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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RProtoBufLib.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RProtoBufLib_2.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RProtoBufLib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RProtoBufLib’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RProtoBufLib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.9Mb
  sub-directories of 1Mb or more:
    include   3.1Mb
    lib       9.7Mb
* 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 ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... WARNING
---- unloading
Warning message:
.onUnload failed in unloadNamespace() for 'RProtoBufLib', details:
  call: dll[["path"]]
  error: subscript out of bounds 
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RProtoBufLib
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking target system type... x86_64-apple-darwin18.7.0
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 '505' 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 whether make supports nested variables... (cached) yes
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 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 -mmacosx-version-min=10.13... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++14... gcc3
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -E
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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
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checking the archiver (ar) interface... ar
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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: -Wall -g -O2
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
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checking for fgrep... /usr/bin/grep -F
checking for ld used by clang -mmacosx-version-min=10.13... /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... 196608
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 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 -mmacosx-version-min=10.13 object... ok
checking for sysroot... no
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checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
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checking for -force_load linker flag... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 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++ -mmacosx-version-min=10.13 -std=gnu++14 -E
checking for ld used by clang++ -mmacosx-version-min=10.13 -std=gnu++14... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++14 option to produce PIC... -fno-common -DPIC
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 PIC flag -fno-common -DPIC works... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 static flag -static works... no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 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++ -mmacosx-version-min=10.13 -std=gnu++14 supports C++11 features by default... yes
checking whether -latomic is needed... no
checking whether clang -mmacosx-version-min=10.13 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-3.13-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++14' 'CXXFLAGS=-Wall -g -O2' 'CC=clang -mmacosx-version-min=10.13' 'CFLAGS=-Wall -g -O2' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... build-aux/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 that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
=== configuring in googletest (/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googletest)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++14' 'CXXFLAGS=-Wall -g -O2' 'CC=clang -mmacosx-version-min=10.13' 'CFLAGS=-Wall -g -O2' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... build-aux/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 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 -mmacosx-version-min=10.13... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++14... gcc3
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang -mmacosx-version-min=10.13... /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... rm: conftest.dSYM: is a directory
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 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 ar... ar
checking for archiver @FILE support... rm: conftest.dSYM: is a directory
no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... rm: conftest.dSYM: is a directory
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 how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 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++ -mmacosx-version-min=10.13 -std=gnu++14 -E
checking for ld used by clang++ -mmacosx-version-min=10.13 -std=gnu++14... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++14 option to produce PIC... -fno-common -DPIC
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 PIC flag -fno-common -DPIC works... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 static flag -static works... no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for python... /usr/bin/python
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 that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gtest-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in googlemock (/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googlemock)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build'  '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=clang++ -mmacosx-version-min=10.13 -std=gnu++14' 'CXXFLAGS=-Wall -g -O2' 'CC=clang -mmacosx-version-min=10.13' 'CFLAGS=-Wall -g -O2' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... build-aux/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking whether clang -mmacosx-version-min=10.13 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 -mmacosx-version-min=10.13... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
checking dependency style of clang++ -mmacosx-version-min=10.13 -std=gnu++14... gcc3
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by clang -mmacosx-version-min=10.13... /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... rm: conftest.dSYM: is a directory
BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 196608
checking how to convert x86_64-apple-darwin18.7.0 file names to x86_64-apple-darwin18.7.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin18.7.0 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 ar... ar
checking for archiver @FILE support... rm: conftest.dSYM: is a directory
no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... rm: conftest.dSYM: is a directory
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 how to run the C preprocessor... clang -mmacosx-version-min=10.13 -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if clang -mmacosx-version-min=10.13 supports -fno-rtti -fno-exceptions... yes
checking for clang -mmacosx-version-min=10.13 option to produce PIC... -fno-common -DPIC
checking if clang -mmacosx-version-min=10.13 PIC flag -fno-common -DPIC works... yes
checking if clang -mmacosx-version-min=10.13 static flag -static works... no
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... yes
checking if clang -mmacosx-version-min=10.13 supports -c -o file.o... (cached) yes
checking whether the clang -mmacosx-version-min=10.13 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 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++ -mmacosx-version-min=10.13 -std=gnu++14 -E
checking for ld used by clang++ -mmacosx-version-min=10.13 -std=gnu++14... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for clang++ -mmacosx-version-min=10.13 -std=gnu++14 option to produce PIC... -fno-common -DPIC
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 PIC flag -fno-common -DPIC works... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 static flag -static works... no
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... yes
checking if clang++ -mmacosx-version-min=10.13 -std=gnu++14 supports -c -o file.o... (cached) yes
checking whether the clang++ -mmacosx-version-min=10.13 -std=gnu++14 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
checking for python... /usr/bin/python
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 for gtest-config... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating scripts/gmock-config
config.status: creating build-aux/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making install in .
make[2]: Nothing to be done for `install-exec-am'.
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Making install in src
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google/protobuf/compiler/cpp/cpp_helpers.cc:171:6: warning: function 'Base63Char' is not needed and will not be emitted [-Wunneeded-internal-declaration]
char Base63Char(int value) {
     ^
1 warning generated.
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In file included from google/protobuf/compiler/csharp/csharp_source_generator_base.cc:39:
./google/protobuf/compiler/csharp/csharp_source_generator_base.h:62:25: warning: private field 'descriptor_' is not used [-Wunused-private-field]
  const FileDescriptor* descriptor_;
                        ^
1 warning generated.
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libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.24.dylib /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.24.dylib
libtool: install: (cd /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.24.dylib libprotobuf-lite.dylib || { rm -f libprotobuf-lite.dylib && ln -s libprotobuf-lite.24.dylib libprotobuf-lite.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.lai /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.24.dylib /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.24.dylib
libtool: install: (cd /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf.24.dylib libprotobuf.dylib || { rm -f libprotobuf.dylib && ln -s libprotobuf.24.dylib libprotobuf.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: install: /usr/bin/install -c .libs/libprotoc.24.dylib /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.24.dylib
libtool: install: (cd /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotoc.24.dylib libprotoc.dylib || { rm -f libprotoc.dylib && ln -s libprotoc.24.dylib libprotoc.dylib; }; })
libtool: install: /usr/bin/install -c .libs/libprotoc.lai /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.la
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c protoc '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/bin'
libtool: install: /usr/bin/install -c .libs/protoc /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/bin/protoc
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/install -c -m 644  google/protobuf/compiler/plugin.proto '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/python'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-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-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 /usr/bin/install -c -m 644  google/protobuf/io/io_win32.h 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-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/java'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util'
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 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby'
 /usr/bin/install -c -m 644  google/protobuf/compiler/ruby/ruby_generator.h '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp'
 /usr/bin/install -c -m 644  google/protobuf/compiler/csharp/csharp_generator.h google/protobuf/compiler/csharp/csharp_names.h '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp'
 .././install-sh -c -d '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/js'
 /usr/bin/install -c -m 644  google/protobuf/compiler/js/js_generator.h google/protobuf/compiler/js/well_known_types_embed.h '/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/js'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -fPIC -I../inst/include/ -I/Users/biocbuild/bbs-3.13-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/4.1/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/google /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf* /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
cp GatingSet_pb_lib/libGatingSet.pb.dylib /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.dylib
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/Users/biocbuild/bbs-3.13-bioc/meat/RProtoBufLib/src/pb_build/include/  -I/usr/local/include   -fPIC  -Wall -g -O2  -c dummy.cpp -o dummy.o
clang++ -mmacosx-version-min=10.13 -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 RProtoBufLib.so dummy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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)