flowWorkspace 3.16.0
Greg Finak ,Mike Jiang
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/flowWorkspace | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowWorkspace_3.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘3.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
src/pb_build/src/google/protobuf/descriptor_database.lo
src/pb_build/src/google/protobuf/descriptor.lo
src/pb_build/src/google/protobuf/descriptor.pb.lo
src/pb_build/src/google/protobuf/dynamic_message.lo
src/pb_build/src/google/protobuf/extension_set_heavy.lo
src/pb_build/src/google/protobuf/extension_set.lo
src/pb_build/src/google/protobuf/generated_message_reflection.lo
src/pb_build/src/google/protobuf/generated_message_util.lo
src/pb_build/src/google/protobuf/io/coded_stream.lo
src/pb_build/src/google/protobuf/io/gzip_stream.lo
src/pb_build/src/google/protobuf/io/printer.lo
src/pb_build/src/google/protobuf/io/strtod.lo
src/pb_build/src/google/protobuf/io/tokenizer.lo
src/pb_build/src/google/protobuf/io/zero_copy_stream_impl_lite.lo
src/pb_build/src/google/protobuf/io/zero_copy_stream_impl.lo
src/pb_build/src/google/protobuf/io/zero_copy_stream.lo
src/pb_build/src/google/protobuf/message_lite.lo
src/pb_build/src/google/protobuf/message.lo
src/pb_build/src/google/protobuf/reflection_ops.lo
src/pb_build/src/google/protobuf/repeated_field.lo
src/pb_build/src/google/protobuf/service.lo
src/pb_build/src/google/protobuf/stubs/atomicops_internals_x86_gcc.lo
src/pb_build/src/google/protobuf/stubs/atomicops_internals_x86_msvc.lo
src/pb_build/src/google/protobuf/stubs/common.lo
src/pb_build/src/google/protobuf/stubs/once.lo
src/pb_build/src/google/protobuf/stubs/stringprintf.lo
src/pb_build/src/google/protobuf/stubs/structurally_valid.lo
src/pb_build/src/google/protobuf/stubs/strutil.lo
src/pb_build/src/google/protobuf/stubs/substitute.lo
src/pb_build/src/google/protobuf/text_format.lo
src/pb_build/src/google/protobuf/unknown_field_set.lo
src/pb_build/src/google/protobuf/wire_format_lite.lo
src/pb_build/src/google/protobuf/wire_format.lo
src/pb_build/src/libprotobuf.la
src/protobuf-2.6.0/src/solaris/libstdc++.la
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
src/pb_build/src/google/protobuf/.dirstamp
src/pb_build/src/google/protobuf/io/.dirstamp
src/pb_build/src/google/protobuf/stubs/.dirstamp
src/pb_build/src/.libs
src/pb_build/src/google/protobuf/.libs
src/pb_build/src/google/protobuf/io/.libs
src/pb_build/src/google/protobuf/stubs/.libs
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... [369s/386s] OK
* checking installed package size ... NOTE
installed size is 16.7Mb
sub-directories of 1Mb or more:
doc 2.7Mb
libs 10.6Mb
tests 2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘gridExtra’
A package should be listed in only one of these fields.
Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
* 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:
‘graphics’ ‘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
GatingSet,GatingHierarchy-character : .local: warning in
list.files(pattern = paste("^", file, "$", sep = ""), path = path,
recursive = TRUE, full = TRUE): partial argument match of 'full' to
'full.names'
getGate,GatingSetList-character : .local: warning in unlist(res, recur
= FALSE): partial argument match of 'recur' to 'recursive'
.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 : <anonymous>: no visible binding
for global variable ‘max_val’
.getTransformations : <anonymous> : f : <anonymous>: no visible binding
for global variable ‘decade’
.getTransformations : <anonymous> : f : <anonymous>: no visible binding
for global variable ‘min_val’
.parse.pData: no visible binding for global variable ‘.’
.preprocessMap: no visible binding for global variable ‘old’
.preprocessMap: no visible binding for global variable ‘.’
.preprocessor: no visible binding for global variable ‘groupName’
.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’
getGate,GatingHierarchy-character : .local: no visible global function
definition for ‘ellipsoidGate’
getPopStats,GatingHierarchy : .local: no visible binding for global
variable ‘node’
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’
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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 ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘run-all.R’ [48s/49s]
[48s/49s] 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
Status: 7 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.
* installing *source* package ‘flowWorkspace’ ...
checking for g++... g++
checking whether the C++ compiler works... yes
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checking whether we are using the GNU C compiler... yes
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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
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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: setting protobuf flags...
configure: No directory was specified for --with-protobuf. Using bundled protocol buffer.
found protobuf-2.6.0 header sources and tar archive;using what is there.
glibtoolize: putting auxiliary files in `.'.
glibtoolize: copying file `./ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
glibtoolize: copying file `m4/libtool.m4'
glibtoolize: copying file `m4/ltoptions.m4'
glibtoolize: copying file `m4/ltsugar.m4'
glibtoolize: copying file `m4/ltversion.m4'
glibtoolize: copying file `m4/lt˜obsolete.m4'
building protobuf...
found pb_build ;using what is there.
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checking build system type... i386-apple-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
checking target system type... i386-apple-darwin10.8.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ../protobuf-2.6.0/install-sh -c -d
checking for gawk... no
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checking whether make sets $(MAKE)... yes
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checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
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checking for suffix of executables...
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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 for style of include used by make... GNU
checking dependency style of gcc... gcc3
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checking whether we are using the GNU C++ compiler... yes
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checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
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checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
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checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r
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checking command to parse /usr/bin/nm output from gcc object... ok
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checking if gcc supports -fno-rtti -fno-exceptions... no
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checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
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checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
checking how to hardcode library paths into programs... immediate
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checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
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checking whether the g++ linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 dyld
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configure: WARNING: Impossible to determine how to use pthreads with shared libraries and -nostdlib
checking the location of hash_map... <tr1/unordered_map>
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating protobuf.pc
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config.status: creating config.h
config.status: config.h is unchanged
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make all-recursive
Making all in .
Making all in src
depbase=`echo google/protobuf/stubs/atomicops_internals_x86_gcc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/atomicops_internals_x86_gcc.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/atomicops_internals_x86_gcc.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_gcc.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/atomicops_internals_x86_gcc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_gcc.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_gcc.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o
depbase=`echo google/protobuf/stubs/atomicops_internals_x86_msvc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/atomicops_internals_x86_msvc.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/atomicops_internals_x86_msvc.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_msvc.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/atomicops_internals_x86_msvc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_msvc.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_msvc.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o
depbase=`echo google/protobuf/stubs/common.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/common.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/common.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/common.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/common.lo -MD -MP -MF google/protobuf/stubs/.deps/common.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/common.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/common.o
depbase=`echo google/protobuf/stubs/once.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/once.lo -MD -MP -MF google/protobuf/stubs/.deps/once.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/once.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/once.o
depbase=`echo google/protobuf/stubs/stringprintf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/stringprintf.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/stringprintf.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/stubs/stringprintf.lo -MD -MP -MF google/protobuf/stubs/.deps/stringprintf.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/stringprintf.o
depbase=`echo google/protobuf/extension_set.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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mv -f $depbase.Tpo $depbase.Plo
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/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/gzip_stream.lo ../../protobuf-2.6.0/src/google/protobuf/io/gzip_stream.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/gzip_stream.lo -MD -MP -MF google/protobuf/io/.deps/gzip_stream.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/gzip_stream.cc -fno-common -DPIC -o google/protobuf/io/.libs/gzip_stream.o
depbase=`echo google/protobuf/io/printer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/printer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/printer.lo ../../protobuf-2.6.0/src/google/protobuf/io/printer.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/printer.lo -MD -MP -MF google/protobuf/io/.deps/printer.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/printer.cc -fno-common -DPIC -o google/protobuf/io/.libs/printer.o
depbase=`echo google/protobuf/io/strtod.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/strtod.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/strtod.lo ../../protobuf-2.6.0/src/google/protobuf/io/strtod.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/strtod.lo -MD -MP -MF google/protobuf/io/.deps/strtod.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/strtod.cc -fno-common -DPIC -o google/protobuf/io/.libs/strtod.o
depbase=`echo google/protobuf/io/tokenizer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/tokenizer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/tokenizer.lo ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/tokenizer.lo -MD -MP -MF google/protobuf/io/.deps/tokenizer.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.cc -fno-common -DPIC -o google/protobuf/io/.libs/tokenizer.o
depbase=`echo google/protobuf/io/zero_copy_stream_impl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/zero_copy_stream_impl.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/zero_copy_stream_impl.lo ../../protobuf-2.6.0/src/google/protobuf/io/zero_copy_stream_impl.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../../protobuf-2.6.0/src -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -MT google/protobuf/io/zero_copy_stream_impl.lo -MD -MP -MF google/protobuf/io/.deps/zero_copy_stream_impl.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/zero_copy_stream_impl.cc -fno-common -DPIC -o google/protobuf/io/.libs/zero_copy_stream_impl.o
/bin/sh ../libtool --tag=CXX --mode=link g++ -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -O2 -g -DNDEBUG -version-info 9:0:0 -export-dynamic -no-undefined -o libprotobuf.la -rpath /usr/local/lib google/protobuf/stubs/atomicops_internals_x86_gcc.lo google/protobuf/stubs/atomicops_internals_x86_msvc.lo google/protobuf/stubs/common.lo google/protobuf/stubs/once.lo google/protobuf/stubs/stringprintf.lo google/protobuf/extension_set.lo google/protobuf/generated_message_util.lo google/protobuf/message_lite.lo google/protobuf/repeated_field.lo google/protobuf/wire_format_lite.lo google/protobuf/io/coded_stream.lo google/protobuf/io/zero_copy_stream.lo google/protobuf/io/zero_copy_stream_impl_lite.lo google/protobuf/stubs/strutil.lo google/protobuf/stubs/substitute.lo google/protobuf/stubs/structurally_valid.lo google/protobuf/descriptor.lo google/protobuf/descriptor.pb.lo google/protobuf/descriptor_database.lo google/protobuf/dynamic_message.lo google/protobuf/extension_set_heavy.lo google/protobuf/generated_message_reflection.lo google/protobuf/message.lo google/protobuf/reflection_ops.lo google/protobuf/service.lo google/protobuf/text_format.lo google/protobuf/unknown_field_set.lo google/protobuf/wire_format.lo google/protobuf/io/gzip_stream.lo google/protobuf/io/printer.lo google/protobuf/io/strtod.lo google/protobuf/io/tokenizer.lo google/protobuf/io/zero_copy_stream_impl.lo -lz
libtool: link: rm -fr .libs/libprotobuf.9.0.0.dylib .libs/libprotobuf.9.dylib .libs/libprotobuf.dylib .libs/libprotobuf.la .libs/libprotobuf.lai
libtool: link: g++ -dynamiclib -o .libs/libprotobuf.9.dylib google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o google/protobuf/stubs/.libs/common.o google/protobuf/stubs/.libs/once.o google/protobuf/stubs/.libs/stringprintf.o google/protobuf/.libs/extension_set.o google/protobuf/.libs/generated_message_util.o google/protobuf/.libs/message_lite.o google/protobuf/.libs/repeated_field.o google/protobuf/.libs/wire_format_lite.o google/protobuf/io/.libs/coded_stream.o google/protobuf/io/.libs/zero_copy_stream.o google/protobuf/io/.libs/zero_copy_stream_impl_lite.o google/protobuf/stubs/.libs/strutil.o google/protobuf/stubs/.libs/substitute.o google/protobuf/stubs/.libs/structurally_valid.o google/protobuf/.libs/descriptor.o google/protobuf/.libs/descriptor.pb.o google/protobuf/.libs/descriptor_database.o google/protobuf/.libs/dynamic_message.o google/protobuf/.libs/extension_set_heavy.o google/protobuf/.libs/generated_message_reflection.o google/protobuf/.libs/message.o google/protobuf/.libs/reflection_ops.o google/protobuf/.libs/service.o google/protobuf/.libs/text_format.o google/protobuf/.libs/unknown_field_set.o google/protobuf/.libs/wire_format.o google/protobuf/io/.libs/gzip_stream.o google/protobuf/io/.libs/printer.o google/protobuf/io/.libs/strtod.o google/protobuf/io/.libs/tokenizer.o google/protobuf/io/.libs/zero_copy_stream_impl.o -lz -install_name /usr/local/lib/libprotobuf.9.dylib -compatibility_version 10 -current_version 10.0 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libprotobuf.dylib" && ln -s "libprotobuf.9.dylib" "libprotobuf.dylib")
libtool: link: (cd ".libs" && rm -f "libprotobuf.9.0.0.dylib" && ln -s "libprotobuf.9.dylib" "libprotobuf.9.0.0.dylib")
libtool: link: ( cd ".libs" && rm -f "libprotobuf.la" && ln -s "../libprotobuf.la" "libprotobuf.la" )
configure: Using the following compilation and linking flags for flowWorkspace
configure: PKG_CPPFLAGS=-I/usr/include/libxml2 -Iprotobuf-2.6.0/src
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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c GatingSet.cpp -o GatingSet.o
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp: In function ‘void boost::serialization::load(Archive&, std::vector<bool, Allocator>&, unsigned int) [with Archive = boost::archive::binary_iarchive, Allocator = std::allocator<bool>]’:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/split_free.hpp:58: instantiated from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/split_free.hpp:74: instantiated from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp:231: instantiated from ‘void boost::serialization::serialize(Archive&, std::vector<bool, Allocator>&, unsigned int) [with Archive = boost::archive::binary_iarchive, Allocator = std::allocator<bool>]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/serialization.hpp:128: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::binary_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/archive/detail/iserializer.hpp:184: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::binary_iarchive, T = std::vector<bool, std::allocator<bool> >]’
GatingSet.cpp:786: instantiated from here
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp:216: warning: comparison between signed and unsigned integer expressions
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp: In function ‘void boost::serialization::load(Archive&, std::vector<bool, Allocator>&, unsigned int) [with Archive = boost::archive::text_iarchive, Allocator = std::allocator<bool>]’:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/split_free.hpp:58: instantiated from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::text_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/split_free.hpp:74: instantiated from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::text_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp:231: instantiated from ‘void boost::serialization::serialize(Archive&, std::vector<bool, Allocator>&, unsigned int) [with Archive = boost::archive::text_iarchive, Allocator = std::allocator<bool>]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/serialization.hpp:128: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::text_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/archive/detail/iserializer.hpp:184: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::text_iarchive, T = std::vector<bool, std::allocator<bool> >]’
GatingSet.cpp:786: instantiated from here
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp:216: warning: comparison between signed and unsigned integer expressions
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp: In function ‘void boost::serialization::load(Archive&, std::vector<bool, Allocator>&, unsigned int) [with Archive = boost::archive::xml_iarchive, Allocator = std::allocator<bool>]’:
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/split_free.hpp:58: instantiated from ‘static void boost::serialization::free_loader<Archive, T>::invoke(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/split_free.hpp:74: instantiated from ‘void boost::serialization::split_free(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp:231: instantiated from ‘void boost::serialization::serialize(Archive&, std::vector<bool, Allocator>&, unsigned int) [with Archive = boost::archive::xml_iarchive, Allocator = std::allocator<bool>]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/serialization.hpp:128: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = std::vector<bool, std::allocator<bool> >]’
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/archive/detail/iserializer.hpp:184: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = std::vector<bool, std::allocator<bool> >]’
GatingSet.cpp:786: instantiated from here
/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include/boost/serialization/vector.hpp:216: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c GatingSet.pb.cc -o GatingSet.pb.o
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h: In static member function ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = unsigned int, google::protobuf::internal::WireFormatLite::FieldType DeclaredType = TYPE_FIXED32]’:
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:413: instantiated from here
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:383: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:393: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h: In static member function ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long unsigned int, google::protobuf::internal::WireFormatLite::FieldType DeclaredType = TYPE_FIXED64]’:
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:414: instantiated from here
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:383: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:393: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h: In static member function ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = int, google::protobuf::internal::WireFormatLite::FieldType DeclaredType = TYPE_SFIXED32]’:
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:415: instantiated from here
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:383: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:393: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h: In static member function ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = long long int, google::protobuf::internal::WireFormatLite::FieldType DeclaredType = TYPE_SFIXED64]’:
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:416: instantiated from here
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:383: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:393: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h: In static member function ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = float, google::protobuf::internal::WireFormatLite::FieldType DeclaredType = TYPE_FLOAT]’:
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:417: instantiated from here
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:383: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:393: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h: In static member function ‘static bool google::protobuf::internal::WireFormatLite::ReadPackedFixedSizePrimitive(google::protobuf::io::CodedInputStream*, google::protobuf::RepeatedField<T>*) [with CType = double, google::protobuf::internal::WireFormatLite::FieldType DeclaredType = TYPE_DOUBLE]’:
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:418: instantiated from here
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:383: warning: comparison between signed and unsigned integer expressions
protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h:393: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c delimitedMessage.cpp -o delimitedMessage.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c transformation.cpp -o transformation.o
include/transformation.hpp: In constructor ‘fasinhTrans::fasinhTrans()’:
include/transformation.hpp:245: warning: ‘fasinhTrans::length’ will be initialized after
include/transformation.hpp:244: warning: ‘double fasinhTrans::maxRange’
transformation.cpp:269: warning: when initialized here
include/transformation.hpp: In constructor ‘fasinhTrans::fasinhTrans(double, double, double, double, double)’:
include/transformation.hpp:245: warning: ‘fasinhTrans::length’ will be initialized after
include/transformation.hpp:244: warning: ‘double fasinhTrans::maxRange’
transformation.cpp:273: warning: when initialized here
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:494:27: warning: "/*" within comment
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/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 -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/archive_exception.cpp -o boost_serialization/archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_archive.cpp -o boost_serialization/basic_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_iarchive.cpp -o boost_serialization/basic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_iserializer.cpp -o boost_serialization/basic_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_oarchive.cpp -o boost_serialization/basic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_oserializer.cpp -o boost_serialization/basic_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_pointer_iserializer.cpp -o boost_serialization/basic_pointer_iserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_pointer_oserializer.cpp -o boost_serialization/basic_pointer_oserializer.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_serializer_map.cpp -o boost_serialization/basic_serializer_map.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_text_iprimitive.cpp -o boost_serialization/basic_text_iprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_text_oprimitive.cpp -o boost_serialization/basic_text_oprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_text_wiprimitive.cpp -o boost_serialization/basic_text_wiprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_text_woprimitive.cpp -o boost_serialization/basic_text_woprimitive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/basic_xml_archive.cpp -o boost_serialization/basic_xml_archive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/binary_iarchive.cpp -o boost_serialization/binary_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/binary_oarchive.cpp -o boost_serialization/binary_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/binary_wiarchive.cpp -o boost_serialization/binary_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/binary_woarchive.cpp -o boost_serialization/binary_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/codecvt_null.cpp -o boost_serialization/codecvt_null.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/extended_type_info.cpp -o boost_serialization/extended_type_info.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/extended_type_info_no_rtti.cpp -o boost_serialization/extended_type_info_no_rtti.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/extended_type_info_typeid.cpp -o boost_serialization/extended_type_info_typeid.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/polymorphic_iarchive.cpp -o boost_serialization/polymorphic_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/polymorphic_oarchive.cpp -o boost_serialization/polymorphic_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/stl_port.cpp -o boost_serialization/stl_port.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/text_iarchive.cpp -o boost_serialization/text_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/text_oarchive.cpp -o boost_serialization/text_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/text_wiarchive.cpp -o boost_serialization/text_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/text_woarchive.cpp -o boost_serialization/text_woarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/utf8_codecvt_facet.cpp -o boost_serialization/utf8_codecvt_facet.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/void_cast.cpp -o boost_serialization/void_cast.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_archive_exception.cpp -o boost_serialization/xml_archive_exception.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_grammar.cpp -o boost_serialization/xml_grammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_iarchive.cpp -o boost_serialization/xml_iarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_oarchive.cpp -o boost_serialization/xml_oarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_wgrammar.cpp -o boost_serialization/xml_wgrammar.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_wiarchive.cpp -o boost_serialization/xml_wiarchive.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -Iboost_serialization -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/BH/include" -fPIC -mtune=core2 -g -O2 -Wall -c boost_serialization/xml_woarchive.cpp -o boost_serialization/xml_woarchive.o
ar rs libboost_serialization.a boost_serialization/archive_exception.o boost_serialization/basic_archive.o boost_serialization/basic_iarchive.o boost_serialization/basic_iserializer.o boost_serialization/basic_oarchive.o boost_serialization/basic_oserializer.o boost_serialization/basic_pointer_iserializer.o boost_serialization/basic_pointer_oserializer.o boost_serialization/basic_serializer_map.o boost_serialization/basic_text_iprimitive.o boost_serialization/basic_text_oprimitive.o boost_serialization/basic_text_wiprimitive.o boost_serialization/basic_text_woprimitive.o boost_serialization/basic_xml_archive.o boost_serialization/binary_iarchive.o boost_serialization/binary_oarchive.o boost_serialization/binary_wiarchive.o boost_serialization/binary_woarchive.o boost_serialization/codecvt_null.o boost_serialization/extended_type_info.o boost_serialization/extended_type_info_no_rtti.o boost_serialization/extended_type_info_typeid.o boost_serialization/polymorphic_iarchive.o boost_serialization/polymorphic_oarchive.o boost_serialization/stl_port.o boost_serialization/text_iarchive.o boost_serialization/text_oarchive.o boost_serialization/text_wiarchive.o boost_serialization/text_woarchive.o boost_serialization/utf8_codecvt_facet.o boost_serialization/void_cast.o boost_serialization/xml_archive_exception.o boost_serialization/xml_grammar.o boost_serialization/xml_iarchive.o boost_serialization/xml_oarchive.o boost_serialization/xml_wgrammar.o boost_serialization/xml_wiarchive.o boost_serialization/xml_woarchive.o
ar: creating archive libboost_serialization.a
/usr/bin/ranlib: file: libboost_serialization.a(stl_port.o) has no symbols
ar rs libprotobuf.a pb_build/src/google/protobuf/.libs/*.o pb_build/src/google/protobuf/stubs/.libs/*.o pb_build/src/google/protobuf/io/.libs/*.o
ar: creating archive libprotobuf.a
/usr/bin/ranlib: file: libprotobuf.a(atomicops_internals_x86_gcc.o) has no symbols
/usr/bin/ranlib: file: libprotobuf.a(atomicops_internals_x86_msvc.o) has no symbols
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 GatingSet.pb.o POPINDICES.o R_API.o R_GatingHierarchy.o R_GatingSet.o RcppExports.o calibrationTable.o delimitedMessage.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o libboost_serialization.a libprotobuf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/flowCore/lib/libboost_regex.a -lxml2 -lz -lpthread -licucore -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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)