BioC 3.4: CHECK report for flowWorkspace on morelia

Package: flowWorkspace

Version: 3.19.24

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowWorkspace_3.19.24.tar.gz

StartedAt: 2016-09-20 06:40:35 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 06:45:49 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 314.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowWorkspace.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowWorkspace_3.19.24.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘3.19.24’
* 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.lo
  src/pb_build/src/google/protobuf/descriptor.pb.lo
  src/pb_build/src/google/protobuf/descriptor_database.lo
  src/pb_build/src/google/protobuf/dynamic_message.lo
  src/pb_build/src/google/protobuf/extension_set.lo
  src/pb_build/src/google/protobuf/extension_set_heavy.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.lo
  src/pb_build/src/google/protobuf/io/zero_copy_stream_impl.lo
  src/pb_build/src/google/protobuf/io/zero_copy_stream_impl_lite.lo
  src/pb_build/src/google/protobuf/message.lo
  src/pb_build/src/google/protobuf/message_lite.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.lo
  src/pb_build/src/google/protobuf/wire_format_lite.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 ... OK
* checking installed package size ... NOTE
  installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    lib   16.4Mb
    libs   3.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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:
  ‘RBGL’ ‘graphics’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘Rgraphviz:::getRenderPar’ ‘flowCore:::.estimateLogicle’
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’
  ‘flowCore:::logicle_transform’ ‘graph:::.makeEdgeKeys’
  ‘lattice:::updateList’ ‘ncdfFlow:::.isValidSamples’
  ‘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:
  ‘.load_gs’ ‘.preprocessMap’ ‘.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: 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: warning in unlist(res, recur = FALSE):
  partial argument match of 'recur' to 'recursive'
.addGatingHierarchies: no visible global function definition for ‘is’
.computeCV : <anonymous>: no visible binding for global variable
  ‘flowJo.count’
.computeCV : <anonymous>: no visible binding for global variable
  ‘flowCore.count’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘IQR’
.computeCV : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘IQR’
.computeCV_gh : <anonymous>: no visible global function definition for
  ‘median’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable ‘max_val’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable ‘decade’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable ‘offset’
.convertTrans : <anonymous> : f : <anonymous>: no visible binding for
  global variable ‘min_val’
.convertTrans : <anonymous>: multiple local function definitions for
  ‘f’ with different formal arguments
.graph_handler : asGraphNEL: no visible global function definition for
  ‘new’
.graph_handler : asGraphNEL: no visible global function definition for
  ‘validObject’
.load_gs: no visible global function definition for ‘new’
.load_gs: no visible global function definition for ‘.hasSlot’
.load_gs: no visible global function definition for ‘slot’
.mergeGates : <anonymous>: no visible global function definition for
  ‘extends’
.parse.pData: no visible binding for global variable ‘.’
.plotGate: no visible global function definition for ‘new’
.plotGate: no visible global function definition for ‘as.formula’
.plotGatingTree: no visible global function definition for ‘dev.prev’
.plotGatingTree: no visible global function definition for ‘dev.off’
.plotGatingTree: no visible global function definition for ‘dev.set’
.preplot: no visible global function definition for ‘as’
.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 : <anonymous>: no visible global function
  definition for ‘symbols’
.renderNodes.svgAnno: no visible global function definition for ‘rect’
.renderNodes.svgAnno : <anonymous>: no visible global function
  definition for ‘polygon’
.renderNodes.svgAnno: no visible global function definition for
  ‘polygon’
.renderNodes.svgAnno: no visible global function definition for
  ‘strwidth’
.renderNodes.svgAnno: no visible global function definition for
  ‘strheight’
.renderNodes.svgAnno: no visible global function definition for
  ‘dev.prev’
.renderNodes.svgAnno: no visible global function definition for
  ‘dev.off’
.renderNodes.svgAnno: no visible global function definition for
  ‘dev.set’
.renderNodes.svgAnno: no visible global function definition for ‘text’
GatingSetList: no visible global function definition for ‘as’
GatingSetList: no visible global function definition for ‘validObject’
booleanFilter: no visible global function definition for ‘new’
char2booleanFilter: no visible global function definition for ‘new’
flowWorkspace.par.init: no visible global function definition for
  ‘gray’
mkformula: no visible global function definition for ‘as.formula’
save_gslist: no visible binding for global variable ‘slot’
transformerList: no visible global function definition for ‘is’
transformerList: no visible binding for global variable ‘is’
GatingSet,GatingHierarchy-character: no visible global function
  definition for ‘new’
GatingSet,character-character: no visible global function definition
  for ‘new’
GatingSet,flowSet-ANY: no visible global function definition for ‘new’
Rm,character-GatingSetList-character: no visible global function
  definition for ‘selectMethod’
[,GatingSet-ANY: no visible global function definition for ‘extends’
[,GatingSetList-ANY: no visible global function definition for
  ‘callNextMethod’
[,GatingSetList-ANY: no visible global function definition for ‘as’
[[,GatingSet-character: no visible global function definition for ‘new’
add,GatingSet-filtersList: no visible global function definition for
  ‘selectMethod’
add,GatingSet-list : <anonymous>: no visible global function definition
  for ‘extends’
add,GatingSet-list: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filter: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filterList: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filters: no visible global function definition for
  ‘selectMethod’
add,GatingSetList-filtersList: no visible global function definition
  for ‘selectMethod’
add,GatingSetList-list: no visible global function definition for
  ‘selectMethod’
getPopStats,GatingHierarchy: no visible binding for global variable
  ‘node’
keyword,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
keyword,GatingSetList-missing: no visible global function definition
  for ‘selectMethod’
openWorkspace,character: no visible global function definition for
  ‘new’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘callNextMethod’
pData<-,GatingSetList-data.frame: no visible global function definition
  for ‘as’
plotGate,GatingSetList-character: no visible global function definition
  for ‘selectMethod’
rbind2,GatingSetList-missing: no visible global function definition for
  ‘new’
rbind2,GatingSetList-missing: no visible binding for global variable
  ‘slot’
recompute,GatingSetList: no visible global function definition for
  ‘selectMethod’
transform,GatingSet: no visible global function definition for ‘is’
Undefined global functions or variables:
  . .hasSlot IQR as as.formula callNextMethod decade dev.off dev.prev
  dev.set extends flowCore.count flowJo.count gray groupName is max_val
  median min_val new node offset old polygon rect selectMethod slot
  strheight strwidth symbols text validObject
Consider adding
  importFrom("grDevices", "dev.off", "dev.prev", "dev.set", "gray")
  importFrom("graphics", "polygon", "rect", "strheight", "strwidth",
             "symbols", "text")
  importFrom("methods", ".hasSlot", "as", "callNextMethod", "extends",
             "is", "new", "selectMethod", "slot", "validObject")
  importFrom("stats", "IQR", "as.formula", "median", "offset")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
S3 methods shown with full name in documentation object 'subset.GatingSet':
  ‘subset.GatingSet’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 8 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

* installing *source* package ‘flowWorkspace’ ...
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 clang++ -std=c++11 accepts -g... yes
checking for gcc... clang
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
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.
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt˜obsolete.m4'
configure.ac:45: installing './compile'
configure.ac:32: installing './missing'
/usr/local/share/automake-1.14/am/ltlibrary.am: warning: 'libprotobuf.la': linking libtool libraries using a non-POSIX
/usr/local/share/automake-1.14/am/ltlibrary.am: archiver requires 'AM_PROG_AR' in 'configure.ac'
src/Makefile.am:81:   while processing Libtool library 'libprotobuf.la'
src/Makefile.am: installing './depcomp'
building protobuf...
found  pb_build  ;using what is there.
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin13.4.0
checking host system type... x86_64-apple-darwin13.4.0
checking target system type... x86_64-apple-darwin13.4.0
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
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=c++11 accepts -g... yes
checking dependency style of clang++ -std=c++11... gcc3
checking how to run the C++ preprocessor... clang++ -std=c++11 -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... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking C++ compiler flags...... use user-supplied: -Wall -mtune=core2 -g -O2
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop
checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from clang object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang supports -fno-rtti -fno-exceptions... yes
checking for clang option to produce PIC... -fno-common -DPIC
checking if clang PIC flag -fno-common -DPIC works... yes
checking if clang static flag -static works... no
checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.4.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... clang++ -std=c++11 -E
checking for ld used by clang++ -std=c++11... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking whether the clang++ -std=c++11 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking for clang++ -std=c++11 option to produce PIC... -fno-common -DPIC
checking if clang++ -std=c++11 PIC flag -fno-common -DPIC works... yes
checking if clang++ -std=c++11 static flag -static works... no
checking if clang++ -std=c++11 supports -c -o file.o... yes
checking if clang++ -std=c++11 supports -c -o file.o... (cached) yes
checking whether the clang++ -std=c++11 linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin13.4.0 dyld
checking how to hardcode library paths into programs... immediate
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... -D_THREAD_SAFE
checking whether to check for GCC pthread/shared inconsistencies... no
checking whether what we have so far is sufficient with -nostdlib... no
checking whether -lpthread saves the day... no
configure: WARNING: Impossible to determine how to use pthreads with shared libraries and -nostdlib
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating protobuf.pc
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/sh /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing aclocal-1.14 -I m4
 cd ../protobuf-2.6.0 && /bin/sh /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing automake-1.14 --foreign
CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/sh /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/00_pkg_src/flowWorkspace/src/protobuf-2.6.0/missing autoconf
/bin/sh ./config.status --recheck
running CONFIG_SHELL=/bin/sh /bin/sh ../protobuf-2.6.0/configure --enable-static=no CXX=clang++ -std=c++11 CXXFLAGS=-Wall -mtune=core2 -g -O2 CC=clang CFLAGS=-Wall -mtune=core2 -g -O2 --no-create --no-recursion
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin13.4.0
checking host system type... x86_64-apple-darwin13.4.0
checking target system type... x86_64-apple-darwin13.4.0
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
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking whether clang understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking for style of include used by make... GNU
checking dependency style of clang... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=c++11 accepts -g... yes
checking dependency style of clang++ -std=c++11... gcc3
checking how to run the C++ preprocessor... clang++ -std=c++11 -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... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:846:21: warning: unused function 'PlaceNum' [-Wunused-function]
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/bin/sh ../libtool  --tag=CXX   --mode=link clang++ -std=c++11 -D_THREAD_SAFE  -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type  -Wall -mtune=core2 -g -O2 -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.dylib .libs/libprotobuf.dylib .libs/libprotobuf.la .libs/libprotobuf.lai
libtool: link: clang++ -std=c++11 -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  -mtune=core2 -g -O2   -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.la" && ln -s "../libprotobuf.la" "libprotobuf.la" )
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from GatingHierarchy.cpp:8:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from GatingHierarchy.cpp:8:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from GatingHierarchy.cpp:8:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from POPINDICES.cpp:8:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from POPINDICES.cpp:8:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from POPINDICES.cpp:8:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c R_API.cpp -o R_API.o
In file included from R_API.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from R_API.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from R_API.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
In file included from R_GatingHierarchy.cpp:17:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from R_GatingHierarchy.cpp:17:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from R_GatingHierarchy.cpp:17:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
R_GatingHierarchy.cpp:326:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)
           ˜^˜
R_GatingHierarchy.cpp:445:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
R_GatingHierarchy.cpp:475:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
R_GatingHierarchy.cpp:486:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
R_GatingHierarchy.cpp:495:6: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        if(u<0)throw(domain_error("not valid vertexID!"));
           ˜^˜
8 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c R_GatingSet.cpp -o R_GatingSet.o
In file included from R_GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from R_GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from R_GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from ./../inst/include/../../src/include/GatingSet.hpp:12:
In file included from ./../inst/include/../../src/include/GatingHierarchy.hpp:13:
In file included from ./../inst/include/../../src/include/populationTree.hpp:11:
In file included from ./../inst/include/../../src/include/nodeProperties.hpp:11:
In file included from ./../inst/include/../../src/include/POPINDICES.hpp:15:
In file included from ./../inst/include/../../src/include/gate.hpp:15:
In file included from ./../inst/include/../../src/include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from ./../inst/include/../../src/include/GatingSet.hpp:12:
In file included from ./../inst/include/../../src/include/GatingHierarchy.hpp:13:
In file included from ./../inst/include/../../src/include/populationTree.hpp:11:
In file included from ./../inst/include/../../src/include/nodeProperties.hpp:11:
In file included from ./../inst/include/../../src/include/POPINDICES.hpp:15:
In file included from ./../inst/include/../../src/include/gate.hpp:15:
In file included from ./../inst/include/../../src/include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/flowWorkspace.h:5:
In file included from ./../inst/include/../../src/include/GatingSet.hpp:12:
In file included from ./../inst/include/../../src/include/GatingHierarchy.hpp:13:
In file included from ./../inst/include/../../src/include/populationTree.hpp:11:
In file included from ./../inst/include/../../src/include/nodeProperties.hpp:11:
In file included from ./../inst/include/../../src/include/POPINDICES.hpp:15:
./../inst/include/../../src/include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c calibrationTable.cpp -o calibrationTable.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c compensation.cpp -o compensation.o
In file included from compensation.cpp:8:
In file included from ./include/compensation.hpp:10:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from compensation.cpp:8:
In file included from ./include/compensation.hpp:10:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
2 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c flowData.cpp -o flowData.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c flowJoWorkspace.cpp -o flowJoWorkspace.o
In file included from flowJoWorkspace.cpp:7:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from flowJoWorkspace.cpp:7:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from flowJoWorkspace.cpp:7:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c gate.cpp -o gate.o
In file included from gate.cpp:10:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from gate.cpp:10:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from gate.cpp:10:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c global.cpp -o global.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
In file included from macFlowJoWorkspace.cpp:9:
In file included from ./include/macFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from macFlowJoWorkspace.cpp:9:
In file included from ./include/macFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from macFlowJoWorkspace.cpp:9:
In file included from ./include/macFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c nodeProperties.cpp -o nodeProperties.o
In file included from nodeProperties.cpp:7:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from nodeProperties.cpp:7:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from nodeProperties.cpp:7:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c spline.cpp -o spline.o
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c transformation.cpp -o transformation.o
In file included from transformation.cpp:8:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from transformation.cpp:8:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
transformation.cpp:273:68: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans():transformation(false,LOG),offset(0),decade(1),T(262144), scale(1){
                                                                   ^
transformation.cpp:278:139: warning: field 'T' will be initialized after field 'scale' [-Wreorder]
logTrans::logTrans(double _offset,double _decade, unsigned _T, unsigned _scale):transformation(false,LOG),offset(_offset),decade(_decade),T(_T), scale(_scale){
                                                                                                                                          ^
transformation.cpp:281:57: warning: field 'length' will be initialized after field 'maxRange' [-Wreorder]
fasinhTrans::fasinhTrans():transformation(false,FASINH),length(256),maxRange(262144), T(262144),A(0),M(4.5){
                                                        ^
transformation.cpp:285:123: warning: field 'length' will be initialized after field 'maxRange' [-Wreorder]
fasinhTrans::fasinhTrans(double _length, double _maxRange, double _T, double _A, double _M):transformation(false, FASINH),length(_length),maxRange(_maxRange), T(_T),A(_A),M(_M){
                                                                                                                          ^
transformation.cpp:431:10: warning: unused variable 'thisMin' [-Wunused-variable]
                double thisMin=0;//input.min();
                       ^
7 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
In file included from winFlowJoWorkspace.cpp:8:
In file included from ./include/winFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from winFlowJoWorkspace.cpp:8:
In file included from ./include/winFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from winFlowJoWorkspace.cpp:8:
In file included from ./include/winFlowJoWorkspace.hpp:10:
In file included from ./include/flowJoWorkspace.hpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
winFlowJoWorkspace.cpp:561:27: warning: '/*' within block comment [-Wcomment]
 * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                          ^
winFlowJoWorkspace.cpp:545:10: warning: variable 'quad' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if(quadPattern == "--")
                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:553:42: note: uninitialized use occurs here
        CurlyGuadGate * g=new CurlyGuadGate(pp, quad);
                                                ^˜˜˜
winFlowJoWorkspace.cpp:545:7: note: remove the 'if' if its condition is always true
        else if(quadPattern == "--")
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
winFlowJoWorkspace.cpp:538:2: note: variable 'quad' is declared here
        QUAD quad;
        ^
5 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c workspace.cpp -o workspace.o
In file included from workspace.cpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from workspace.cpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from workspace.cpp:11:
In file included from ./include/workspace.hpp:14:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include"   -fPIC  -Wall -mtune=core2 -g -O2 -c wsNode.cpp -o wsNode.o
In file included from wsNode.cpp:10:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:97:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from wsNode.cpp:10:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:15:
In file included from ./include/transformation.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/regex.hpp:108:
/Library/Frameworks/R.framework/Versions/3.3/Resources/library/BH/include/boost/regex/v4/instances.hpp:124:34: warning: unknown warning group '-Wkeyword-macro', ignored [-Wunknown-pragmas]
#pragma clang diagnostic ignored "-Wkeyword-macro"
                                 ^
In file included from wsNode.cpp:10:
In file included from ./include/wsNode.hpp:10:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:414:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
        CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
                                                                  ^
3 warnings generated.
mkdir -p "/Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib"
ar rs "/Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/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 /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a(atomicops_internals_x86_gcc.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a(atomicops_internals_x86_msvc.o) has no symbols
clang++ -std=c++11 -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 -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 compensation.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 /Users/biocbuild/bbs-3.4-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/lib/libprotobuf.a /Library/Frameworks/R.framework/Versions/3.3/Resources/library/flowCore/lib/libboost_regex.a -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-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)

name	user	system	elapsed
GatingHierarchy-class	2.241	0.179	2.638
GatingSet-class	1.442	0.142	1.589
GatingSet-methods	0	0	0
GatingSetList-class	0.002	0.001	0.002
add	0.001	0.000	0.002
asinh_Gml2	0.001	0.000	0.001
asinhtGml2_trans	0.001	0.000	0.001
checkRedundantNodes	0.001	0.000	0.000
clone	0	0	0
compensate	0.000	0.000	0.001
dropRedundantChannels	0.001	0.000	0.000
dropRedundantNodes	0.000	0.000	0.001
estimateLogicle.GatingHierarchy	0.000	0.001	0.001
flowJo.fasinh	0.001	0.000	0.001
flowJoTrans	0.002	0.000	0.002
flowJoWorkspace-class	0.034	0.004	0.041
flowJo_biexp_trans	0.601	0.049	0.650
flowJo_fasinh_trans	0.001	0.000	0.001
flowWorkspace.par.get	0.001	0.000	0.000
flow_breaks	0.605	0.033	0.638
getCompensationMatrices	0.001	0.000	0.000
getData-methods	0.000	0.000	0.001
getGate	0.001	0.000	0.000
getIndices-GatingSet-name-method	0.000	0.000	0.001
getIndices	0	0	0
getKeywords	0.194	0.025	0.294
getParent	0.000	0.000	0.001
getPopStats	0.001	0.000	0.001
getSampleGroups	0.000	0.000	0.001
getSamples	0	0	0
getSingleCellExpression	0.000	0.000	0.001
getTransformations	0.001	0.000	0.001
groupByChannels	0.000	0.000	0.001
groupByTree	0.001	0.000	0.000
insertGate	0.000	0.000	0.001
keyword	0	0	0
logicleGml2_trans	0.001	0.000	0.001
logicle_trans	0.002	0.000	0.001
loglevel	0	0	0
markernames	0.001	0.000	0.000
mkformula	0.001	0.000	0.002
openWorkspace	0	0	0
parseWorkspace	0.001	0.000	0.001
plot-methods	0.000	0.000	0.001
plotGate-methods	0.001	0.000	0.001
plotPopCV	0	0	0
prettyAxis	0.001	0.000	0.001
sampleNames	0.001	0.000	0.000
save_gs	0.000	0.000	0.001
setGate	0.001	0.000	0.000
setNode-methods	0.001	0.000	0.001
transform	0	0	0
transformerList	0.009	0.000	0.009
updateChannels	0.001	0.000	0.000