[package - main-amd64-default][biology/mothur] Failed for mothur-1.48.0 in build
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Date: Mon, 26 Jun 2023 22:21:46 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: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p4785b313b958_se8efee297c/logs/mothur-1.48.0.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p4785b313b958_se8efee297c
Log:
=>> Building biology/mothur
build started at Mon Jun 26 22:02:26 UTC 2023
port directory: /usr/ports/biology/mothur
package name: mothur-1.48.0
building for: FreeBSD main-amd64-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400091
Job Id: 08
!!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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yuri@FreeBSD.org
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MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mothur/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mothur/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mothur/work/.cache HOME=/wrkdirs/usr/ports/biology/mothur/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mothur/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mothur/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> mothur-1.48.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-08] Installing pkg-1.19.1_1...
[main-amd64-default-job-08] Extracting pkg-1.19.1_1: .......... done
===> mothur-1.48.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mothur-1.48.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by mothur-1.48.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by mothur-1.48.0 for building
=> SHA256 Checksum OK for mothur-mothur-v1.48.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by mothur-1.48.0 for building
===> Extracting for mothur-1.48.0
=> SHA256 Checksum OK for mothur-mothur-v1.48.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for mothur-1.48.0
===> Applying FreeBSD patches for mothur-1.48.0 from /usr/ports/biology/mothur/files
===========================================================================
=======================<phase: build-depends >============================
===> mothur-1.48.0 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.2.15.pkg
[main-amd64-default-job-08] Installing bash-5.2.15...
[main-amd64-default-job-08] `-- Installing gettext-runtime-0.21.1...
<snip>
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
source/utils.cpp:1612:1: warning: '/*' within block comment [-Wcomment]
/***********************************************************************
^
source/utils.cpp:1624:1: warning: '/*' within block comment [-Wcomment]
/***********************************************************************/
^
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
2 warnings generated.
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -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=c++ && gmake clean && gmake && mv uchime ../../ && cd ..
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.48.0/source/uchime_src'
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.48.0/source/uchime_src'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.48.0/source/uchime_src'
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
In file included from addtargets2.cpp:3:
./myutils.h:176:1: error: reference to 'byte' is ambiguous
byte *ReadAllStdioFile(FILE *f, off_t &FileSize);
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
In file included from addtargets2.cpp:3:
./myutils.h:177:1: error: reference to 'byte' is ambiguous
byte *ReadAllStdioFile(const string &FileName, off_t &FileSize);
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
In file included from addtargets2.cpp:4:
In file included from ./chime.h:4:
./seq.h:9:8: error: reference to 'byte' is ambiguous
const byte *Seq;
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
In file included from addtargets2.cpp:5:
In file included from ./ultra.h:4:
./seqdb.h:20:2: error: reference to 'byte' is ambiguous
byte **m_Seqs;
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
In file included from addtargets2.cpp:5:
In file included from ./ultra.h:4:
./seqdb.h:35:43: error: reference to 'byte' is ambiguous
unsigned AddSeq(const char *Label, const byte *Seq, unsigned L);
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
In file included from addtargets2.cpp:5:
In file included from ./ultra.h:4:
./seqdb.h:37:2: error: reference to 'byte' is ambiguous
byte *GetSeq(unsigned SeqIndex) const
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
In file included from addtargets2.cpp:5:
In file included from ./ultra.h:4:
./seqdb.h:106:12: error: reference to 'byte' is ambiguous
bool isgap(byte c);
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
addtargets2.cpp:12:34: error: reference to 'byte' is ambiguous
double GetFractIdGivenPath(const byte *A, const byte *B, const char *Path);
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
addtargets2.cpp:12:49: error: reference to 'byte' is ambiguous
double GetFractIdGivenPath(const byte *A, const byte *B, const char *Path);
^
./myutils.h:42:23: note: candidate found by name lookup is 'byte'
typedef unsigned char byte;
^
/usr/include/c++/v1/cstddef:72:12: note: candidate found by name lookup is 'std::byte'
enum class byte : unsigned char {};
^
9 errors generated.
gmake[2]: *** [<builtin>: addtargets2.o] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.48.0/source/uchime_src'
gmake[1]: *** [Makefile:131: uchime] Error 2
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mothur/work/mothur-1.48.0'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/mothur