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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RProtoBufLib_2.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RProtoBufLib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RProtoBufLib’ version ‘2.18.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RProtoBufLib’ can be installed ... WARNING
Found the following significant warnings:
  ./google/protobuf/util/internal/default_value_objectwriter.h:122:37: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:98:29: warning: 'StartObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:99:29: warning: 'EndObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:100:29: warning: 'StartList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:101:29: warning: 'EndList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:102:29: warning: 'RenderBool' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:103:29: warning: 'RenderInt32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:104:29: warning: 'RenderUint32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:105:29: warning: 'RenderInt64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:106:29: warning: 'RenderUint64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:107:29: warning: 'RenderDouble' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:108:29: warning: 'RenderFloat' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:109:29: warning: 'RenderString' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:111:29: warning: 'RenderBytes' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  ./google/protobuf/util/internal/json_objectwriter.h:112:29: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  google/protobuf/compiler/cpp/cpp_helpers.cc:171:6: warning: function 'Base63Char' is not needed and will not be emitted [-Wunneeded-internal-declaration]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 13.4Mb
  sub-directories of 1Mb or more:
    include   2.8Mb
    lib      10.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  BSD_3_clause
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'RProtoBufLib', details:
  call: dll[["path"]]
  error: subscript out of bounds 
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RProtoBufLib
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... clang -arch x86_64
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 -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking target system type... x86_64-apple-darwin21.6.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./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 whether UID '503' is supported by ustar format... yes
checking whether GID '20' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking for gcc... clang -arch x86_64
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 -arch x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking whether clang -arch x86_64 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of clang -arch x86_64... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
checking dependency style of clang++ -arch x86_64 -std=gnu++17... gcc3
checking how to run the C preprocessor... clang -arch x86_64 -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++17 -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -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 for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... yes
checking whether gcc accepts -g... yes
checking dependency style of gcc... gcc3
checking C++ compiler flags...... use user-supplied: -falign-functions=64 -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 -arch x86_64... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/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... 786432
checking how to convert x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
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 archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang -arch x86_64 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 -arch x86_64 supports -fno-rtti -fno-exceptions... yes
checking for clang -arch x86_64 option to produce PIC... -fno-common -DPIC
checking if clang -arch x86_64 PIC flag -fno-common -DPIC works... yes
checking if clang -arch x86_64 static flag -static works... no
checking if clang -arch x86_64 supports -c -o file.o... yes
checking if clang -arch x86_64 supports -c -o file.o... (cached) yes
checking whether the clang -arch x86_64 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin21.6.0 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++ -arch x86_64 -std=gnu++17 -E
checking for ld used by clang++ -arch x86_64 -std=gnu++17... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -arch x86_64 -std=gnu++17 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -arch x86_64 -std=gnu++17 option to produce PIC... -fno-common -DPIC
checking if clang++ -arch x86_64 -std=gnu++17 PIC flag -fno-common -DPIC works... yes
checking if clang++ -arch x86_64 -std=gnu++17 static flag -static works... no
checking if clang++ -arch x86_64 -std=gnu++17 supports -c -o file.o... yes
checking if clang++ -arch x86_64 -std=gnu++17 supports -c -o file.o... (cached) yes
checking whether the clang++ -arch x86_64 -std=gnu++17 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin21.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether the linker supports version scripts... no
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 whether clang++ -arch x86_64 -std=gnu++17 supports C++11 features by default... yes
checking whether -latomic is needed... no
checking whether clang -arch x86_64 is Clang... yes
checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
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 benchmarks/Makefile
config.status: creating conformance/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
=== configuring in third_party/googletest (/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/protobuf-3.8.0/third_party/googletest)
configure: WARNING: no configuration information is in third_party/googletest
Making install in .
make[2]: Nothing to be done for `install-exec-am'.
 ./install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/pkgconfig'
 /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/pkgconfig'
Making install in src
depbase=`echo google/protobuf/compiler/main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/compiler/main.o -MD -MP -MF $depbase.Tpo -c -o google/protobuf/compiler/main.o google/protobuf/compiler/main.cc &&\
	mv -f $depbase.Tpo $depbase.Po
depbase=`echo google/protobuf/stubs/bytestream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/bytestream.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/bytestream.lo google/protobuf/stubs/bytestream.cc &&\
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/bytestream.lo -MD -MP -MF google/protobuf/stubs/.deps/bytestream.Tpo -c google/protobuf/stubs/bytestream.cc  -fno-common -DPIC -o google/protobuf/stubs/.libs/bytestream.o
depbase=`echo google/protobuf/stubs/common.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/common.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/common.lo google/protobuf/stubs/common.cc &&\
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/common.lo -MD -MP -MF google/protobuf/stubs/.deps/common.Tpo -c google/protobuf/stubs/common.cc  -fno-common -DPIC -o google/protobuf/stubs/.libs/common.o
depbase=`echo google/protobuf/stubs/int128.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/int128.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/int128.lo google/protobuf/stubs/int128.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/int128.lo -MD -MP -MF google/protobuf/stubs/.deps/int128.Tpo -c google/protobuf/stubs/int128.cc  -fno-common -DPIC -o google/protobuf/stubs/.libs/int128.o
depbase=`echo google/protobuf/io/io_win32.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/io/io_win32.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/io/io_win32.lo google/protobuf/io/io_win32.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/io/io_win32.lo -MD -MP -MF google/protobuf/io/.deps/io_win32.Tpo -c google/protobuf/io/io_win32.cc  -fno-common -DPIC -o google/protobuf/io/.libs/io_win32.o
depbase=`echo google/protobuf/stubs/status.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/status.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/status.lo google/protobuf/stubs/status.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/status.lo -MD -MP -MF google/protobuf/stubs/.deps/status.Tpo -c google/protobuf/stubs/status.cc  -fno-common -DPIC -o google/protobuf/stubs/.libs/status.o
depbase=`echo google/protobuf/stubs/statusor.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ../libtool  --tag=CXX   --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I..   -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/statusor.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/stubs/statusor.lo google/protobuf/stubs/statusor.cc &&\
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/stubs/statusor.lo -MD -MP -MF google/protobuf/stubs/.deps/statusor.Tpo -c google/protobuf/stubs/statusor.cc  -fno-common -DPIC -o google/protobuf/stubs/.libs/statusor.o
depbase=`echo google/protobuf/stubs/stringpiece.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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In file included from google/protobuf/util/internal/default_value_objectwriter.cc:31:
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  virtual ObjectWriter* RenderNull(StringPiece name) = 0;
                        ^
1 warning generated.
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In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:98:29: warning: 'StartObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* StartObject(StringPiece name);
                            ^
./google/protobuf/util/internal/object_writer.h:65:25: note: overridden virtual function is here
  virtual ObjectWriter* StartObject(StringPiece name) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:99:29: warning: 'EndObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* EndObject();
                            ^
./google/protobuf/util/internal/object_writer.h:68:25: note: overridden virtual function is here
  virtual ObjectWriter* EndObject() = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:100:29: warning: 'StartList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* StartList(StringPiece name);
                            ^
./google/protobuf/util/internal/object_writer.h:71:25: note: overridden virtual function is here
  virtual ObjectWriter* StartList(StringPiece name) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:101:29: warning: 'EndList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* EndList();
                            ^
./google/protobuf/util/internal/object_writer.h:74:25: note: overridden virtual function is here
  virtual ObjectWriter* EndList() = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:102:29: warning: 'RenderBool' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderBool(StringPiece name, bool value);
                            ^
./google/protobuf/util/internal/object_writer.h:77:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderBool(StringPiece name, bool value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:103:29: warning: 'RenderInt32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderInt32(StringPiece name, int32 value);
                            ^
./google/protobuf/util/internal/object_writer.h:80:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderInt32(StringPiece name, int32 value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:104:29: warning: 'RenderUint32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderUint32(StringPiece name, uint32 value);
                            ^
./google/protobuf/util/internal/object_writer.h:83:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderUint32(StringPiece name, uint32 value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:105:29: warning: 'RenderInt64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderInt64(StringPiece name, int64 value);
                            ^
./google/protobuf/util/internal/object_writer.h:86:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderInt64(StringPiece name, int64 value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:106:29: warning: 'RenderUint64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderUint64(StringPiece name, uint64 value);
                            ^
./google/protobuf/util/internal/object_writer.h:89:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderUint64(StringPiece name, uint64 value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:107:29: warning: 'RenderDouble' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderDouble(StringPiece name, double value);
                            ^
./google/protobuf/util/internal/object_writer.h:92:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderDouble(StringPiece name, double value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:108:29: warning: 'RenderFloat' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderFloat(StringPiece name, float value);
                            ^
./google/protobuf/util/internal/object_writer.h:95:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderFloat(StringPiece name, float value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:109:29: warning: 'RenderString' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderString(StringPiece name,
                            ^
./google/protobuf/util/internal/object_writer.h:98:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderString(StringPiece name,
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:111:29: warning: 'RenderBytes' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderBytes(StringPiece name, StringPiece value);
                            ^
./google/protobuf/util/internal/object_writer.h:102:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderBytes(StringPiece name, StringPiece value) = 0;
                        ^
In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
./google/protobuf/util/internal/json_objectwriter.h:112:29: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderNull(StringPiece name);
                            ^
./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderNull(StringPiece name) = 0;
                        ^
14 warnings generated.
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/type_info_test_helper.lo -MD -MP -MF google/protobuf/util/internal/.deps/type_info_test_helper.Tpo -c google/protobuf/util/internal/type_info_test_helper.cc  -fno-common -DPIC -o google/protobuf/util/internal/.libs/type_info_test_helper.o
In file included from google/protobuf/util/internal/type_info_test_helper.cc:31:
In file included from ./google/protobuf/util/internal/type_info_test_helper.h:39:
./google/protobuf/util/internal/default_value_objectwriter.h:122:37: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual DefaultValueObjectWriter* RenderNull(StringPiece name);
                                    ^
./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderNull(StringPiece name) = 0;
                        ^
1 warning generated.
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/json_util.lo -MD -MP -MF google/protobuf/util/.deps/json_util.Tpo -c google/protobuf/util/json_util.cc  -fno-common -DPIC -o google/protobuf/util/.libs/json_util.o
In file included from google/protobuf/util/json_util.cc:37:
./google/protobuf/util/internal/default_value_objectwriter.h:122:37: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual DefaultValueObjectWriter* RenderNull(StringPiece name);
                                    ^
./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderNull(StringPiece name) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:98:29: warning: 'StartObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* StartObject(StringPiece name);
                            ^
./google/protobuf/util/internal/object_writer.h:65:25: note: overridden virtual function is here
  virtual ObjectWriter* StartObject(StringPiece name) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:99:29: warning: 'EndObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* EndObject();
                            ^
./google/protobuf/util/internal/object_writer.h:68:25: note: overridden virtual function is here
  virtual ObjectWriter* EndObject() = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:100:29: warning: 'StartList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* StartList(StringPiece name);
                            ^
./google/protobuf/util/internal/object_writer.h:71:25: note: overridden virtual function is here
  virtual ObjectWriter* StartList(StringPiece name) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:101:29: warning: 'EndList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* EndList();
                            ^
./google/protobuf/util/internal/object_writer.h:74:25: note: overridden virtual function is here
  virtual ObjectWriter* EndList() = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:102:29: warning: 'RenderBool' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderBool(StringPiece name, bool value);
                            ^
./google/protobuf/util/internal/object_writer.h:77:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderBool(StringPiece name, bool value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:103:29: warning: 'RenderInt32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderInt32(StringPiece name, int32 value);
                            ^
./google/protobuf/util/internal/object_writer.h:80:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderInt32(StringPiece name, int32 value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:104:29: warning: 'RenderUint32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderUint32(StringPiece name, uint32 value);
                            ^
./google/protobuf/util/internal/object_writer.h:83:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderUint32(StringPiece name, uint32 value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:105:29: warning: 'RenderInt64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderInt64(StringPiece name, int64 value);
                            ^
./google/protobuf/util/internal/object_writer.h:86:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderInt64(StringPiece name, int64 value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:106:29: warning: 'RenderUint64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderUint64(StringPiece name, uint64 value);
                            ^
./google/protobuf/util/internal/object_writer.h:89:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderUint64(StringPiece name, uint64 value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:107:29: warning: 'RenderDouble' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderDouble(StringPiece name, double value);
                            ^
./google/protobuf/util/internal/object_writer.h:92:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderDouble(StringPiece name, double value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:108:29: warning: 'RenderFloat' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderFloat(StringPiece name, float value);
                            ^
./google/protobuf/util/internal/object_writer.h:95:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderFloat(StringPiece name, float value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:109:29: warning: 'RenderString' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderString(StringPiece name,
                            ^
./google/protobuf/util/internal/object_writer.h:98:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderString(StringPiece name,
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:111:29: warning: 'RenderBytes' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderBytes(StringPiece name, StringPiece value);
                            ^
./google/protobuf/util/internal/object_writer.h:102:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderBytes(StringPiece name, StringPiece value) = 0;
                        ^
In file included from google/protobuf/util/json_util.cc:39:
./google/protobuf/util/internal/json_objectwriter.h:112:29: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override]
  virtual JsonObjectWriter* RenderNull(StringPiece name);
                            ^
./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here
  virtual ObjectWriter* RenderNull(StringPiece name) = 0;
                        ^
15 warnings generated.
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/compiler/cpp/cpp_service.lo -MD -MP -MF google/protobuf/compiler/cpp/.deps/cpp_service.Tpo -c google/protobuf/compiler/cpp/cpp_service.cc  -fno-common -DPIC -o google/protobuf/compiler/cpp/.libs/cpp_service.o
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libtool: compile:  clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/compiler/cpp/cpp_string_field.lo -MD -MP -MF google/protobuf/compiler/cpp/.deps/cpp_string_field.Tpo -c google/protobuf/compiler/cpp/cpp_string_field.cc  -fno-common -DPIC -o google/protobuf/compiler/cpp/.libs/cpp_string_field.o
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libtool: link: clang++ -arch x86_64 -std=gnu++17 -dynamiclib  -o .libs/libprotoc.19.dylib  google/protobuf/compiler/.libs/code_generator.o google/protobuf/compiler/.libs/command_line_interface.o google/protobuf/compiler/.libs/plugin.o google/protobuf/compiler/.libs/plugin.pb.o google/protobuf/compiler/.libs/subprocess.o google/protobuf/compiler/.libs/zip_writer.o google/protobuf/compiler/cpp/.libs/cpp_enum.o google/protobuf/compiler/cpp/.libs/cpp_enum_field.o google/protobuf/compiler/cpp/.libs/cpp_extension.o google/protobuf/compiler/cpp/.libs/cpp_field.o google/protobuf/compiler/cpp/.libs/cpp_file.o google/protobuf/compiler/cpp/.libs/cpp_generator.o google/protobuf/compiler/cpp/.libs/cpp_helpers.o google/protobuf/compiler/cpp/.libs/cpp_map_field.o google/protobuf/compiler/cpp/.libs/cpp_message.o google/protobuf/compiler/cpp/.libs/cpp_message_field.o google/protobuf/compiler/cpp/.libs/cpp_padding_optimizer.o google/protobuf/compiler/cpp/.libs/cpp_primitive_field.o google/protobuf/compiler/cpp/.libs/cpp_service.o google/protobuf/compiler/cpp/.libs/cpp_string_field.o   -L/opt/R/x86_64/lib ./.libs/libprotobuf.dylib -lz  -arch x86_64 -pthread -g -O2   -pthread -install_name  /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.19.dylib -compatibility_version 20 -current_version 20.0 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libprotoc.dylib" && ln -s "libprotoc.19.dylib" "libprotoc.dylib")
libtool: link: ( cd ".libs" && rm -f "libprotoc.la" && ln -s "../libprotoc.la" "libprotoc.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link clang++ -arch x86_64 -std=gnu++17 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -pthread -L/opt/R/x86_64/lib -o protoc google/protobuf/compiler/main.o  libprotobuf.la libprotoc.la -lz 
libtool: link: clang++ -arch x86_64 -std=gnu++17 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -pthread -o .libs/protoc google/protobuf/compiler/main.o  -L/opt/R/x86_64/lib ./.libs/libprotobuf.dylib ./.libs/libprotoc.dylib /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/protobuf-3.8.0/src/.libs/libprotobuf.dylib -lz -pthread
/bin/sh ../libtool  --tag=CXX   --mode=link clang++ -arch x86_64 -std=gnu++17 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -falign-functions=64 -Wall -g -O2 -version-info 19:0:0 -export-dynamic -no-undefined  -L/opt/R/x86_64/lib -o libprotobuf-lite.la -rpath /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib google/protobuf/stubs/bytestream.lo google/protobuf/stubs/common.lo google/protobuf/stubs/int128.lo google/protobuf/io/io_win32.lo google/protobuf/stubs/status.lo google/protobuf/stubs/statusor.lo google/protobuf/stubs/stringpiece.lo google/protobuf/stubs/stringprintf.lo google/protobuf/stubs/structurally_valid.lo google/protobuf/stubs/strutil.lo google/protobuf/stubs/time.lo google/protobuf/any_lite.lo google/protobuf/arena.lo google/protobuf/extension_set.lo google/protobuf/generated_message_util.lo google/protobuf/generated_message_table_driven_lite.lo google/protobuf/implicit_weak_message.lo google/protobuf/message_lite.lo google/protobuf/parse_context.lo google/protobuf/repeated_field.lo google/protobuf/wire_format_lite.lo google/protobuf/io/coded_stream.lo google/protobuf/io/strtod.lo google/protobuf/io/zero_copy_stream.lo google/protobuf/io/zero_copy_stream_impl_lite.lo   -lz 
libtool: link: clang++ -arch x86_64 -std=gnu++17 -dynamiclib  -o .libs/libprotobuf-lite.19.dylib  google/protobuf/stubs/.libs/bytestream.o google/protobuf/stubs/.libs/common.o google/protobuf/stubs/.libs/int128.o google/protobuf/io/.libs/io_win32.o google/protobuf/stubs/.libs/status.o google/protobuf/stubs/.libs/statusor.o google/protobuf/stubs/.libs/stringpiece.o google/protobuf/stubs/.libs/stringprintf.o google/protobuf/stubs/.libs/structurally_valid.o google/protobuf/stubs/.libs/strutil.o google/protobuf/stubs/.libs/time.o google/protobuf/.libs/any_lite.o google/protobuf/.libs/arena.o google/protobuf/.libs/extension_set.o google/protobuf/.libs/generated_message_util.o google/protobuf/.libs/generated_message_table_driven_lite.o google/protobuf/.libs/implicit_weak_message.o google/protobuf/.libs/message_lite.o google/protobuf/.libs/parse_context.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/strtod.o google/protobuf/io/.libs/zero_copy_stream.o google/protobuf/io/.libs/zero_copy_stream_impl_lite.o   -L/opt/R/x86_64/lib -lz  -arch x86_64 -pthread -g -O2   -pthread -install_name  /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.19.dylib -compatibility_version 20 -current_version 20.0 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libprotobuf-lite.dylib" && ln -s "libprotobuf-lite.19.dylib" "libprotobuf-lite.dylib")
libtool: link: ( cd ".libs" && rm -f "libprotobuf-lite.la" && ln -s "../libprotobuf-lite.la" "libprotobuf-lite.la" )
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib'
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libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.19.dylib /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.19.dylib
libtool: install: (cd /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.19.dylib libprotobuf-lite.dylib || { rm -f libprotobuf-lite.dylib && ln -s libprotobuf-lite.19.dylib libprotobuf-lite.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.lai /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.19.dylib /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.19.dylib
libtool: install: (cd /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf.19.dylib libprotobuf.dylib || { rm -f libprotobuf.dylib && ln -s libprotobuf.19.dylib libprotobuf.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: install: /usr/bin/install -c .libs/libprotoc.19.dylib /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.19.dylib
libtool: install: (cd /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotoc.19.dylib libprotoc.dylib || { rm -f libprotoc.dylib && ln -s libprotoc.19.dylib libprotoc.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libprotoc.lai /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.la
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c protoc '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/bin'
libtool: install: /usr/bin/install -c .libs/protoc /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/bin/protoc
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /usr/bin/install -c -m 644  google/protobuf/descriptor.proto google/protobuf/any.proto google/protobuf/api.proto google/protobuf/duration.proto google/protobuf/empty.proto google/protobuf/field_mask.proto google/protobuf/source_context.proto google/protobuf/struct.proto google/protobuf/timestamp.proto google/protobuf/type.proto google/protobuf/wrappers.proto '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/install -c -m 644  google/protobuf/compiler/plugin.proto '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /usr/bin/install -c -m 644  google/protobuf/any.pb.h google/protobuf/api.pb.h google/protobuf/any.h google/protobuf/arena.h google/protobuf/arena_impl.h google/protobuf/arenastring.h google/protobuf/descriptor_database.h google/protobuf/descriptor.h google/protobuf/descriptor.pb.h google/protobuf/duration.pb.h google/protobuf/dynamic_message.h google/protobuf/empty.pb.h google/protobuf/extension_set.h google/protobuf/extension_set_inl.h google/protobuf/field_mask.pb.h google/protobuf/generated_enum_reflection.h google/protobuf/generated_enum_util.h google/protobuf/generated_message_reflection.h google/protobuf/generated_message_table_driven.h google/protobuf/generated_message_util.h google/protobuf/has_bits.h google/protobuf/implicit_weak_message.h google/protobuf/inlined_string_field.h google/protobuf/map_entry.h google/protobuf/map_entry_lite.h google/protobuf/map_field.h google/protobuf/map_field_inl.h google/protobuf/map_field_lite.h google/protobuf/map.h google/protobuf/map_type_handler.h google/protobuf/message.h google/protobuf/message_lite.h google/protobuf/metadata.h google/protobuf/metadata_lite.h google/protobuf/parse_context.h google/protobuf/port.h google/protobuf/port_def.inc google/protobuf/port_undef.inc google/protobuf/reflection.h google/protobuf/reflection_ops.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
 /usr/bin/install -c -m 644  google/protobuf/compiler/cpp/cpp_generator.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 /usr/bin/install -c -m 644  google/protobuf/stubs/callback.h google/protobuf/stubs/bytestream.h google/protobuf/stubs/casts.h google/protobuf/stubs/common.h google/protobuf/stubs/fastmem.h google/protobuf/stubs/hash.h google/protobuf/stubs/logging.h google/protobuf/stubs/macros.h google/protobuf/stubs/mutex.h google/protobuf/stubs/once.h google/protobuf/stubs/platform_macros.h google/protobuf/stubs/port.h google/protobuf/stubs/status.h google/protobuf/stubs/stl_util.h google/protobuf/stubs/stringpiece.h google/protobuf/stubs/strutil.h google/protobuf/stubs/template_util.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 /usr/bin/install -c -m 644  google/protobuf/io/coded_stream.h google/protobuf/io/gzip_stream.h google/protobuf/io/printer.h google/protobuf/io/strtod.h google/protobuf/io/tokenizer.h google/protobuf/io/zero_copy_stream.h google/protobuf/io/zero_copy_stream_impl.h google/protobuf/io/zero_copy_stream_impl_lite.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 /usr/bin/install -c -m 644  google/protobuf/repeated_field.h google/protobuf/service.h google/protobuf/source_context.pb.h google/protobuf/struct.pb.h google/protobuf/text_format.h google/protobuf/timestamp.pb.h google/protobuf/type.pb.h google/protobuf/unknown_field_set.h google/protobuf/wire_format.h google/protobuf/wire_format_lite.h google/protobuf/wrappers.pb.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/install -c -m 644  google/protobuf/compiler/code_generator.h google/protobuf/compiler/command_line_interface.h google/protobuf/compiler/importer.h google/protobuf/compiler/parser.h google/protobuf/compiler/plugin.h google/protobuf/compiler/plugin.pb.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util'
 /usr/bin/install -c -m 644  google/protobuf/util/type_resolver.h google/protobuf/util/delimited_message_util.h google/protobuf/util/field_comparator.h google/protobuf/util/field_mask_util.h google/protobuf/util/json_util.h google/protobuf/util/time_util.h google/protobuf/util/type_resolver_util.h google/protobuf/util/message_differencer.h '/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -fPIC -I../inst/include/ -I/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.dylib GatingSet_pb_lib/GatingSet.pb.cc
mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/google /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf* /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
cp GatingSet_pb_lib/libGatingSet.pb.dylib /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.dylib
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/Users/biocbuild/bbs-3.20-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c dummy.cpp -o dummy.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o RProtoBufLib.so dummy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RProtoBufLib)