Package: flowWorkspace

Version: 1.5.90

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_1.5.90.tar.gz

StartedAt: 2013-03-25 02:30:05 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:38:22 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 496.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowWorkspace.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '1.5.90'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'multicore' 'Rmpi'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/algorithm/iteration/detail/preprocessed/reverse_fold.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/algorithm/iteration/detail/segmented_for_each.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/deque/detail/preprocessed/deque10_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/deque/detail/preprocessed/deque20_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/deque/detail/preprocessed/deque30_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/deque/detail/preprocessed/deque40_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/deque/detail/preprocessed/deque50_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/deque/detail/preprocessed/deque_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/list/detail/preprocessed/list10_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/list/detail/preprocessed/list20_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/list/detail/preprocessed/list30_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/list/detail/preprocessed/list40_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/list/detail/preprocessed/list50_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector10.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector10_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector20.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector20_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector30.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector30_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector40.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector40_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector50.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector50_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vector_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vvector10_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vvector20_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vvector30_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vvector40_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/container/vector/detail/preprocessed/vvector50_fwd.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/sequence/intrinsic/detail/segmented_begin_impl.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/view/iterator_range/detail/segmented_iterator_range.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/fusion/view/transform_view/detail/apply_transform_result.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/aux_/preprocessed/bcc_pre590/reverse_iter_fold_impl.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/aux_/preprocessed/no_ctps/reverse_iter_fold_impl.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/vector/aux_/preprocessed/typeof_based/vector10_c.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/vector/aux_/preprocessed/typeof_based/vector20_c.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/vector/aux_/preprocessed/typeof_based/vector30_c.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/vector/aux_/preprocessed/typeof_based/vector40_c.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/mpl/vector/aux_/preprocessed/typeof_based/vector50_c.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/numeric/conversion/detail/preprocessed/numeric_cast_traits_common.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/numeric/conversion/detail/preprocessed/numeric_cast_traits_long_long.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/proto/transform/detail/preprocessed/construct_pod_funop.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/proto/transform/detail/preprocessed/make_gcc_workaround.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/proto/transform/detail/preprocessed/pass_through_impl.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/spirit/home/classic/core/composite/impl/exclusive_or.ipp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/spirit/home/classic/core/composite/impl/intersection.ipp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/spirit/home/classic/core/composite/impl/sequential_and.ipp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/spirit/home/classic/core/composite/impl/sequential_or.ipp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/spirit/home/classic/core/non_terminal/impl/object_with_id.ipp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/spirit/home/classic/core/non_terminal/parser_context.hpp
  flowWorkspace/src/trimmed_boost_1_52_0/boost/xpressive/detail/core/matcher/logical_newline_matcher.hpp

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowWorkspace' can be installed ... [269s/277s] OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    lib    3.8Mb
    libs   3.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getTransformations,GatingHierarchyInternal : <anonymous>: multiple
  local function definitions for 'f' with different formal arguments
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs/i386/flowWorkspace.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'GatingHierarchy.o', 'GatingSet.o', 'flowJoWorkspace.o',
      'gate.o', 'macFlowJoWorkspace.o', 'transformation.o',
      'winFlowJoWorkspace.o', 'workspace.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [27s/27s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
GatingHierarchy-class 8.937  1.861  10.927
GatingSet-class       5.449  1.710   7.247
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'run-all.R' [17s/18s]
 [18s/18s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 6 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/00check.log'
for details.

* installing *source* package 'flowWorkspace' ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: No directory was specified for --with-boost. Using bundled boost.
found  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.Rcheck/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)

name	user	system	elapsed
GatingHierarchy-class	8.937	1.861	10.927
GatingSet-class	5.449	1.710	7.247
GatingSetList-class	0.004	0.010	0.014
add	0.019	0.038	0.058
archive	0.003	0.006	0.009
clone	0.005	0.012	0.018
ellipsoidGate2FlowJoVertices	0.016	0.010	0.027
execute	0.003	0.006	0.009
exportAsFlowJoXML	0.004	0.007	0.011
flowJoWorkspace-class	0.088	0.024	0.117
flowWorkspace2flowCore	0.016	0.021	0.039
getBoundaries	0.006	0.013	0.021
getCompensationMatrices	0.004	0.009	0.014
getData	0.006	0.012	0.017
getGate	0.004	0.009	0.014
getIndices	0.003	0.007	0.010
getKeywords	0.009	0.015	0.026
getNodes	0.003	0.006	0.009
getParent	0.005	0.011	0.016
getPopStats	0.005	0.010	0.014
getSample	0.003	0.007	0.009
getSampleGroups	0.006	0.012	0.017
getSamples	0.003	0.007	0.010
getTransformations	0.003	0.007	0.011
includedChannel2ExcludedChannel	0.005	0.013	0.018
includedGate2ExcludedGate	0.003	0.007	0.010
openWorkspace	0.004	0.008	0.011
parseWorkspace	0.006	0.013	0.021
plot	0.003	0.007	0.011
plotGate	0.003	0.007	0.011
plotPopCV	0.003	0.005	0.009
plotWf	0.004	0.009	0.013