##############################################################################
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###
### Running command:
###
### rm -rf RProtoBufLib.buildbin-libdir && mkdir RProtoBufLib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RProtoBufLib_2.19.0.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_2.19.0.tar.gz'
>>>>>>>
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... clang -arch arm64
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
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checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... arm-apple-darwin22.6.0
checking host system type... arm-apple-darwin22.6.0
checking target system type... arm-apple-darwin22.6.0
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checking whether more special flags are required for pthreads... no
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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
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=== configuring in third_party/googletest (/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/pkgconfig'
/usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/pkgconfig'
Making install in src
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In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
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In file included from google/protobuf/util/internal/json_objectwriter.cc:31:
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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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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);
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./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here
virtual ObjectWriter* RenderNull(StringPiece name) = 0;
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1 warning generated.
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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]
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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++ -arch arm64 -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/arm64/lib -o libprotoc.la -rpath /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib google/protobuf/compiler/code_generator.lo google/protobuf/compiler/command_line_interface.lo google/protobuf/compiler/plugin.lo google/protobuf/compiler/plugin.pb.lo google/protobuf/compiler/subprocess.lo google/protobuf/compiler/zip_writer.lo google/protobuf/compiler/cpp/cpp_enum.lo google/protobuf/compiler/cpp/cpp_enum_field.lo google/protobuf/compiler/cpp/cpp_extension.lo google/protobuf/compiler/cpp/cpp_field.lo google/protobuf/compiler/cpp/cpp_file.lo google/protobuf/compiler/cpp/cpp_generator.lo google/protobuf/compiler/cpp/cpp_helpers.lo google/protobuf/compiler/cpp/cpp_map_field.lo google/protobuf/compiler/cpp/cpp_message.lo google/protobuf/compiler/cpp/cpp_message_field.lo google/protobuf/compiler/cpp/cpp_padding_optimizer.lo google/protobuf/compiler/cpp/cpp_primitive_field.lo google/protobuf/compiler/cpp/cpp_service.lo google/protobuf/compiler/cpp/cpp_string_field.lo libprotobuf.la -lz
libtool: link: clang++ -arch arm64 -std=gnu++17 -r -keep_private_externs -nostdlib -o .libs/libprotoc.19.dylib-master.o 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
libtool: link: clang++ -arch arm64 -std=gnu++17 -dynamiclib -o .libs/libprotoc.19.dylib .libs/libprotoc.19.dylib-master.o -L/opt/R/arm64/lib ./.libs/libprotobuf.dylib -lz -arch arm64 -pthread -g -O2 -pthread -install_name /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotoc.19.dylib -compatibility_version 20 -current_version 20.0
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 arm64 -std=gnu++17 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -pthread -L/opt/R/arm64/lib -o protoc google/protobuf/compiler/main.o libprotobuf.la libprotoc.la -lz
libtool: link: clang++ -arch arm64 -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/arm64/lib ./.libs/libprotobuf.dylib ./.libs/libprotoc.dylib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/protobuf-3.8.0/src/.libs/libprotobuf.dylib -lz -pthread
/bin/sh ../libtool --tag=CXX --mode=link clang++ -arch arm64 -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/arm64/lib -o libprotobuf-lite.la -rpath /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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 arm64 -std=gnu++17 -r -keep_private_externs -nostdlib -o .libs/libprotobuf-lite.19.dylib-master.o 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
libtool: link: clang++ -arch arm64 -std=gnu++17 -dynamiclib -o .libs/libprotobuf-lite.19.dylib .libs/libprotobuf-lite.19.dylib-master.o -L/opt/R/arm64/lib -lz -arch arm64 -pthread -g -O2 -pthread -install_name /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.19.dylib -compatibility_version 20 -current_version 20.0
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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib'
/bin/sh ../libtool --mode=install /usr/bin/install -c libprotobuf-lite.la libprotobuf.la libprotoc.la '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib'
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.19.dylib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.19.dylib
libtool: install: (cd /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la
libtool: install: /usr/bin/install -c .libs/libprotobuf.19.dylib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotobuf.19.dylib
libtool: install: (cd /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotobuf.la
libtool: install: /usr/bin/install -c .libs/libprotoc.19.dylib /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotoc.19.dylib
libtool: install: (cd /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotoc.la
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c protoc '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/bin'
libtool: install: /usr/bin/install -c .libs/protoc /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/bin/protoc
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
/usr/bin/install -c -m 644 google/protobuf/compiler/plugin.proto '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
/usr/bin/install -c -m 644 google/protobuf/compiler/cpp/cpp_generator.h '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/io'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
.././install-sh -c -d '/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/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/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google/protobuf/util'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -fPIC -I../inst/include/ -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.dylib GatingSet_pb_lib/GatingSet.pb.cc
mkdir -p "/Users/biocbuild/bbs-3.21-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/google /Users/biocbuild/bbs-3.21-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/Users/biocbuild/bbs-3.21-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/lib/libprotobuf* /Users/biocbuild/bbs-3.21-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
cp GatingSet_pb_lib/libGatingSet.pb.dylib /Users/biocbuild/bbs-3.21-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.dylib
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/Rtmp16vfXx/R.INSTALL82fd777acc75/RProtoBufLib/src/pb_build/include/ -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c dummy.cpp -o dummy.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RProtoBufLib.so dummy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-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 PATHS TO DYNAMIC LIBRARIES FOR RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so
>>>>>>>
>>>>>>> Paths before fix:
RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so:
RProtoBufLib.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-arm64/Resources/lib/libquadmath.0.dylib" "RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so"
>>>>>>> Paths after fix:
RProtoBufLib.buildbin-libdir/RProtoBufLib/libs/RProtoBufLib.so:
RProtoBufLib.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)