Multiple platform build/check report for BioC 3.15 - BUILD BIN results for RProtoBufLib on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
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###
### Running command:
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###   rm -rf RProtoBufLib.buildbin-libdir && mkdir RProtoBufLib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RProtoBufLib_2.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RProtoBufLib.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RProtoBufLib.buildbin-libdir RProtoBufLib_2.8.0.tar.gz'
>>>>>>> 

* 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 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
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rm: conftest.dSYM: is a directory
yes
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checking the name lister (/usr/bin/nm -B) interface... BSD nm
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checking how to convert x86_64-apple-darwin18.7.0 file names to toolchain format... func_convert_file_noop
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checking how to recognize dependent libraries... pass_all
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checking command to parse /usr/bin/nm -B output from clang -mmacosx-version-min=10.13 object... ok
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checking dynamic linker characteristics... darwin18.7.0 dyld
checking how to hardcode library paths into programs... immediate
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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
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checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
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checking for ftruncate... yes
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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 (/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/pkgconfig'
 /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/pkgconfig'
Making install in src
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libtool: compile:  clang++ -mmacosx-version-min=10.13 -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -Wall -g -O2 -MT google/protobuf/util/internal/default_value_objectwriter.lo -MD -MP -MF google/protobuf/util/internal/.deps/default_value_objectwriter.Tpo -c google/protobuf/util/internal/default_value_objectwriter.cc  -fno-common -DPIC -o google/protobuf/util/internal/.libs/default_value_objectwriter.o
In file included from google/protobuf/util/internal/default_value_objectwriter.cc:31:
./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);
                                    ^
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  virtual ObjectWriter* RenderNull(StringPiece name) = 0;
                        ^
1 warning generated.
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libtool: compile:  clang++ -mmacosx-version-min=10.13 -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -Wall -g -O2 -MT google/protobuf/util/internal/json_objectwriter.lo -MD -MP -MF google/protobuf/util/internal/.deps/json_objectwriter.Tpo -c google/protobuf/util/internal/json_objectwriter.cc  -fno-common -DPIC -o google/protobuf/util/internal/.libs/json_objectwriter.o
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
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                        ^
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++ -mmacosx-version-min=10.13 -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -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++ -mmacosx-version-min=10.13 -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -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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/bin/sh ../libtool  --tag=CXX   --mode=link clang++ -mmacosx-version-min=10.13 -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -Wall -g -O2 -pthread  -o protoc google/protobuf/compiler/main.o  libprotobuf.la libprotoc.la -lz 
libtool: link: clang++ -mmacosx-version-min=10.13 -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -Wall -g -O2 -pthread -o .libs/protoc google/protobuf/compiler/main.o -Wl,-bind_at_load  ./.libs/libprotobuf.dylib ./.libs/libprotoc.dylib /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/protobuf-3.8.0/src/.libs/libprotobuf.dylib -lz -pthread
/bin/sh ../libtool  --tag=CXX   --mode=link clang++ -mmacosx-version-min=10.13 -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare  -Wall -g -O2 -version-info 19:0:0 -export-dynamic -no-undefined   -o libprotobuf-lite.la -rpath /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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++ -mmacosx-version-min=10.13 -std=gnu++14 -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   -lz  -mmacosx-version-min=10.13 -pthread -g -O2   -pthread -install_name  /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libprotobuf-lite.la libprotobuf.la libprotoc.la '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib'
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.19.dylib /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.19.dylib
libtool: install: (cd /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.19.dylib /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotobuf.19.dylib
libtool: install: (cd /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: install: /usr/bin/install -c .libs/libprotoc.19.dylib /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotoc.19.dylib
libtool: install: (cd /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotoc.la
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/install -c protoc '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/bin'
libtool: install: /usr/bin/install -c .libs/protoc /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/bin/protoc
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 /usr/bin/install -c -m 644  google/protobuf/compiler/plugin.proto '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
 /usr/bin/install -c -m 644  google/protobuf/compiler/cpp/cpp_generator.h '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/io'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
 .././install-sh -c -d '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 '/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google/protobuf/util'
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/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.dylib GatingSet_pb_lib/GatingSet.pb.cc
mkdir -p "/Users/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/include/google /Users/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/Users/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/RProtoBufLib/src/pb_build/lib/libprotobuf* /Users/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
cp GatingSet_pb_lib/libGatingSet.pb.dylib /Users/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.buildbin-libdir/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/private/tmp/Rtmp6C3l5M/R.INSTALL5738767b10a5/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 /Users/biocbuild/bbs-3.15-bioc/meat/RProtoBufLib.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING LINKS FOR RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so"
BUILD BIN results for RProtoBufLib on merida1

Summary

Command output
