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BioC 2.13: BUILD BIN report for flowWorkspace on perceval

This page was generated on 2014-04-05 09:52:38 -0700 (Sat, 05 Apr 2014).

Package 266/750HostnameOS / ArchBUILDCHECKBUILD BIN
flowWorkspace 3.8.61
Greg Finak ,Mike Jiang
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace
Last Changed Rev: 86756 / Revision: 88450
Last Changed Date: 2014-02-24 14:24:01 -0800 (Mon, 24 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: flowWorkspace
Version: 3.8.61
Command: rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_3.8.61.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowWorkspace.buildbin-libdir
StartedAt: 2014-04-05 05:23:04 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:28:47 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 343.1 seconds
RetCode: 0
Status:  OK 
PackageFile: flowWorkspace_3.8.61.tgz
PackageFileSize: 6.13 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.8.61.tar.gz'
>>>>>>> 

* installing *source* package ‘flowWorkspace’ ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: No directory was specified for --with-boost. Using bundled boost.
found  bst  header sources and tar archive;using what is there.
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2 
configure:    PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GatingHierarchy.cpp -o GatingHierarchy.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GatingSet.cpp -o GatingSet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c POPINDICES.cpp -o POPINDICES.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_GatingSet.cpp -o R_GatingSet.o
R_GatingSet.cpp: In function ‘SEXPREC* R_combineGatingSet(SEXPREC*, SEXPREC*)’:
R_GatingSet.cpp:192: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c calibrationTable.cpp -o calibrationTable.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c flowData.cpp -o flowData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c flowJoWorkspace.cpp -o flowJoWorkspace.o
flowJoWorkspace.cpp: In member function ‘virtual std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > flowJoWorkspace::getSampleID(short unsigned int)’:
flowJoWorkspace.cpp:43: warning: comparison is always false due to limited range of data type
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c gate.cpp -o gate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nodeProperties.cpp -o nodeProperties.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c spline.cpp -o spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c transformation.cpp -o transformation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:456:27: warning: "/*" within comment
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c workspace.cpp -o workspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c wsNode.cpp -o wsNode.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/archive_exception.cpp -o bst/libs/serialization/src/archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_archive.cpp -o bst/libs/serialization/src/basic_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_iarchive.cpp -o bst/libs/serialization/src/basic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_iserializer.cpp -o bst/libs/serialization/src/basic_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_oarchive.cpp -o bst/libs/serialization/src/basic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_oserializer.cpp -o bst/libs/serialization/src/basic_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_pointer_iserializer.cpp -o bst/libs/serialization/src/basic_pointer_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_pointer_oserializer.cpp -o bst/libs/serialization/src/basic_pointer_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_serializer_map.cpp -o bst/libs/serialization/src/basic_serializer_map.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_iprimitive.cpp -o bst/libs/serialization/src/basic_text_iprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_oprimitive.cpp -o bst/libs/serialization/src/basic_text_oprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_wiprimitive.cpp -o bst/libs/serialization/src/basic_text_wiprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_woprimitive.cpp -o bst/libs/serialization/src/basic_text_woprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_xml_archive.cpp -o bst/libs/serialization/src/basic_xml_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_iarchive.cpp -o bst/libs/serialization/src/binary_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_oarchive.cpp -o bst/libs/serialization/src/binary_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_wiarchive.cpp -o bst/libs/serialization/src/binary_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_woarchive.cpp -o bst/libs/serialization/src/binary_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/codecvt_null.cpp -o bst/libs/serialization/src/codecvt_null.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/extended_type_info.cpp -o bst/libs/serialization/src/extended_type_info.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/extended_type_info_no_rtti.cpp -o bst/libs/serialization/src/extended_type_info_no_rtti.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/extended_type_info_typeid.cpp -o bst/libs/serialization/src/extended_type_info_typeid.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/polymorphic_iarchive.cpp -o bst/libs/serialization/src/polymorphic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/polymorphic_oarchive.cpp -o bst/libs/serialization/src/polymorphic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/shared_ptr_helper.cpp -o bst/libs/serialization/src/shared_ptr_helper.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/stl_port.cpp -o bst/libs/serialization/src/stl_port.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_iarchive.cpp -o bst/libs/serialization/src/text_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_oarchive.cpp -o bst/libs/serialization/src/text_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_wiarchive.cpp -o bst/libs/serialization/src/text_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_woarchive.cpp -o bst/libs/serialization/src/text_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/utf8_codecvt_facet.cpp -o bst/libs/serialization/src/utf8_codecvt_facet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/void_cast.cpp -o bst/libs/serialization/src/void_cast.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_archive_exception.cpp -o bst/libs/serialization/src/xml_archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_grammar.cpp -o bst/libs/serialization/src/xml_grammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_iarchive.cpp -o bst/libs/serialization/src/xml_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_oarchive.cpp -o bst/libs/serialization/src/xml_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_wgrammar.cpp -o bst/libs/serialization/src/xml_wgrammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_wiarchive.cpp -o bst/libs/serialization/src/xml_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_woarchive.cpp -o bst/libs/serialization/src/xml_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/c_regex_traits.cpp -o bst/libs/regex/src/c_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/cpp_regex_traits.cpp -o bst/libs/regex/src/cpp_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/cregex.cpp -o bst/libs/regex/src/cregex.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/fileiter.cpp -o bst/libs/regex/src/fileiter.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/icu.cpp -o bst/libs/regex/src/icu.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/instances.cpp -o bst/libs/regex/src/instances.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/posix_api.cpp -o bst/libs/regex/src/posix_api.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex.cpp -o bst/libs/regex/src/regex.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex_debug.cpp -o bst/libs/regex/src/regex_debug.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex_raw_buffer.cpp -o bst/libs/regex/src/regex_raw_buffer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex_traits_defaults.cpp -o bst/libs/regex/src/regex_traits_defaults.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/static_mutex.cpp -o bst/libs/regex/src/static_mutex.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/usinstances.cpp -o bst/libs/regex/src/usinstances.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/w32_regex_traits.cpp -o bst/libs/regex/src/w32_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/wc_regex_traits.cpp -o bst/libs/regex/src/wc_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/wide_posix_api.cpp -o bst/libs/regex/src/wide_posix_api.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/winstances.cpp -o bst/libs/regex/src/winstances.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o bst/libs/serialization/src/archive_exception.o bst/libs/serialization/src/basic_archive.o bst/libs/serialization/src/basic_iarchive.o bst/libs/serialization/src/basic_iserializer.o bst/libs/serialization/src/basic_oarchive.o bst/libs/serialization/src/basic_oserializer.o bst/libs/serialization/src/basic_pointer_iserializer.o bst/libs/serialization/src/basic_pointer_oserializer.o bst/libs/serialization/src/basic_serializer_map.o bst/libs/serialization/src/basic_text_iprimitive.o bst/libs/serialization/src/basic_text_oprimitive.o bst/libs/serialization/src/basic_text_wiprimitive.o bst/libs/serialization/src/basic_text_woprimitive.o bst/libs/serialization/src/basic_xml_archive.o bst/libs/serialization/src/binary_iarchive.o bst/libs/serialization/src/binary_oarchive.o bst/libs/serialization/src/binary_wiarchive.o bst/libs/serialization/src/binary_woarchive.o bst/libs/serialization/src/codecvt_null.o bst/libs/serialization/src/extended_type_info.o bst/libs/serialization/src/extended_type_info_no_rtti.o bst/libs/serialization/src/extended_type_info_typeid.o bst/libs/serialization/src/polymorphic_iarchive.o bst/libs/serialization/src/polymorphic_oarchive.o bst/libs/serialization/src/shared_ptr_helper.o bst/libs/serialization/src/stl_port.o bst/libs/serialization/src/text_iarchive.o bst/libs/serialization/src/text_oarchive.o bst/libs/serialization/src/text_wiarchive.o bst/libs/serialization/src/text_woarchive.o bst/libs/serialization/src/utf8_codecvt_facet.o bst/libs/serialization/src/void_cast.o bst/libs/serialization/src/xml_archive_exception.o bst/libs/serialization/src/xml_grammar.o bst/libs/serialization/src/xml_iarchive.o bst/libs/serialization/src/xml_oarchive.o bst/libs/serialization/src/xml_wgrammar.o bst/libs/serialization/src/xml_wiarchive.o bst/libs/serialization/src/xml_woarchive.o bst/libs/regex/src/c_regex_traits.o bst/libs/regex/src/cpp_regex_traits.o bst/libs/regex/src/cregex.o bst/libs/regex/src/fileiter.o bst/libs/regex/src/icu.o bst/libs/regex/src/instances.o bst/libs/regex/src/posix_api.o bst/libs/regex/src/regex.o bst/libs/regex/src/regex_debug.o bst/libs/regex/src/regex_raw_buffer.o bst/libs/regex/src/regex_traits_defaults.o bst/libs/regex/src/static_mutex.o bst/libs/regex/src/usinstances.o bst/libs/regex/src/w32_regex_traits.o bst/libs/regex/src/wc_regex_traits.o bst/libs/regex/src/wide_posix_api.o bst/libs/regex/src/winstances.o -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cp flowWorkspace.so libflowWorkspace.dylib 
cp libflowWorkspace.dylib ../inst/lib
rm libflowWorkspace.dylib
installing to /Users/biocbuild/bbs-2.13-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (flowWorkspace)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"