[package - main-armv6-default][biology/mothur] Failed for mothur-1.46.1 in build
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Date: Mon, 13 Sep 2021 06:28:33 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: http://beefy8.nyi.freebsd.org/data/main-armv6-default/p37fb990074a9_s98168a6e6c/logs/mothur-1.46.1.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=p37fb990074a9_s98168a6e6c
Log:
=>> Building biology/mothur
build started at Mon Sep 13 05:44:40 UTC 2021
port directory: /usr/ports/biology/mothur
package name: mothur-1.46.1
building for: FreeBSD main-armv6-default-job-02 14.0-CURRENT FreeBSD 14.0-CURRENT 1400032 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
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Host OSVERSION: 1300121
Jail OSVERSION: 1400032
Job Id: 02
!!! Jail is newer than host. (Jail: 1400032, Host: 1300121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> mothur-1.46.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.1.pkg
[main-armv6-default-job-02] Installing pkg-1.17.1...
[main-armv6-default-job-02] Extracting pkg-1.17.1: .......... done
===> mothur-1.46.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mothur-1.46.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
=> mothur-mothur-v1.46.1_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/mothur/mothur/tar.gz/v1.46.1?dummy=/mothur-mothur-v1.46.1_GH0.tar.gz
fetch: https://codeload.github.com/mothur/mothur/tar.gz/v1.46.1?dummy=/mothur-mothur-v1.46.1_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/mothur/mothur/tar.gz/v1.46.1?dummy=/mothur-mothur-v1.46.1_GH0.tar.gz: size of remote file is not known
mothur-mothur-v1.46.1_GH0.tar.gz 1599 kB 5740 kBps 01s
<snip>
/******************************************************************************************************************/
^
1 warning generated.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/biom.o source/datastructures/biom.cpp
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/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/kmerdb.o source/datastructures/kmerdb.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/listvector.o source/datastructures/listvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/nameassignment.o source/datastructures/nameassignment.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/oligos.o source/datastructures/oligos.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optiblastmatrix.o source/datastructures/optiblastmatrix.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optidata.o source/datastructures/optidata.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optidb.o source/datastructures/optidb.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optimatrix.o source/datastructures/optimatrix.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/optirefmatrix.o source/datastructures/optirefmatrix.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/ordervector.o source/datastructures/ordervector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/picrust.o source/datastructures/picrust.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/protein.o source/datastructures/protein.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/proteindb.o source/datastructures/proteindb.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/qualityscores.o source/datastructures/qualityscores.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/rabundfloatvector.o source/datastructures/rabundfloatvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/rabundvector.o source/datastructures/rabundvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/report.o source/datastructures/report.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sabundvector.o source/datastructures/sabundvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequence.o source/datastructures/sequence.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequencecountparser.o source/datastructures/sequencecountparser.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequencedb.o source/datastructures/sequencedb.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sequenceparser.o source/datastructures/sequenceparser.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sffheader.o source/datastructures/sffheader.cpp
In file included from source/datastructures/sffheader.cpp:9:
source/datastructures/sffheader.hpp:22:2: warning: '/*' within block comment [-Wcomment]
/*
^
1 warning generated.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sffread.o source/datastructures/sffread.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedclrvector.o source/datastructures/sharedclrvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedclrvectors.o source/datastructures/sharedclrvectors.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedlistvector.o source/datastructures/sharedlistvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedordervector.o source/datastructures/sharedordervector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundfloatvectors.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sharedrabundvectors.o source/datastructures/sharedrabundvectors.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sparsedistancematrix.o source/datastructures/sparsedistancematrix.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/sparsematrix.o source/datastructures/sparsematrix.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixdb.o source/datastructures/suffixdb.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixnodes.o source/datastructures/suffixnodes.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/suffixtree.o source/datastructures/suffixtree.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/taxonomy.o source/datastructures/taxonomy.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/tree.o source/datastructures/tree.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/treemap.o source/datastructures/treemap.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/datastructures/treenode.o source/datastructures/treenode.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/engines/batchengine.o source/engines/batchengine.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/engines/interactengine.o source/engines/interactengine.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/engines/scriptengine.o source/engines/scriptengine.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/metastats/mothurfisher.o source/metastats/mothurfisher.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/metastats/mothurmetastats.o source/metastats/mothurmetastats.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readblast.o source/read/readblast.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readcluster.o source/read/readcluster.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readcolumn.o source/read/readcolumn.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readphylip.o source/read/readphylip.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readphylipvector.o source/read/readphylipvector.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/readtree.o source/read/readtree.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/splitmatrix.o source/read/splitmatrix.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/read/treereader.o source/read/treereader.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/svm/svm.o source/svm/svm.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/alignreport.o source/alignreport.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/averagelinkage.o source/averagelinkage.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/calcsparcc.o source/calcsparcc.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/cluster.o source/cluster.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/clusterclassic.o source/clusterclassic.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/collect.o source/collect.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commandfactory.o source/commandfactory.cpp
In file included from source/commandfactory.cpp:77:
In file included from source/commands/sffinfocommand.h:18:
source/datastructures/sffheader.hpp:22:2: warning: '/*' within block comment [-Wcomment]
/*
^
1 warning generated.
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/commandoptionparser.o source/commandoptionparser.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/completelinkage.o source/completelinkage.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/consensus.o source/consensus.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/currentfile.o source/currentfile.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/dlibshuff.o source/dlibshuff.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/fileoutput.o source/fileoutput.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/gotohoverlap.o source/gotohoverlap.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/heatmap.o source/heatmap.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/heatmapsim.o source/heatmapsim.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/inputdata.o source/inputdata.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/libshuff.o source/libshuff.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/linearalgebra.o source/linearalgebra.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/mothur.o source/mothur.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/mothurout.o source/mothurout.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/myseqdist.o source/myseqdist.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/nast.o source/nast.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/needlemanoverlap.o source/needlemanoverlap.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/noalign.o source/noalign.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/opticluster.o source/opticluster.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/optifitcluster.o source/optifitcluster.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/optionparser.o source/optionparser.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/overlap.o source/overlap.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/raredisplay.o source/raredisplay.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/rarefact.o source/rarefact.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/refchimeratest.o source/refchimeratest.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/sensspeccalc.o source/sensspeccalc.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/seqnoise.o source/seqnoise.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/singlelinkage.o source/singlelinkage.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/slibshuff.o source/slibshuff.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/subsample.o source/subsample.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/summary.o source/summary.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/trialSwap2.o source/trialSwap2.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/trimoligos.o source/trimoligos.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/utils.o source/utils.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/validcalculator.o source/validcalculator.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/validparameter.o source/validparameter.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/venn.o source/venn.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/weightedlinkage.o source/weightedlinkage.cpp
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -I/usr/local/include -isystem /usr/local/include -c -o source/wilcox.o source/wilcox.cpp
cd source/uchime_src && export CXX=/nxb-bin/usr/bin/c++ && gmake clean && gmake && mv uchime ../../ && cd ..
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.46.1/source/uchime_src'
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.46.1/source/uchime_src'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.46.1/source/uchime_src'
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o addtargets2.o addtargets2.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o alignchime.o alignchime.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o alignchimel.o alignchimel.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o alnparams.o alnparams.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o alpha.o alpha.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o alpha2.o alpha2.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o fractid.o fractid.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o getparents.o getparents.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o globalalign2.o globalalign2.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o make3way.o make3way.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o mx.o mx.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o myutils.o myutils.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o path.o path.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o searchchime.o searchchime.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o seqdb.o seqdb.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o setnucmx.o setnucmx.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o sfasta.o sfasta.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o tracebackbit.o tracebackbit.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o uchime_main.o uchime_main.cpp
uchime_main.cpp:186:19: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
AlnParams &AP = *(AlnParams *) 0;
^~~~~~~~~~~~~~~~
uchime_main.cpp:187:23: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
AlnHeuristics &AH = *(AlnHeuristics *) 0;
^~~~~~~~~~~~~~~~~~~~
uchime_main.cpp:188:19: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference]
HSPFinder &HF = *(HSPFinder *) 0;
^~~~~~~~~~~~~~~~
3 warnings generated.
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o usort.o usort.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o viterbifast.o viterbifast.cpp
/nxb-bin/usr/bin/c++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -I/usr/local/include -isystem /usr/local/include -c -o writechhit.o writechhit.cpp
/nxb-bin/usr/bin/c++ -g -o uchime addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o -L/usr/local/lib -lreadline
ld: error: addtargets2.o is incompatible with /usr/lib/crt1.o
ld: error: alignchime.o is incompatible with /usr/lib/crt1.o
ld: error: alignchimel.o is incompatible with /usr/lib/crt1.o
ld: error: alnparams.o is incompatible with /usr/lib/crt1.o
ld: error: alpha.o is incompatible with /usr/lib/crt1.o
ld: error: alpha2.o is incompatible with /usr/lib/crt1.o
ld: error: fractid.o is incompatible with /usr/lib/crt1.o
ld: error: getparents.o is incompatible with /usr/lib/crt1.o
ld: error: globalalign2.o is incompatible with /usr/lib/crt1.o
ld: error: make3way.o is incompatible with /usr/lib/crt1.o
ld: error: mx.o is incompatible with /usr/lib/crt1.o
ld: error: myutils.o is incompatible with /usr/lib/crt1.o
ld: error: path.o is incompatible with /usr/lib/crt1.o
ld: error: searchchime.o is incompatible with /usr/lib/crt1.o
ld: error: seqdb.o is incompatible with /usr/lib/crt1.o
ld: error: setnucmx.o is incompatible with /usr/lib/crt1.o
ld: error: sfasta.o is incompatible with /usr/lib/crt1.o
ld: error: tracebackbit.o is incompatible with /usr/lib/crt1.o
ld: error: uchime_main.o is incompatible with /usr/lib/crt1.o
ld: error: usort.o is incompatible with /usr/lib/crt1.o
ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
c++: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[2]: *** [makefile:13: uchime] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.46.1/source/uchime_src'
gmake[1]: *** [Makefile:131: uchime] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.46.1'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/mothur