flowWorkspace 3.24.4
Greg Finak ,Mike Jiang
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/flowWorkspace | | Last Changed Rev: 131240 / Revision: 131943 | | Last Changed Date: 2017-07-14 17:48:43 -0400 (Fri, 14 Jul 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / 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 INSTALL flowWorkspace
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* 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=gnu++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.
untarring protobuf ...
glibtoolize: putting auxiliary files in '.'.
glibtoolize: copying file './ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIRS, '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'
configure.ac:45: installing './compile'
configure.ac:32: installing './missing'
/usr/local/Cellar/automake/1.15/share/automake-1.15/am/ltlibrary.am: warning: 'libprotobuf.la': linking libtool libraries using a non-POSIX
/usr/local/Cellar/automake/1.15/share/automake-1.15/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...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking target system type... x86_64-apple-darwin15.6.0
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checking for suffix of executables...
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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
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checking whether clang++ -std=gnu++11 accepts -g... yes
checking dependency style of clang++ -std=gnu++11... gcc3
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rm: conftest.dSYM: is a directory
yes
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checking C++ compiler flags...... use user-supplied: -Wall -g -O2
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checking whether ln -s works... yes
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checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
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checking if libtool supports shared libraries... yes
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checking how to run the C++ preprocessor... clang++ -std=gnu++11 -E
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checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
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checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
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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: executing depfiles commands
config.status: executing libtool commands
CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/sh /Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace/src/protobuf-2.6.0/missing aclocal-1.15 -I m4
cd ../protobuf-2.6.0 && /bin/sh /Users/biocbuild/bbs-3.5-bioc/meat/flowWorkspace/src/protobuf-2.6.0/missing automake-1.15 --foreign
CDPATH="${ZSH_VERSION+.}:" && cd ../protobuf-2.6.0 && /bin/sh /Users/biocbuild/bbs-3.5-bioc/meat/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=gnu++11 CXXFLAGS=-Wall -g -O2 CC=clang CFLAGS=-Wall -g -O2 --no-create --no-recursion
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking target system type... x86_64-apple-darwin15.6.0
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 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=gnu++11 accepts -g... yes
checking dependency style of clang++ -std=gnu++11... gcc3
checking how to run the C++ preprocessor... clang++ -std=gnu++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 -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... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) 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-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin15.6.0 file names to toolchain format... func_convert_file_noop
checking for /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 -B 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
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checking if clang supports -c -o file.o... yes
checking if clang supports -c -o file.o... (cached) yes
checking whether the clang linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 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=gnu++11 -E
checking for ld used by clang++ -std=gnu++11... /usr/bin/ld
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checking whether the clang++ -std=gnu++11 linker (/usr/bin/ld) supports shared libraries... yes
checking for clang++ -std=gnu++11 option to produce PIC... -fno-common -DPIC
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checking if clang++ -std=gnu++11 static flag -static works... no
checking if clang++ -std=gnu++11 supports -c -o file.o... yes
checking if clang++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the clang++ -std=gnu++11 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 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
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checking that generated files are newer than configure... done
configure: creating ./config.status
/bin/sh ./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-3.5-bioc/meat/flowWorkspace/src/protobuf-2.6.0/missing autoheader)
rm -f stamp-h1
touch ../protobuf-2.6.0/config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
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 clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/atomicops_internals_x86_gcc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_gcc.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_gcc.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/atomicops_internals_x86_gcc.o
depbase=`echo google/protobuf/stubs/atomicops_internals_x86_msvc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/atomicops_internals_x86_msvc.lo -MD -MP -MF google/protobuf/stubs/.deps/atomicops_internals_x86_msvc.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_msvc.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/atomicops_internals_x86_msvc.o
depbase=`echo google/protobuf/stubs/common.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/common.lo -MD -MP -MF google/protobuf/stubs/.deps/common.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/common.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/common.o
depbase=`echo google/protobuf/stubs/once.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/once.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/once.lo ../../protobuf-2.6.0/src/google/protobuf/stubs/once.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/once.lo -MD -MP -MF google/protobuf/stubs/.deps/once.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/once.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/once.o
depbase=`echo google/protobuf/stubs/stringprintf.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/stringprintf.lo -MD -MP -MF google/protobuf/stubs/.deps/stringprintf.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/stringprintf.o
../../protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc:164:59: warning: unused typedef 'arg_count_mismatch' [-Wunused-local-typedef]
GOOGLE_COMPILE_ASSERT(kStringPrintfVectorMaxArgs == 32, arg_count_mismatch);
^
1 warning generated.
depbase=`echo google/protobuf/extension_set.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/extension_set.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/extension_set.lo ../../protobuf-2.6.0/src/google/protobuf/extension_set.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/extension_set.lo -MD -MP -MF google/protobuf/.deps/extension_set.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/extension_set.cc -fno-common -DPIC -o google/protobuf/.libs/extension_set.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/extension_set.cc:43:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
^
2 warnings generated.
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:846:21: warning: unused function 'PlaceNum' [-Wunused-function]
static inline char* PlaceNum(char* p, int num, char prev_sep) {
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:33:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:1172:39: warning: unused typedef 'DBL_DIG_is_too_big' [-Wunused-local-typedef]
GOOGLE_COMPILE_ASSERT(DBL_DIG < 20, DBL_DIG_is_too_big);
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc:1227:39: warning: unused typedef 'FLT_DIG_is_too_big' [-Wunused-local-typedef]
GOOGLE_COMPILE_ASSERT(FLT_DIG < 10, FLT_DIG_is_too_big);
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libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/stubs/substitute.lo -MD -MP -MF google/protobuf/stubs/.deps/substitute.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.cc -fno-common -DPIC -o google/protobuf/stubs/.libs/substitute.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.cc:33:
In file included from ../../protobuf-2.6.0/src/google/protobuf/stubs/substitute.h:36:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
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2 warnings generated.
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In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor.cc:57:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
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In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor.cc:59:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
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../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
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4 warnings generated.
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In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.cc:41:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
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../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
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In file included from ../../protobuf-2.6.0/src/google/protobuf/descriptor_database.cc:43:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
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../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
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4 warnings generated.
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libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/message.lo -MD -MP -MF google/protobuf/.deps/message.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/message.cc -fno-common -DPIC -o google/protobuf/.libs/message.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/message.cc:50:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/message.cc:51:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
^
4 warnings generated.
depbase=`echo google/protobuf/reflection_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/reflection_ops.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/reflection_ops.lo ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/reflection_ops.lo -MD -MP -MF google/protobuf/.deps/reflection_ops.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.cc -fno-common -DPIC -o google/protobuf/.libs/reflection_ops.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/reflection_ops.cc:42:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
^
2 warnings generated.
depbase=`echo google/protobuf/service.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/service.lo -MD -MP -MF google/protobuf/.deps/service.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/service.cc -fno-common -DPIC -o google/protobuf/.libs/service.o
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/text_format.lo -MD -MP -MF google/protobuf/.deps/text_format.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/text_format.cc -fno-common -DPIC -o google/protobuf/.libs/text_format.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/text_format.cc:53:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
^
In file included from ../../protobuf-2.6.0/src/google/protobuf/text_format.cc:54:
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:356:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
^
../../protobuf-2.6.0/src/google/protobuf/stubs/map_util.h:367:43: warning: unused typedef 'value_type' [-Wunused-local-typedef]
typedef typename Collection::value_type value_type;
^
4 warnings generated.
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libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/unknown_field_set.lo -MD -MP -MF google/protobuf/.deps/unknown_field_set.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/unknown_field_set.cc -fno-common -DPIC -o google/protobuf/.libs/unknown_field_set.o
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/wire_format.lo -MD -MP -MF google/protobuf/.deps/wire_format.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/wire_format.cc -fno-common -DPIC -o google/protobuf/.libs/wire_format.o
../../protobuf-2.6.0/src/google/protobuf/wire_format.cc:60:12: warning: unused function 'GetEnumNumber' [-Wunused-function]
inline int GetEnumNumber(const EnumValueDescriptor* descriptor) {
^
1 warning generated.
depbase=`echo google/protobuf/io/gzip_stream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 &&\
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libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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
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mv -f $depbase.Tpo $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/printer.lo -MD -MP -MF google/protobuf/io/.deps/printer.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/printer.cc -fno-common -DPIC -o google/protobuf/io/.libs/printer.o
depbase=`echo google/protobuf/io/strtod.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/strtod.lo -MD -MP -MF google/protobuf/io/.deps/strtod.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/strtod.cc -fno-common -DPIC -o google/protobuf/io/.libs/strtod.o
depbase=`echo google/protobuf/io/tokenizer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 $depbase.Plo
libtool: compile: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -MT google/protobuf/io/tokenizer.lo -MD -MP -MF google/protobuf/io/.deps/tokenizer.Tpo -c ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.cc -fno-common -DPIC -o google/protobuf/io/.libs/tokenizer.o
In file included from ../../protobuf-2.6.0/src/google/protobuf/io/tokenizer.cc:96:
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:341:25: warning: unused typedef 'sizeof_int64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_int64_is_not_sizeof_long_long);
^
../../protobuf-2.6.0/src/google/protobuf/stubs/strutil.h:347:25: warning: unused typedef 'sizeof_uint64_is_not_sizeof_long_long' [-Wunused-local-typedef]
sizeof_uint64_is_not_sizeof_long_long);
^
2 warnings generated.
depbase=`echo google/protobuf/io/zero_copy_stream_impl.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool --tag=CXX --mode=compile clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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: clang++ -std=gnu++11 -DHAVE_CONFIG_H -I. -I../../protobuf-2.6.0/src -I.. -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -g -O2 -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 clang++ -std=gnu++11 -D_THREAD_SAFE -Wall -Wwrite-strings -Woverloaded-virtual -Wno-sign-compare -Wno-return-type -Wall -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: clang++ -std=gnu++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 -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/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900
configure: PB_INCLUDE=protobuf-2.6.0/src
configure: PKG_LIBS=-lxml2 -lz -lpthread -licucore -lm
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace"
cp include/* /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include/flowWorkspace
cp -r protobuf-2.6.0/src/google /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include
cp GatingSet.pb.h /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/include #GatingSet.pb.h is autogenerated by protoc and thus kept at the same folder as GatingSet.proto
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from POPINDICES.cpp:8:
In file included from ./include/POPINDICES.hpp:15:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: 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!"));
˜^˜
6 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./../inst/include/../../src/include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c compensation.cpp -o compensation.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c delimitedMessage.cpp -o delimitedMessage.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c flowData.cpp -o flowData.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c gate.cpp -o gate.o
In file included from gate.cpp:10:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c getSingleCellExpression.cpp -o getSingleCellExpression.o
In file included from getSingleCellExpression.cpp:2:
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:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c global.cpp -o global.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c spline.cpp -o spline.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -g -O2 -c transformation.cpp -o transformation.o
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();
^
5 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: 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;
^
3 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -I/usr/include/libxml2 -Iprotobuf-2.6.0/src -ftemplate-depth=900 -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I/usr/local/include -fPIC -Wall -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:
./include/gate.hpp:440:60: warning: field 'quadrant' will be initialized after field 'interpolated' [-Wreorder]
CurlyGuadGate(paramPoly _inter, QUAD _quad):polygonGate(),quadrant(_quad),interpolated(false){
^
1 warning generated.
mkdir -p "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libprotobuf.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libprotobuf.a(atomicops_internals_x86_gcc.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libprotobuf.a(atomicops_internals_x86_msvc.o) has no symbols
mkdir -p "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib"
ar rs "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a" 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 ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o
ar: creating archive /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libflowWorkspace.a
clang++ -std=gnu++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 ellipse2points.o flowData.o flowJoWorkspace.o gate.o getSingleCellExpression.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o /Library/Frameworks/R.framework/Versions/3.4/Resources/library/flowWorkspace/lib/libprotobuf.a /Library/Frameworks/R.framework/Versions/3.4/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 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/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)