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BUILD BIN report for DNABarcodes on merida2

This page was generated on 2018-10-17 08:55:21 -0400 (Wed, 17 Oct 2018).

Package 401/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DNABarcodes 1.10.0
Tilo Buschmann
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/DNABarcodes
Branch: RELEASE_3_7
Last Commit: 9f40368
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DNABarcodes
Version: 1.10.0
Command: rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNABarcodes_1.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNABarcodes.buildbin-libdir
StartedAt: 2018-10-17 01:14:21 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:16:15 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 113.8 seconds
RetCode: 0
Status:  OK 
PackageFile: DNABarcodes_1.10.0.tgz
PackageFileSize: 481.9 KiB

Command output

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###
### Running command:
###
###   rm -rf DNABarcodes.buildbin-libdir && mkdir DNABarcodes.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DNABarcodes_1.10.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DNABarcodes.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DNABarcodes.buildbin-libdir DNABarcodes_1.10.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DNABarcodes’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c DNABarcodes_init.c -o DNABarcodes_init.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c analyse_barcodes.cpp -o analyse_barcodes.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c barcode_set_distances.cpp -o barcode_set_distances.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c cachedistance.cpp -o cachedistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c chromosome.cpp -o chromosome.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c code_falsification.cpp -o code_falsification.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c conway.cpp -o conway.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c create_distance_func.cpp -o create_distance_func.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c create_dnabarcodes.cpp -o create_dnabarcodes.o
In file included from create_dnabarcodes.cpp:26:
In file included from ./maxclique_pattabiraman_heuristic.h:10:
In file included from ./maxclique.h:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/graph/adjacency_list.hpp:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_set.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_set.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c create_pool.cpp -o create_pool.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c demultiplex.cpp -o demultiplex.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c distance_for_R.cpp -o distance_for_R.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c genericchromosome.cpp -o genericchromosome.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c greedyevolution.cpp -o greedyevolution.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c hammingdistance.cpp -o hammingdistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c helpers.cpp -o helpers.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c levenshteindistance.cpp -o levenshteindistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c maxclique_pattabiraman_heuristic.cpp -o maxclique_pattabiraman_heuristic.o
In file included from maxclique_pattabiraman_heuristic.cpp:6:
In file included from ./maxclique_pattabiraman_heuristic.h:10:
In file included from ./maxclique.h:12:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/graph/adjacency_list.hpp:21:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered_set.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/unordered/unordered_set.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c phaseshiftdist.cpp -o phaseshiftdist.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c sequence.cpp -o sequence.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c sequencelevenshteindistance.cpp -o sequencelevenshteindistance.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c sequencepool.cpp -o sequencepool.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o DNABarcodes.so DNABarcodes_init.o RcppExports.o analyse_barcodes.o barcode_set_distances.o cachedistance.o chromosome.o code_falsification.o conway.o create_distance_func.o create_dnabarcodes.o create_pool.o demultiplex.o distance_for_R.o genericchromosome.o greedyevolution.o hammingdistance.o helpers.o levenshteindistance.o maxclique_pattabiraman_heuristic.o phaseshiftdist.o sequence.o sequencelevenshteindistance.o sequencepool.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/DNABarcodes.buildbin-libdir/DNABarcodes/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DNABarcodes)


>>>>>>> 
>>>>>>> FIXING LINKS FOR DNABarcodes.buildbin-libdir/DNABarcodes/libs//DNABarcodes.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "DNABarcodes.buildbin-libdir/DNABarcodes/libs//DNABarcodes.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "DNABarcodes.buildbin-libdir/DNABarcodes/libs//DNABarcodes.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "DNABarcodes.buildbin-libdir/DNABarcodes/libs//DNABarcodes.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "DNABarcodes.buildbin-libdir/DNABarcodes/libs//DNABarcodes.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "DNABarcodes.buildbin-libdir/DNABarcodes/libs//DNABarcodes.so"