscommand.o source/commands/sracommand.o source/commands/parsimonycommand.o source/commands/setdircommand.o source/commands/screenseqscommand.o source/commands/clearcutcommand.o source/commands/countgroupscommand.o source/commands/parsefastaqcommand.o source/commands/getsharedotucommand.o source/commands/chimerabellerophoncommand.o source/commands/chimeraccodecommand.o source/commands/removelineagecommand.o source/commands/getrelabundcommand.o source/commands/otuhierarchycommand.o source/commands/seqerrorcommand.o source/commands/systemcommand.o source/commands/unifracunweightedcommand.o source/commands/summarytaxcommand.o source/commands/removerarecommand.o source/commands/degapseqscommand.o source/commands/clustercommand.o source/commands/heatmapsimcommand.o source/commands/listseqscommand.o source/commands/normalizesharedcommand.o source/commands/parselistscommand.o source/commands/sffmultiplecommand.o source/commands/splitgroupscommand.o source/commands/mimarksattributescommand.o source/commands/unifracweightedcommand.o source/commands/summaryqualcommand.o source/commands/getdistscommand.o source/commands/makefilecommand.o source/commands/classifyseqscommand.o source/commands/getcoremicrobiomecommand.o source/commands/makegroupcommand.o source/commands/renameseqscommand.o source/commands/venncommand.o source/commands/removeseqscommand.o source/commands/getotulabelscommand.o source/commands/quitcommand.o source/commands/kruskalwalliscommand.o source/commands/treegroupscommand.o source/commands/clusterfragmentscommand.o source/commands/seqsummarycommand.o source/commands/mgclustercommand.o source/commands/indicatorcommand.o source/commands/removegroupscommand.o source/commands/subsamplecommand.o source/commands/matrixoutputcommand.o source/commands/classifyrfsharedcommand.o source/commands/sensspeccommand.o source/commands/mergetaxsummarycommand.o source/commands/heatmapcommand.o source/commands/clusterdoturcommand.o source/commands/diversityestimatorcommand.o source/commands/distancecommand.o source/commands/collectcommand.o source/commands/setlogfilecommand.o source/commands/getsabundcommand.o source/commands/reversecommand.o source/commands/summarycommand.o source/commands/newcommandtemplate.o source/commands/rarefactsharedcommand.o source/commands/phylotypecommand.o source/commands/sparcccommand.o source/commands/nocommands.o source/commands/getoturepcommand.o source/commands/mergecountcommand.o source/commands/mergegroupscommand.o source/commands/pairwiseseqscommand.o source/commands/clustersplitcommand.o source/commands/chimeracheckcommand.o source/commands/libshuffcommand.o source/commands/chimerauchimecommand.o source/commands/countseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/filterseqscommand.o source/commands/classifyotucommand.o source/commands/renamefilecommand.o source/commands/amovacommand.o source/commands/homovacommand.o source/commands/removedistscommand.o source/commands/otuassociationcommand.o source/commands/sortseqscommand.o source/commands/createdatabasecommand.o source/commands/trimflowscommand.o source/commands/binsequencecommand.o source/commands/deuniquetreecommand.o source/commands/chimeraperseuscommand.o source/commands/anosimcommand.o source/commands/pcrseqscommand.o source/commands/helpcommand.o source/commands/makefastqcommand.o source/commands/getgroupcommand.o source/commands/biominfocommand.o source/commands/pcoacommand.o source/commands/shhhseqscommand.o source/commands/mergefilecommand.o source/commands/sharedcommand.o source/commands/getcurrentcommand.o source/commands/setseedcommand.o source/commands/getmetacommunitycommand.o source/commands/setcurrentcommand.o source/commands/getmimarkspackagecommand.o source/commands/deuniqueseqscommand.o source/commands/collectsharedcommand.o source/commands/getseqscommand.o source/commands/clusterfitcommand.o source/commands/classifytreecommand.o source/commands/preclustercommand.o source/commands/cooccurrencecommand.o source/commands/corraxescommand.o source/commands/consensusseqscommand.o source/commands/getlabelcommand.o source/commands/aligncommand.o source/commands/makebiomcommand.o source/commands/sffinfocommand.o source/commands/chopseqscommand.o source/commands/chimeraslayercommand.o source/commands/getrabundcommand.o source/commands/metastatscommand.o source/commands/pcacommand.o source/commands/secondarystructurecommand.o source/commands/mergesfffilecommand.o source/commands/shhhercommand.o source/commands/filtersharedcommand.o source/commands/makelefsecommand.o source/commands/phylodiversitycommand.o source/commands/removeotulabelscommand.o source/commands/lefsecommand.o source/commands/listotulabelscommand.o source/commands/getcommandinfocommand.o source/commands/chimeravsearchcommand.o source/commands/nmdscommand.o source/commands/getlineagecommand.o source/commands/summarysharedcommand.o source/commands/rarefactcommand.o source/commands/makelookupcommand.o source/commands/makecontigscommand.o source/communitytype/qFinderDMM.o source/communitytype/kmeans.o source/communitytype/pam.o source/communitytype/communitytype.o source/datastructures/optidata.o source/datastructures/alignmentdb.o source/datastructures/treemap.o source/datastructures/sequencecountparser.o source/datastructures/listvector.o source/datastructures/reportfile.o source/datastructures/sequenceparser.o source/datastructures/optiblastmatrix.o source/datastructures/optirefmatrix.o source/datastructures/suffixtree.o source/datastructures/alignment.o source/datastructures/fullmatrix.o source/datastructures/sparsematrix.o source/datastructures/flowdata.o source/datastructures/kmer.o source/datastructures/suffixdb.o source/datastructures/fastqread.o source/datastructures/sharedordervector.o source/datastructures/distancedb.o source/datastructures/filefile.o source/datastructures/sabundvector.o source/datastructures/sharedlistvector.o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundvectors.o source/datastructures/designmap.o source/datastructures/sequencedb.o source/datastructures/sequence.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundvector.o source/datastructures/blastdb.o source/datastructures/kmerdb.o source/datastructures/counttable.o source/datastructures/oligos.o source/datastructures/sparsedistancematrix.o source/datastructures/groupmap.o source/datastructures/qualityscores.o source/datastructures/rabundfloatvector.o source/datastructures/rabundvector.o source/datastructures/treenode.o source/datastructures/blastalign.o source/datastructures/kmeralign.o source/datastructures/tree.o source/datastructures/suffixnodes.o source/datastructures/nameassignment.o source/datastructures/alignmentcell.o source/datastructures/fastamap.o source/datastructures/optimatrix.o source/datastructures/ordervector.o source/metastats/mothurmetastats.o source/metastats/mothurfisher.o source/randomforest/forest.o source/randomforest/randomforest.o source/randomforest/abstractdecisiontree.o source/randomforest/decisiontree.o source/randomforest/rftreenode.o source/randomforest/regularizeddecisiontree.o source/read/readphylip.o source/read/formatphylip.o source/read/readtree.o source/read/treereader.o source/read/readcluster.o source/read/readcolumn.o source/read/readphylipvector.o source/read/splitmatrix.o source/read/formatcolumn.o source/read/readblast.o source/svm/svm.o -L/usr/local/lib -lreadline gmake[1]: Leaving directory '/construction/biology/mothur/mothur-v.1.42.2' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for mothur-1.42.2 ===> Generating temporary packing list install -s -m 555 /construction/biology/mothur/mothur-v.1.42.2/mothur /construction/biology/mothur/stage/usr/local/bin install -s -m 555 /construction/biology/mothur/mothur-v.1.42.2/uchime /construction/biology/mothur/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for mothur-1.42.2 file sizes/checksums [5]: . done packing files [5]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:38:40 UTC Duration: 00:14:43