>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_1.5.90.tar.gz'
>>>>>>>
* installing *source* package 'flowWorkspace' ...
removing .o files
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 trimmed_boost_1_52_0 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=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from GatingHierarchy.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from GatingHierarchy.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
GatingHierarchy.cpp: In member function 'VertexID GatingHierarchy::getChildren(VertexID, std::string)':
GatingHierarchy.cpp:885: warning: 'curNodeID' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c GatingSet.cpp -o GatingSet.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c POPINDICES.cpp -o POPINDICES.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from POPINDICES.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from POPINDICES.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/R_GatingHierarchy.hpp:18,
from R_GatingHierarchy.cpp:17:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/R_GatingHierarchy.hpp:18,
from R_GatingHierarchy.cpp:17:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c R_GatingSet.cpp -o R_GatingSet.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from include/R_GatingSet.hpp:19,
from R_GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from include/R_GatingSet.hpp:19,
from R_GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
R_GatingSet.cpp: In function 'SEXPREC* R_combineGatingSet(SEXPREC*, SEXPREC*)':
R_GatingSet.cpp:186: warning: comparison between signed and unsigned integer expressions
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -pedantic -c bitOps.c -o bitOps.o
cc1: warning: command line option "-Wno-deprecated" is valid for C++/ObjC++ but not for C
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c calibrationTable.cpp -o calibrationTable.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from calibrationTable.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from calibrationTable.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c flowData.cpp -o flowData.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from flowData.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from flowData.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from flowJoWorkspace.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from flowJoWorkspace.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
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:28: warning: comparison is always false due to limited range of data type
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c gate.cpp -o gate.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from gate.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from gate.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -pedantic -c init.c -o init.o
cc1: warning: command line option "-Wno-deprecated" is valid for C++/ObjC++ but not for C
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/macFlowJoWorkspace.hpp:10,
from macFlowJoWorkspace.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/macFlowJoWorkspace.hpp:10,
from macFlowJoWorkspace.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c ncdfFlow.cpp -o ncdfFlow.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/ncdfFlow.hpp:11,
from ncdfFlow.cpp:1:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/ncdfFlow.hpp:11,
from ncdfFlow.cpp:1:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c nodeProperties.cpp -o nodeProperties.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from nodeProperties.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from nodeProperties.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c spline.cpp -o spline.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c transformation.cpp -o transformation.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from include/transformation.hpp:21,
from transformation.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from include/transformation.hpp:21,
from transformation.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/winFlowJoWorkspace.hpp:10,
from winFlowJoWorkspace.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/winFlowJoWorkspace.hpp:10,
from winFlowJoWorkspace.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c workspace.cpp -o workspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from workspace.cpp:11:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from workspace.cpp:11:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c wsNode.cpp -o wsNode.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from wsNode.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from wsNode.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/archive_exception.cpp -o trimmed_boost_1_52_0/libs/serialization/src/archive_exception.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_archive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_archive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.o
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp: In instantiation of 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >':
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> > >'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:50: instantiated from 'boost::detail::transform_iterator_base<boost::archive::iterators::detail::to_6_bit<char>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:76: instantiated from 'boost::transform_iterator<boost::archive::iterators::detail::to_6_bit<char>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/binary_from_base64.hpp:91: instantiated from 'boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>'
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >'
trimmed_boost_1_52_0/boost/detail/iterator.hpp:83: instantiated from 'boost::detail::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >'
trimmed_boost_1_52_0/boost/iterator/iterator_traits.hpp:49: instantiated from 'boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >'
trimmed_boost_1_52_0/boost/mpl/eval_if.hpp:38: instantiated from 'boost::mpl::eval_if<boost::is_same<boost::use_default, boost::use_default>, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >, boost::mpl::identity<boost::use_default> >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:166: instantiated from 'boost::detail::ia_dflt_help<boost::use_default, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> > >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:217: instantiated from 'boost::detail::iterator_adaptor_base<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, char, boost::single_pass_traversal_tag, char, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:265: instantiated from 'boost::iterator_adaptor<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, char, boost::single_pass_traversal_tag, char, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/transform_width.hpp:56: instantiated from 'boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>'
trimmed_boost_1_52_0/boost/archive/impl/basic_text_iprimitive.ipp:90: instantiated from 'void boost::archive::basic_text_iprimitive<IStream>::load_binary(void*, size_t) [with IStream = std::basic_istream<char, std::char_traits<char> >]'
trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.cpp:25: instantiated from here
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >' has a field 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >::<anonymous>' whose type uses the anonymous namespace
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >' has a base 'boost::archive::iterators::filter_iterator<<unnamed>::remove_whitespace_predicate<char>, boost::archive::iterators::istream_iterator<char> >' whose type uses the anonymous namespace
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.o
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp: In instantiation of 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >':
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> > >'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:50: instantiated from 'boost::detail::transform_iterator_base<boost::archive::iterators::detail::to_6_bit<wchar_t>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:76: instantiated from 'boost::transform_iterator<boost::archive::iterators::detail::to_6_bit<wchar_t>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/binary_from_base64.hpp:91: instantiated from 'boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>'
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >'
trimmed_boost_1_52_0/boost/detail/iterator.hpp:83: instantiated from 'boost::detail::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >'
trimmed_boost_1_52_0/boost/iterator/iterator_traits.hpp:49: instantiated from 'boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >'
trimmed_boost_1_52_0/boost/mpl/eval_if.hpp:38: instantiated from 'boost::mpl::eval_if<boost::is_same<boost::use_default, boost::use_default>, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >, boost::mpl::identity<boost::use_default> >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:166: instantiated from 'boost::detail::ia_dflt_help<boost::use_default, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> > >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:217: instantiated from 'boost::detail::iterator_adaptor_base<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, 8, 6, wchar_t>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, wchar_t, boost::single_pass_traversal_tag, wchar_t, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:265: instantiated from 'boost::iterator_adaptor<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, 8, 6, wchar_t>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, wchar_t, boost::single_pass_traversal_tag, wchar_t, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/transform_width.hpp:56: instantiated from 'boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, 8, 6, wchar_t>'
trimmed_boost_1_52_0/boost/archive/impl/basic_text_iprimitive.ipp:90: instantiated from 'void boost::archive::basic_text_iprimitive<IStream>::load_binary(void*, size_t) [with IStream = std::basic_istream<wchar_t, std::char_traits<wchar_t> >]'
trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.cpp:30: instantiated from here
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >' has a field 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >::<anonymous>' whose type uses the anonymous namespace
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >' has a base 'boost::archive::iterators::filter_iterator<<unnamed>::remove_whitespace_predicate<wchar_t>, boost::archive::iterators::istream_iterator<wchar_t> >' whose type uses the anonymous namespace
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_woprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_woprimitive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.cpp -o trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.cpp -o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.cpp -o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.cpp -o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.cpp -o trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/stl_port.cpp -o trimmed_boost_1_52_0/libs/serialization/src/stl_port.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/utf8_codecvt_facet.cpp -o trimmed_boost_1_52_0/libs/serialization/src/utf8_codecvt_facet.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/void_cast.cpp -o trimmed_boost_1_52_0/libs/serialization/src/void_cast.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.o
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o bitOps.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o init.o macFlowJoWorkspace.o ncdfFlow.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o trimmed_boost_1_52_0/libs/serialization/src/archive_exception.o trimmed_boost_1_52_0/libs/serialization/src/basic_archive.o trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_woprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.o trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.o trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.o trimmed_boost_1_52_0/libs/serialization/src/stl_port.o trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.o trimmed_boost_1_52_0/libs/serialization/src/utf8_codecvt_facet.o trimmed_boost_1_52_0/libs/serialization/src/void_cast.o trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.o trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.o trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.o trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/lib/i386/libRcpp.a -L/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/lib/i386 -lncdfFlow -L/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Scalable Robust Estimators with High Breakdown Point (version 1.3-02)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
cp flowWorkspace.so libflowWorkspace.dylib
cp libflowWorkspace.dylib ../inst/lib/i386
rm libflowWorkspace.dylib
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'flowWorkspace.Rnw'
** testing if installed package can be loaded
* DONE (flowWorkspace)
>>>>>>>
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/i386/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/i386/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/i386/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/i386/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/i386/flowWorkspace.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=flowWorkspace.buildbin-libdir --libs-only flowWorkspace_1.5.90.tar.gz'
>>>>>>>
* installing *source* package 'flowWorkspace' ...
removing .o files
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 trimmed_boost_1_52_0 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=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from GatingHierarchy.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from GatingHierarchy.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
GatingHierarchy.cpp: In member function 'VertexID GatingHierarchy::getChildren(VertexID, std::string)':
GatingHierarchy.cpp:885: warning: 'curNodeID' may be used uninitialized in this function
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c GatingSet.cpp -o GatingSet.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c POPINDICES.cpp -o POPINDICES.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from POPINDICES.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from POPINDICES.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/R_GatingHierarchy.hpp:18,
from R_GatingHierarchy.cpp:17:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/R_GatingHierarchy.hpp:18,
from R_GatingHierarchy.cpp:17:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c R_GatingSet.cpp -o R_GatingSet.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from include/R_GatingSet.hpp:19,
from R_GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/populationTree.hpp:11,
from include/GatingHierarchy.hpp:13,
from include/GatingSet.hpp:12,
from include/R_GatingSet.hpp:19,
from R_GatingSet.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
R_GatingSet.cpp: In function 'SEXPREC* R_combineGatingSet(SEXPREC*, SEXPREC*)':
R_GatingSet.cpp:186: warning: comparison between signed and unsigned integer expressions
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -pedantic -c bitOps.c -o bitOps.o
cc1: warning: command line option "-Wno-deprecated" is valid for C++/ObjC++ but not for C
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c calibrationTable.cpp -o calibrationTable.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from calibrationTable.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from calibrationTable.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c flowData.cpp -o flowData.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from flowData.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from flowData.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from flowJoWorkspace.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from flowJoWorkspace.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
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:28: warning: comparison is always false due to limited range of data type
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c gate.cpp -o gate.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from gate.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from gate.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -pedantic -c init.c -o init.o
cc1: warning: command line option "-Wno-deprecated" is valid for C++/ObjC++ but not for C
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/macFlowJoWorkspace.hpp:10,
from macFlowJoWorkspace.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/macFlowJoWorkspace.hpp:10,
from macFlowJoWorkspace.cpp:9:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c ncdfFlow.cpp -o ncdfFlow.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/ncdfFlow.hpp:11,
from ncdfFlow.cpp:1:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/ncdfFlow.hpp:11,
from ncdfFlow.cpp:1:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c nodeProperties.cpp -o nodeProperties.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from nodeProperties.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from nodeProperties.cpp:7:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c spline.cpp -o spline.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c transformation.cpp -o transformation.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from include/transformation.hpp:21,
from transformation.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/calibrationTable.hpp:27,
from include/transformation.hpp:21,
from transformation.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/winFlowJoWorkspace.hpp:10,
from winFlowJoWorkspace.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from include/flowJoWorkspace.hpp:11,
from include/winFlowJoWorkspace.hpp:10,
from winFlowJoWorkspace.cpp:8:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c workspace.cpp -o workspace.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from workspace.cpp:11:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from include/workspace.hpp:14,
from workspace.cpp:11:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c wsNode.cpp -o wsNode.o
In file included from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:26,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from wsNode.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: "BOOST_concept" redefined
In file included from trimmed_boost_1_52_0/boost/graph/buffer_concepts.hpp:9,
from trimmed_boost_1_52_0/boost/graph/graph_concepts.hpp:21,
from trimmed_boost_1_52_0/boost/graph/detail/adjacency_list.hpp:31,
from trimmed_boost_1_52_0/boost/graph/adjacency_list.hpp:245,
from trimmed_boost_1_52_0/boost/graph/adj_list_serialize.hpp:12,
from include/flowData.hpp:34,
from include/gate.hpp:14,
from include/POPINDICES.hpp:15,
from include/nodeProperties.hpp:11,
from include/wsNode.hpp:10,
from wsNode.cpp:10:
trimmed_boost_1_52_0/boost/concept/detail/concept_def.hpp:34:1: warning: this is the location of the previous definition
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/archive_exception.cpp -o trimmed_boost_1_52_0/libs/serialization/src/archive_exception.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_archive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_archive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.o
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp: In instantiation of 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >':
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> > >'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:50: instantiated from 'boost::detail::transform_iterator_base<boost::archive::iterators::detail::to_6_bit<char>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:76: instantiated from 'boost::transform_iterator<boost::archive::iterators::detail::to_6_bit<char>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/binary_from_base64.hpp:91: instantiated from 'boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>'
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >'
trimmed_boost_1_52_0/boost/detail/iterator.hpp:83: instantiated from 'boost::detail::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >'
trimmed_boost_1_52_0/boost/iterator/iterator_traits.hpp:49: instantiated from 'boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >'
trimmed_boost_1_52_0/boost/mpl/eval_if.hpp:38: instantiated from 'boost::mpl::eval_if<boost::is_same<boost::use_default, boost::use_default>, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> >, boost::mpl::identity<boost::use_default> >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:166: instantiated from 'boost::detail::ia_dflt_help<boost::use_default, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char> > >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:217: instantiated from 'boost::detail::iterator_adaptor_base<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, char, boost::single_pass_traversal_tag, char, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:265: instantiated from 'boost::iterator_adaptor<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, char, boost::single_pass_traversal_tag, char, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/transform_width.hpp:56: instantiated from 'boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >, char>, 8, 6, char>'
trimmed_boost_1_52_0/boost/archive/impl/basic_text_iprimitive.ipp:90: instantiated from 'void boost::archive::basic_text_iprimitive<IStream>::load_binary(void*, size_t) [with IStream = std::basic_istream<char, std::char_traits<char> >]'
trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.cpp:25: instantiated from here
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >' has a field 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >::<anonymous>' whose type uses the anonymous namespace
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<char> >' has a base 'boost::archive::iterators::filter_iterator<<unnamed>::remove_whitespace_predicate<char>, boost::archive::iterators::istream_iterator<char> >' whose type uses the anonymous namespace
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.o
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp: In instantiation of 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >':
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> > >'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:50: instantiated from 'boost::detail::transform_iterator_base<boost::archive::iterators::detail::to_6_bit<wchar_t>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/transform_iterator.hpp:76: instantiated from 'boost::transform_iterator<boost::archive::iterators::detail::to_6_bit<wchar_t>, boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, boost::use_default, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/binary_from_base64.hpp:91: instantiated from 'boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>'
/usr/include/c++/4.0.0/bits/stl_iterator_base_types.h:129: instantiated from 'std::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >'
trimmed_boost_1_52_0/boost/detail/iterator.hpp:83: instantiated from 'boost::detail::iterator_traits<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >'
trimmed_boost_1_52_0/boost/iterator/iterator_traits.hpp:49: instantiated from 'boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >'
trimmed_boost_1_52_0/boost/mpl/eval_if.hpp:38: instantiated from 'boost::mpl::eval_if<boost::is_same<boost::use_default, boost::use_default>, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> >, boost::mpl::identity<boost::use_default> >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:166: instantiated from 'boost::detail::ia_dflt_help<boost::use_default, boost::iterator_difference<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t> > >'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:217: instantiated from 'boost::detail::iterator_adaptor_base<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, 8, 6, wchar_t>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, wchar_t, boost::single_pass_traversal_tag, wchar_t, boost::use_default>'
trimmed_boost_1_52_0/boost/iterator/iterator_adaptor.hpp:265: instantiated from 'boost::iterator_adaptor<boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, 8, 6, wchar_t>, boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, wchar_t, boost::single_pass_traversal_tag, wchar_t, boost::use_default>'
trimmed_boost_1_52_0/boost/archive/iterators/transform_width.hpp:56: instantiated from 'boost::archive::iterators::transform_width<boost::archive::iterators::binary_from_base64<boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >, wchar_t>, 8, 6, wchar_t>'
trimmed_boost_1_52_0/boost/archive/impl/basic_text_iprimitive.ipp:90: instantiated from 'void boost::archive::basic_text_iprimitive<IStream>::load_binary(void*, size_t) [with IStream = std::basic_istream<wchar_t, std::char_traits<wchar_t> >]'
trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.cpp:30: instantiated from here
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >' has a field 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >::<anonymous>' whose type uses the anonymous namespace
trimmed_boost_1_52_0/boost/archive/iterators/remove_whitespace.hpp:150: warning: 'boost::archive::iterators::remove_whitespace<boost::archive::iterators::istream_iterator<wchar_t> >' has a base 'boost::archive::iterators::filter_iterator<<unnamed>::remove_whitespace_predicate<wchar_t>, boost::archive::iterators::istream_iterator<wchar_t> >' whose type uses the anonymous namespace
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_text_woprimitive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_text_woprimitive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.cpp -o trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.cpp -o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.cpp -o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.cpp -o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.cpp -o trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/stl_port.cpp -o trimmed_boost_1_52_0/libs/serialization/src/stl_port.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/utf8_codecvt_facet.cpp -o trimmed_boost_1_52_0/libs/serialization/src/utf8_codecvt_facet.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/void_cast.cpp -o trimmed_boost_1_52_0/libs/serialization/src/void_cast.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -Wno-deprecated -I/usr/include/libxml2 -Itrimmed_boost_1_52_0/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/include" -fPIC -g -O2 -Wall -fasm-blocks -c trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.o
Error in tools:::file_path_as_absolute(base:::system.file(..., package = "Rcpp")) :
file '' does not exist
Calls: <Anonymous> ... RcppLdFlags -> RcppLdPath -> Rcpp.system.file -> <Anonymous>
Execution halted
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o bitOps.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o init.o macFlowJoWorkspace.o ncdfFlow.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o trimmed_boost_1_52_0/libs/serialization/src/archive_exception.o trimmed_boost_1_52_0/libs/serialization/src/basic_archive.o trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_iserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_pointer_oserializer.o trimmed_boost_1_52_0/libs/serialization/src/basic_serializer_map.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_iprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_oprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_wiprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_text_woprimitive.o trimmed_boost_1_52_0/libs/serialization/src/basic_xml_archive.o trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.o trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.o trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_no_rtti.o trimmed_boost_1_52_0/libs/serialization/src/extended_type_info_typeid.o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/shared_ptr_helper.o trimmed_boost_1_52_0/libs/serialization/src/stl_port.o trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.o trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.o trimmed_boost_1_52_0/libs/serialization/src/utf8_codecvt_facet.o trimmed_boost_1_52_0/libs/serialization/src/void_cast.o trimmed_boost_1_52_0/libs/serialization/src/xml_archive_exception.o trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.o trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.o trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.o trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.o -L/usr/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in tools:::file_path_as_absolute(base:::system.file(..., package = "Rcpp")) :
file '' does not exist
Calls: <Anonymous> ... RcppLdFlags -> RcppLdPath -> Rcpp.system.file -> <Anonymous>
Execution halted
cp flowWorkspace.so libflowWorkspace.dylib
cp libflowWorkspace.dylib ../inst/lib/x86_64
rm libflowWorkspace.dylib
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64
* DONE (flowWorkspace)
>>>>>>>
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs/x86_64/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/x86_64/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/x86_64/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/x86_64/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/x86_64/flowWorkspace.so"