BioC 3.5: BUILD BIN report for flowCore on veracruz2

Package: flowCore

Version: 1.42.3

Command: rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_1.42.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowCore.buildbin-libdir

StartedAt: 2017-10-18 10:53:19 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 10:55:34 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 135.6 seconds

RetCode: 0

Status:  OK

PackageFile: flowCore_1.42.3.tgz

PackageFileSize: 10.09 MiB

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### Running command:
###
###   rm -rf flowCore.buildbin-libdir && mkdir flowCore.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowCore_1.42.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowCore.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowCore.buildbin-libdir flowCore_1.42.3.tar.gz'
>>>>>>> 

* installing *source* package ‘flowCore’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c FastLogicle.cpp -o FastLogicle.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Hyperlog.cpp -o Hyperlog.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Logicle.cpp -o Logicle.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c biexponential.cpp -o biexponential.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c convertRawBytes.cpp -o convertRawBytes.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c fcsTextParse.cpp -o fcsTextParse.o
fcsTextParse.cpp:45:133: warning: multi-line // comment [-Wcomment]
                        txt = boost::regex_replace(txt, boost::regex(doubleDelimiter), magicString);//somehow boost::replace_all won't do the job for \\\\
                                                                                                                                                         ^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c hyperlogTransform.cpp -o hyperlogTransform.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c inPolygon.cpp -o inPolygon.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c inPolytope.cpp -o inPolytope.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c logicleTransform.cpp -o logicleTransform.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c sortBytes.cpp -o sortBytes.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c uint2double.cpp -o uint2double.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c zeroin.cpp -o zeroin.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib"
ar rs "/Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating archive /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a(icu.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a(regex_debug.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a(usinstances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a(w32_regex_traits.o) has no symbols
clang++ -std=gnu++11 -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 flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o convertRawBytes.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o pairVectorRcppWrap.o sortBytes.o uint2double.o zeroin.o /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/flowCore.buildbin-libdir/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "flowCore.buildbin-libdir/flowCore/libs//flowCore.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "flowCore.buildbin-libdir/flowCore/libs//flowCore.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "flowCore.buildbin-libdir/flowCore/libs//flowCore.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "flowCore.buildbin-libdir/flowCore/libs//flowCore.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "flowCore.buildbin-libdir/flowCore/libs//flowCore.so"