Back to the "Multiple platform build/check report" A  B  C  D  E [F] G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.0: CHECK report for flowWorkspace on perceval

This page was generated on 2015-04-10 09:55:52 -0700 (Fri, 10 Apr 2015).

Package 324/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowWorkspace 3.12.06
Greg Finak ,Mike Jiang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowWorkspace
Last Changed Rev: 100927 / Revision: 102249
Last Changed Date: 2015-03-20 10:30:59 -0700 (Fri, 20 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: flowWorkspace
Version: 3.12.06
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_3.12.06.tar.gz
StartedAt: 2015-04-10 01:34:46 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:43:56 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 550.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowWorkspace.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_3.12.06.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.12.06’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... [328s/341s] OK
* checking installed package size ... NOTE
  installed size is 26.0Mb
  sub-directories of 1Mb or more:
    doc     2.7Mb
    lib     9.9Mb
    libs   10.1Mb
    tests   2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’ ‘Biobase’ ‘gridExtra’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘RSVGTipsDevice’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘graphics’ ‘IDPmisc’ ‘RBGL’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
  ‘graph:::.makeEdgeKeys’ ‘lattice:::updateList’
  ‘ncdfFlow:::.isValidSamples’ ‘Rgraphviz:::getRenderPar’
  ‘stats:::.splinefun’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.addTrans’ ‘.load_gs’ ‘.uuid_gen’ ‘isNegated’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.addGatingHierarchies: no visible global function definition for
  ‘read.ncdfFlowSet’
.addGatingHierarchies : <anonymous>: no visible global function
  definition for ‘flowFrame’
.addGatingHierarchies: no visible global function definition for
  ‘flowSet’
.computeCV : <anonymous>: no visible binding for global variable
  ‘flowJo.count’
.computeCV : <anonymous>: no visible binding for global variable
  ‘flowCore.count’
.getTransformations : <anonymous> : f: no visible binding for global
  variable ‘max_val’
.getTransformations : <anonymous> : f: no visible binding for global
  variable ‘decade’
.getTransformations : <anonymous> : f: no visible binding for global
  variable ‘min_val’
.plotGate: no visible global function definition for ‘sampleNames<-’
.plotGate : <anonymous>: no visible global function definition for
  ‘sampleNames<-’
.renderNodes.svgAnno: no visible global function definition for ‘nodes’
GatingSetList: no visible global function definition for ‘ncdfFlowList’
getData,GatingSetList-ANY: no visible global function definition for
  ‘ncdfFlowList’
pData<-,GatingSet-data.frame: no visible global function definition for
  ‘varMetadata’
pData<-,GatingSet-data.frame: no visible global function definition for
  ‘phenoData’
pData<-,GatingSet-data.frame: no visible global function definition for
  ‘varMetadata<-’
pData<-,GatingSet-data.frame: no visible global function definition for
  ‘phenoData<-’
rbind2,GatingSetList-missing: no visible global function definition for
  ‘ncdfFlowList’
sampleNames<-,GatingSet-ANY: no visible global function definition for
  ‘sampleNames<-’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
GatingHierarchy-class 6.006  0.404   6.564
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run-all.R’ [41s/42s]
 [41s/42s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

flowWorkspace.Rcheck/00install.out:

* installing *source* package ‘flowWorkspace’ ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: No directory was specified for --with-boost. Using bundled boost.
found  bst  header sources and tar archive;using what is there.
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/usr/include/libxml2 
configure:    PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GatingHierarchy.cpp -o GatingHierarchy.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GatingSet.cpp -o GatingSet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c POPINDICES.cpp -o POPINDICES.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_API.cpp -o R_API.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c R_GatingSet.cpp -o R_GatingSet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RcppExports.cpp -o RcppExports.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c calibrationTable.cpp -o calibrationTable.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c flowData.cpp -o flowData.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c flowJoWorkspace.cpp -o flowJoWorkspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c gate.cpp -o gate.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c global.cpp -o global.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nodeProperties.cpp -o nodeProperties.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c spline.cpp -o spline.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c transformation.cpp -o transformation.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:488:27: warning: "/*" within comment
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c workspace.cpp -o workspace.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c wsNode.cpp -o wsNode.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/archive_exception.cpp -o bst/libs/serialization/src/archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_archive.cpp -o bst/libs/serialization/src/basic_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_iarchive.cpp -o bst/libs/serialization/src/basic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_iserializer.cpp -o bst/libs/serialization/src/basic_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_oarchive.cpp -o bst/libs/serialization/src/basic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_oserializer.cpp -o bst/libs/serialization/src/basic_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_pointer_iserializer.cpp -o bst/libs/serialization/src/basic_pointer_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_pointer_oserializer.cpp -o bst/libs/serialization/src/basic_pointer_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_serializer_map.cpp -o bst/libs/serialization/src/basic_serializer_map.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_iprimitive.cpp -o bst/libs/serialization/src/basic_text_iprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_oprimitive.cpp -o bst/libs/serialization/src/basic_text_oprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_wiprimitive.cpp -o bst/libs/serialization/src/basic_text_wiprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_text_woprimitive.cpp -o bst/libs/serialization/src/basic_text_woprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/basic_xml_archive.cpp -o bst/libs/serialization/src/basic_xml_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_iarchive.cpp -o bst/libs/serialization/src/binary_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_oarchive.cpp -o bst/libs/serialization/src/binary_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_wiarchive.cpp -o bst/libs/serialization/src/binary_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/binary_woarchive.cpp -o bst/libs/serialization/src/binary_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/codecvt_null.cpp -o bst/libs/serialization/src/codecvt_null.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/extended_type_info.cpp -o bst/libs/serialization/src/extended_type_info.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/extended_type_info_no_rtti.cpp -o bst/libs/serialization/src/extended_type_info_no_rtti.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/extended_type_info_typeid.cpp -o bst/libs/serialization/src/extended_type_info_typeid.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/polymorphic_iarchive.cpp -o bst/libs/serialization/src/polymorphic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/polymorphic_oarchive.cpp -o bst/libs/serialization/src/polymorphic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/shared_ptr_helper.cpp -o bst/libs/serialization/src/shared_ptr_helper.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/stl_port.cpp -o bst/libs/serialization/src/stl_port.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_iarchive.cpp -o bst/libs/serialization/src/text_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_oarchive.cpp -o bst/libs/serialization/src/text_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_wiarchive.cpp -o bst/libs/serialization/src/text_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/text_woarchive.cpp -o bst/libs/serialization/src/text_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/utf8_codecvt_facet.cpp -o bst/libs/serialization/src/utf8_codecvt_facet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/void_cast.cpp -o bst/libs/serialization/src/void_cast.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_archive_exception.cpp -o bst/libs/serialization/src/xml_archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_grammar.cpp -o bst/libs/serialization/src/xml_grammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_iarchive.cpp -o bst/libs/serialization/src/xml_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_oarchive.cpp -o bst/libs/serialization/src/xml_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_wgrammar.cpp -o bst/libs/serialization/src/xml_wgrammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_wiarchive.cpp -o bst/libs/serialization/src/xml_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/serialization/src/xml_woarchive.cpp -o bst/libs/serialization/src/xml_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/c_regex_traits.cpp -o bst/libs/regex/src/c_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/cpp_regex_traits.cpp -o bst/libs/regex/src/cpp_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/cregex.cpp -o bst/libs/regex/src/cregex.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/fileiter.cpp -o bst/libs/regex/src/fileiter.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/icu.cpp -o bst/libs/regex/src/icu.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/instances.cpp -o bst/libs/regex/src/instances.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/posix_api.cpp -o bst/libs/regex/src/posix_api.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex.cpp -o bst/libs/regex/src/regex.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex_debug.cpp -o bst/libs/regex/src/regex_debug.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex_raw_buffer.cpp -o bst/libs/regex/src/regex_raw_buffer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/regex_traits_defaults.cpp -o bst/libs/regex/src/regex_traits_defaults.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/static_mutex.cpp -o bst/libs/regex/src/static_mutex.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/usinstances.cpp -o bst/libs/regex/src/usinstances.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/w32_regex_traits.cpp -o bst/libs/regex/src/w32_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/wc_regex_traits.cpp -o bst/libs/regex/src/wc_regex_traits.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/wide_posix_api.cpp -o bst/libs/regex/src/wide_posix_api.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/usr/include/libxml2  -Ibst/ -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bst/libs/regex/src/winstances.cpp -o bst/libs/regex/src/winstances.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o bst/libs/serialization/src/archive_exception.o bst/libs/serialization/src/basic_archive.o bst/libs/serialization/src/basic_iarchive.o bst/libs/serialization/src/basic_iserializer.o bst/libs/serialization/src/basic_oarchive.o bst/libs/serialization/src/basic_oserializer.o bst/libs/serialization/src/basic_pointer_iserializer.o bst/libs/serialization/src/basic_pointer_oserializer.o bst/libs/serialization/src/basic_serializer_map.o bst/libs/serialization/src/basic_text_iprimitive.o bst/libs/serialization/src/basic_text_oprimitive.o bst/libs/serialization/src/basic_text_wiprimitive.o bst/libs/serialization/src/basic_text_woprimitive.o bst/libs/serialization/src/basic_xml_archive.o bst/libs/serialization/src/binary_iarchive.o bst/libs/serialization/src/binary_oarchive.o bst/libs/serialization/src/binary_wiarchive.o bst/libs/serialization/src/binary_woarchive.o bst/libs/serialization/src/codecvt_null.o bst/libs/serialization/src/extended_type_info.o bst/libs/serialization/src/extended_type_info_no_rtti.o bst/libs/serialization/src/extended_type_info_typeid.o bst/libs/serialization/src/polymorphic_iarchive.o bst/libs/serialization/src/polymorphic_oarchive.o bst/libs/serialization/src/shared_ptr_helper.o bst/libs/serialization/src/stl_port.o bst/libs/serialization/src/text_iarchive.o bst/libs/serialization/src/text_oarchive.o bst/libs/serialization/src/text_wiarchive.o bst/libs/serialization/src/text_woarchive.o bst/libs/serialization/src/utf8_codecvt_facet.o bst/libs/serialization/src/void_cast.o bst/libs/serialization/src/xml_archive_exception.o bst/libs/serialization/src/xml_grammar.o bst/libs/serialization/src/xml_iarchive.o bst/libs/serialization/src/xml_oarchive.o bst/libs/serialization/src/xml_wgrammar.o bst/libs/serialization/src/xml_wiarchive.o bst/libs/serialization/src/xml_woarchive.o bst/libs/regex/src/c_regex_traits.o bst/libs/regex/src/cpp_regex_traits.o bst/libs/regex/src/cregex.o bst/libs/regex/src/fileiter.o bst/libs/regex/src/icu.o bst/libs/regex/src/instances.o bst/libs/regex/src/posix_api.o bst/libs/regex/src/regex.o bst/libs/regex/src/regex_debug.o bst/libs/regex/src/regex_raw_buffer.o bst/libs/regex/src/regex_traits_defaults.o bst/libs/regex/src/static_mutex.o bst/libs/regex/src/usinstances.o bst/libs/regex/src/w32_regex_traits.o bst/libs/regex/src/wc_regex_traits.o bst/libs/regex/src/wide_posix_api.o bst/libs/regex/src/winstances.o -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cp flowWorkspace.so libflowWorkspace.dylib 
cp libflowWorkspace.dylib ../inst/lib
rm libflowWorkspace.dylib
installing to /Users/biocbuild/bbs-3.0-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)

flowWorkspace.Rcheck/flowWorkspace-Ex.timings:

nameusersystemelapsed
GatingHierarchy-class6.0060.4046.564
GatingSet-class3.9680.3324.348
GatingSet-methods000
GatingSetList-class0.0030.0010.003
add0.0020.0010.003
clone0.0000.0000.001
flowJoWorkspace-class0.0850.0090.114
flowWorkspace.par.get0.0020.0010.003
getCompensationMatrices0.0000.0000.001
getData-methods0.0010.0000.001
getGate0.0010.0000.002
getIndices-GatingSet-name-method0.0010.0000.001
getIndices0.0010.0000.001
getKeywords0.3820.0870.571
getNodes0.0010.0010.001
getParent0.0010.0000.001
getPopStats0.0010.0010.001
getSample0.0010.0000.002
getSampleGroups0.0000.0000.001
getSamples0.0000.0010.001
getSingleCellExpression0.0010.0000.001
getTransformations0.0010.0010.001
insertGate000
keyword0.0010.0010.001
loglevel0.0020.0000.002
mkformula0.0030.0000.003
openWorkspace0.0010.0000.001
parseWorkspace0.0010.0000.002
plot-methods0.0010.0000.001
plotGate-methods0.0020.0000.002
plotPopCV0.0000.0000.001
prettyAxis0.0010.0000.001
sampleNames0.0000.0000.001
save_gs0.0010.0000.001
setGate0.0010.0000.001
setNode-methods0.0010.0000.001
transform0.0010.0000.001