flowWorkspace 1.6.1
Greg Finak ,Mike Jiang
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/flowWorkspace | | Last Changed Rev: 78306 / Revision: 81334 | | Last Changed Date: 2013-07-10 16:09:35 -0700 (Wed, 10 Jul 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ ERROR ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowWorkspace/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowWorkspace' version '1.6.1'
* 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 ... [302s/310s] OK
* checking installed package size ... NOTE
installed size is 11.2Mb
sub-directories of 1Mb or more:
lib 4.9Mb
libs 5.1Mb
* 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/flowWorkspace.so':
Found '__ZSt4cout', possibly from 'std::cout' (C++)
Objects: 'GatingHierarchy.o', 'GatingSet.o', 'flowJoWorkspace.o',
'gate.o', 'macFlowJoWorkspace.o', 'nodeProperties.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 ... [29s/31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
GatingHierarchy-class 10.514 0.839 12.665
GatingSet-class 6.041 0.847 7.095
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running 'run-all.R'/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 62445 Segmentation fault ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
[10s/16s]
ERROR
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
13: try(parseWorkspace(ws, execute = TRUE, path = d, name = 1))
14: eval(expr, envir, enclos)
15: eval(i, envir)
16: sys.source(file, chdir = TRUE, envir = new.env(parent = env))
17: FUN("/Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/tests/test-workspace_import.R"[[1L]], ...)
18: lapply(files, function(file) { sys.source(file, chdir = TRUE, envir = new.env(parent = env)) end_context()})
19: force(code)
20: with_reporter(reporter, lapply(files, function(file) { sys.source(file, chdir = TRUE, envir = new.env(parent = env)) end_context()}))
21: test_dir(test_path, reporter = reporter, env = env, filter = filter)
22: test_package("flowWorkspace")
aborting ...
* 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... no
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=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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 -mtune=core2 -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c GatingSet.cpp -o GatingSet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c POPINDICES.cpp -o POPINDICES.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c bitOps.c -o bitOps.o
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c calibrationTable.cpp -o calibrationTable.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c flowData.cpp -o flowData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
flowJoWorkspace.cpp: In member function 'virtual std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > flowJoWorkspace::getSampleID(short unsigned int)':
flowJoWorkspace.cpp:28: warning: comparison is always false due to limited range of data type
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -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 -mtune=core2 -g -O2 -c gate.cpp -o gate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c init.c -o init.o
cc1: warning: command line option "-Wno-deprecated" is valid for C++/Java/ObjC++ but not for C
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c ncdfFlow.cpp -o ncdfFlow.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c nodeProperties.cpp -o nodeProperties.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c spline.cpp -o spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c transformation.cpp -o transformation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c workspace.cpp -o workspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c wsNode.cpp -o wsNode.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/archive_exception.cpp -o trimmed_boost_1_52_0/libs/serialization/src/archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/basic_archive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.cpp -o trimmed_boost_1_52_0/libs/serialization/src/basic_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/binary_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.cpp -o trimmed_boost_1_52_0/libs/serialization/src/codecvt_null.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/polymorphic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/stl_port.cpp -o trimmed_boost_1_52_0/libs/serialization/src/stl_port.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/text_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/void_cast.cpp -o trimmed_boost_1_52_0/libs/serialization/src/void_cast.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_grammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_wgrammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -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 -mtune=core2 -g -O2 -c trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.cpp -o trimmed_boost_1_52_0/libs/serialization/src/xml_woarchive.o
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o 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/libRcpp.a -L/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/lib -lncdfFlow -Wl,-rpath,/Library/Frameworks/R.framework/Versions/3.0/Resources/library/ncdfFlow/lib -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
cp flowWorkspace.so libflowWorkspace.dylib
cp libflowWorkspace.dylib ../inst/lib
rm libflowWorkspace.dylib
installing to /Users/biocbuild/bbs-2.12-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowWorkspace)