############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf RProtoBufLib.buildbin-libdir && mkdir RProtoBufLib.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RProtoBufLib_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R RProtoBufLib.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RProtoBufLib.buildbin-libdir RProtoBufLib_2.16.0.tar.gz' >>>>>>> * installing *source* package ‘RProtoBufLib’ ... ** using staged installation checking for gcc... clang -arch x86_64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes untarring protobuf ... building protobuf... checking whether to enable maintainer-specific portions of Makefiles... yes checking build system type... x86_64-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking target system type... x86_64-apple-darwin21.6.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '503' is supported by ustar format... yes checking whether GID '20' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking for gcc... clang -arch x86_64 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to accept ISO C89... none needed checking whether clang -arch x86_64 understands -c and -o together... rm: conftest.dSYM: is a directory yes checking whether make supports the include directive... yes (GNU style) checking dependency style of clang -arch x86_64... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes checking dependency style of clang++ -arch x86_64 -std=gnu++17... gcc3 checking how to run the C preprocessor... clang -arch x86_64 -E checking for gcc... gcc checking whether we are using the GNU C compiler... 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(cached) yes checking for working memcmp... yes checking for working strtod... yes checking for ftruncate... yes checking for memset... yes checking for mkdir... yes checking for strchr... yes checking for strerror... yes checking for strtol... yes checking zlib version... ok (1.2.0.4 or later) checking for library containing zlibVersion... -lz checking whether clang++ -arch x86_64 -std=gnu++17 supports C++11 features by default... yes checking whether -latomic is needed... no checking whether clang -arch x86_64 is Clang... yes checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking the location of hash_map... 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/RtmppV3i2M/R.INSTALLed252643dff9/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/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/lib/pkgconfig' /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/lib/pkgconfig' Making install in src depbase=`echo google/protobuf/compiler/main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/compiler/main.o -MD -MP -MF $depbase.Tpo -c -o google/protobuf/compiler/main.o google/protobuf/compiler/main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo google/protobuf/stubs/bytestream.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 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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 virtual ObjectWriter* StartObject(StringPiece name) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:99:29: warning: 'EndObject' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* EndObject(); ^ ./google/protobuf/util/internal/object_writer.h:68:25: note: overridden virtual function is here virtual ObjectWriter* EndObject() = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:100:29: warning: 'StartList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* StartList(StringPiece name); ^ ./google/protobuf/util/internal/object_writer.h:71:25: note: overridden virtual function is here virtual ObjectWriter* StartList(StringPiece name) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:101:29: warning: 'EndList' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* EndList(); ^ ./google/protobuf/util/internal/object_writer.h:74:25: note: overridden virtual function is here virtual ObjectWriter* EndList() = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:102:29: warning: 'RenderBool' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderBool(StringPiece name, bool value); ^ ./google/protobuf/util/internal/object_writer.h:77:25: note: overridden virtual function is here virtual ObjectWriter* RenderBool(StringPiece name, bool value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:103:29: warning: 'RenderInt32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderInt32(StringPiece name, int32 value); ^ ./google/protobuf/util/internal/object_writer.h:80:25: note: overridden virtual function is here virtual ObjectWriter* RenderInt32(StringPiece name, int32 value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:104:29: warning: 'RenderUint32' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderUint32(StringPiece name, uint32 value); ^ ./google/protobuf/util/internal/object_writer.h:83:25: note: overridden virtual function is here virtual ObjectWriter* RenderUint32(StringPiece name, uint32 value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:105:29: warning: 'RenderInt64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderInt64(StringPiece name, int64 value); ^ ./google/protobuf/util/internal/object_writer.h:86:25: note: overridden virtual function is here virtual ObjectWriter* RenderInt64(StringPiece name, int64 value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:106:29: warning: 'RenderUint64' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderUint64(StringPiece name, uint64 value); ^ ./google/protobuf/util/internal/object_writer.h:89:25: note: overridden virtual function is here virtual ObjectWriter* RenderUint64(StringPiece name, uint64 value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:107:29: warning: 'RenderDouble' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderDouble(StringPiece name, double value); ^ ./google/protobuf/util/internal/object_writer.h:92:25: note: overridden virtual function is here virtual ObjectWriter* RenderDouble(StringPiece name, double value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:108:29: warning: 'RenderFloat' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderFloat(StringPiece name, float value); ^ ./google/protobuf/util/internal/object_writer.h:95:25: note: overridden virtual function is here virtual ObjectWriter* RenderFloat(StringPiece name, float value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:109:29: warning: 'RenderString' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderString(StringPiece name, ^ ./google/protobuf/util/internal/object_writer.h:98:25: note: overridden virtual function is here virtual ObjectWriter* RenderString(StringPiece name, ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:111:29: warning: 'RenderBytes' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderBytes(StringPiece name, StringPiece value); ^ ./google/protobuf/util/internal/object_writer.h:102:25: note: overridden virtual function is here virtual ObjectWriter* RenderBytes(StringPiece name, StringPiece value) = 0; ^ In file included from google/protobuf/util/internal/json_objectwriter.cc:31: ./google/protobuf/util/internal/json_objectwriter.h:112:29: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual JsonObjectWriter* RenderNull(StringPiece name); ^ ./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here virtual ObjectWriter* RenderNull(StringPiece name) = 0; ^ 14 warnings generated. depbase=`echo google/protobuf/util/internal/json_stream_parser.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/json_stream_parser.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/json_stream_parser.lo google/protobuf/util/internal/json_stream_parser.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/json_stream_parser.lo -MD -MP -MF google/protobuf/util/internal/.deps/json_stream_parser.Tpo -c google/protobuf/util/internal/json_stream_parser.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/json_stream_parser.o depbase=`echo google/protobuf/util/internal/object_writer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/object_writer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/object_writer.lo google/protobuf/util/internal/object_writer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/object_writer.lo -MD -MP -MF google/protobuf/util/internal/.deps/object_writer.Tpo -c google/protobuf/util/internal/object_writer.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/object_writer.o depbase=`echo google/protobuf/util/internal/protostream_objectsource.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/protostream_objectsource.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/protostream_objectsource.lo google/protobuf/util/internal/protostream_objectsource.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/protostream_objectsource.lo -MD -MP -MF google/protobuf/util/internal/.deps/protostream_objectsource.Tpo -c google/protobuf/util/internal/protostream_objectsource.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/protostream_objectsource.o depbase=`echo google/protobuf/util/internal/protostream_objectwriter.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/protostream_objectwriter.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/protostream_objectwriter.lo google/protobuf/util/internal/protostream_objectwriter.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/protostream_objectwriter.lo -MD -MP -MF google/protobuf/util/internal/.deps/protostream_objectwriter.Tpo -c google/protobuf/util/internal/protostream_objectwriter.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/protostream_objectwriter.o depbase=`echo google/protobuf/util/internal/proto_writer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/proto_writer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/proto_writer.lo google/protobuf/util/internal/proto_writer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/proto_writer.lo -MD -MP -MF google/protobuf/util/internal/.deps/proto_writer.Tpo -c google/protobuf/util/internal/proto_writer.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/proto_writer.o depbase=`echo google/protobuf/util/internal/type_info.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/type_info.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/type_info.lo google/protobuf/util/internal/type_info.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/type_info.lo -MD -MP -MF google/protobuf/util/internal/.deps/type_info.Tpo -c google/protobuf/util/internal/type_info.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/type_info.o depbase=`echo google/protobuf/util/internal/type_info_test_helper.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/type_info_test_helper.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/type_info_test_helper.lo google/protobuf/util/internal/type_info_test_helper.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/type_info_test_helper.lo -MD -MP -MF google/protobuf/util/internal/.deps/type_info_test_helper.Tpo -c google/protobuf/util/internal/type_info_test_helper.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/type_info_test_helper.o In file included from google/protobuf/util/internal/type_info_test_helper.cc:31: In file included from ./google/protobuf/util/internal/type_info_test_helper.h:39: ./google/protobuf/util/internal/default_value_objectwriter.h:122:37: warning: 'RenderNull' overrides a member function but is not marked 'override' [-Winconsistent-missing-override] virtual DefaultValueObjectWriter* RenderNull(StringPiece name); ^ ./google/protobuf/util/internal/object_writer.h:105:25: note: overridden virtual function is here virtual ObjectWriter* RenderNull(StringPiece name) = 0; ^ 1 warning generated. depbase=`echo google/protobuf/util/internal/utility.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/utility.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/internal/utility.lo google/protobuf/util/internal/utility.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/internal/utility.lo -MD -MP -MF google/protobuf/util/internal/.deps/utility.Tpo -c google/protobuf/util/internal/utility.cc -fno-common -DPIC -o google/protobuf/util/internal/.libs/utility.o depbase=`echo google/protobuf/util/json_util.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/json_util.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/json_util.lo google/protobuf/util/json_util.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/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. depbase=`echo google/protobuf/util/message_differencer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/message_differencer.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/message_differencer.lo google/protobuf/util/message_differencer.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/message_differencer.lo -MD -MP -MF google/protobuf/util/.deps/message_differencer.Tpo -c google/protobuf/util/message_differencer.cc -fno-common -DPIC -o google/protobuf/util/.libs/message_differencer.o depbase=`echo google/protobuf/util/time_util.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/time_util.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/time_util.lo google/protobuf/util/time_util.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/time_util.lo -MD -MP -MF google/protobuf/util/.deps/time_util.Tpo -c google/protobuf/util/time_util.cc -fno-common -DPIC -o google/protobuf/util/.libs/time_util.o depbase=`echo google/protobuf/util/type_resolver_util.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile clang++ -arch x86_64 -std=gnu++17 -DHAVE_CONFIG_H -I. -I.. -I/opt/R/x86_64/include -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -falign-functions=64 -Wall -g -O2 -MT google/protobuf/util/type_resolver_util.lo -MD -MP -MF $depbase.Tpo -c -o google/protobuf/util/type_resolver_util.lo google/protobuf/util/type_resolver_util.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: clang++ -arch x86_64 -std=gnu++17 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'/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/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/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/google/protobuf/io' .././install-sh -c -d '/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/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/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/google/protobuf' .././install-sh -c -d '/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/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/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/google/protobuf/compiler' .././install-sh -c -d '/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/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/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/google/protobuf/util' configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -fPIC -I../inst/include/ -I/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.dylib GatingSet_pb_lib/GatingSet.pb.cc mkdir -p "/Users/biocbuild/bbs-3.19-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include" cp -r /private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/google /Users/biocbuild/bbs-3.19-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/include mkdir -p "/Users/biocbuild/bbs-3.19-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/" cp /private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/lib/libprotobuf* /Users/biocbuild/bbs-3.19-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/ cp GatingSet_pb_lib/libGatingSet.pb.dylib /Users/biocbuild/bbs-3.19-bioc/meat/RProtoBufLib.buildbin-libdir/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.dylib clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I/private/tmp/RtmppV3i2M/R.INSTALLed252643dff9/RProtoBufLib/src/pb_build/include/ -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dummy.cpp -o dummy.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o RProtoBufLib.so dummy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/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/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)