############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RProtoBufLib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’ * installing *source* package ‘RProtoBufLib’ ... ** using staged installation checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether g++ -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-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1002' is supported by ustar format... yes checking whether GID '1002' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports nested variables... (cached) yes checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++14 accepts -g... yes checking dependency style of g++ -std=gnu++14... gcc3 checking how to run the C preprocessor... gcc -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... g++ -std=gnu++14 -E checking for g++... g++ checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for ar... ar checking the archiver (ar) interface... ar checking for gcc... gcc checking whether we are using the GNU Objective C compiler... yes checking whether gcc accepts -g... yes checking dependency style of gcc... gcc3 checking C++ compiler flags...... use user-supplied: -g -O2 -Wall checking whether __SUNPRO_CC is declared... no checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking for ld used by g++ -std=gnu++14... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++14 static flag -static works... yes checking if g++ -std=gnu++14 supports -c -o file.o... yes checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether the linker supports version scripts... yes checking for ANSI C header files... (cached) yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for working memcmp... yes checking for working strtod... yes checking for ftruncate... yes checking for memset... yes checking for mkdir... yes checking for strchr... yes checking for strerror... yes checking for strtol... yes checking zlib version... ok (1.2.0.4 or later) checking for library containing zlibVersion... -lz checking whether g++ -std=gnu++14 supports C++11 features by default... yes checking whether -latomic is needed... no checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes 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 (/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build' '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-g -O2 -Wall' 'CC=gcc' 'CFLAGS=-g -O2 -Wall' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile === configuring in googletest (/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googletest) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build' '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-g -O2 -Wall' 'CC=gcc' 'CFLAGS=-g -O2 -Wall' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++14 accepts -g... yes checking dependency style of g++ -std=gnu++14... gcc3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking for ld used by g++ -std=gnu++14... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++14 static flag -static works... yes checking if g++ -std=gnu++14 supports -c -o file.o... yes checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for python... : checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking whether to check for GCC pthread/shared inconsistencies... yes checking whether -pthread is sufficient with -shared... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating scripts/gtest-config config.status: creating build-aux/config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in googlemock (/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/third_party/googletest/googlemock) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build' '--enable-static=no' '--with-pic=yes' '--enable-shared=yes' '--libdir=/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' 'CXX=g++ -std=gnu++14' 'CXXFLAGS=-g -O2 -Wall' 'CC=gcc' 'CFLAGS=-g -O2 -Wall' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++14 accepts -g... yes checking dependency style of g++ -std=gnu++14... gcc3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking for ld used by g++ -std=gnu++14... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=gnu++14 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++14 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++14 static flag -static works... yes checking if g++ -std=gnu++14 supports -c -o file.o... yes checking if g++ -std=gnu++14 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++14 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for python... : checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking whether to check for GCC pthread/shared inconsistencies... yes checking whether -pthread is sufficient with -shared... yes checking for gtest-config... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating scripts/gmock-config config.status: creating build-aux/config.h config.status: executing depfiles commands config.status: executing libtool commands Making install in . make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0' make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/pkgconfig' /usr/bin/install -c -m 644 protobuf.pc protobuf-lite.pc '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/pkgconfig' make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0' make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0' Making install in src make[1]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src' CXX google/protobuf/compiler/main.o CXX google/protobuf/stubs/bytestream.lo CXX google/protobuf/stubs/common.lo CXX google/protobuf/stubs/int128.lo CXX google/protobuf/io/io_win32.lo CXX google/protobuf/stubs/status.lo CXX google/protobuf/stubs/statusor.lo CXX google/protobuf/stubs/stringpiece.lo CXX google/protobuf/stubs/stringprintf.lo CXX google/protobuf/stubs/structurally_valid.lo CXX google/protobuf/stubs/strutil.lo CXX google/protobuf/stubs/time.lo CXX google/protobuf/any_lite.lo CXX google/protobuf/arena.lo CXX google/protobuf/extension_set.lo CXX google/protobuf/generated_enum_util.lo CXX google/protobuf/generated_message_util.lo CXX google/protobuf/generated_message_table_driven_lite.lo CXX google/protobuf/implicit_weak_message.lo CXX google/protobuf/message_lite.lo In file included from /usr/include/string.h:495, from ./google/protobuf/stubs/port.h:39, from ./google/protobuf/stubs/macros.h:34, from ./google/protobuf/stubs/common.h:46, from ./google/protobuf/message_lite.h:45, from google/protobuf/message_lite.cc:36: In function 'void* memcpy(void*, const void*, size_t)', inlined from 'google::protobuf::uint8* google::protobuf::io::EpsCopyOutputStream::WriteRaw(const void*, int, google::protobuf::uint8*)' at ./google/protobuf/io/coded_stream.h:699:16, inlined from 'virtual google::protobuf::uint8* google::protobuf::internal::ImplicitWeakMessage::_InternalSerialize(google::protobuf::uint8*, google::protobuf::io::EpsCopyOutputStream*) const' at ./google/protobuf/implicit_weak_message.h:85:28, inlined from 'bool google::protobuf::MessageLite::SerializePartialToZeroCopyStream(google::protobuf::io::ZeroCopyOutputStream*) const' at google/protobuf/message_lite.cc:419:30: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:33: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' specified size between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX google/protobuf/parse_context.lo CXX google/protobuf/repeated_field.lo CXX google/protobuf/wire_format_lite.lo CXX google/protobuf/io/coded_stream.lo CXX google/protobuf/io/strtod.lo CXX google/protobuf/io/zero_copy_stream.lo CXX google/protobuf/io/zero_copy_stream_impl.lo CXX google/protobuf/io/zero_copy_stream_impl_lite.lo CXX google/protobuf/any.pb.lo CXX google/protobuf/api.pb.lo CXX google/protobuf/any.lo CXX google/protobuf/descriptor.lo CXX google/protobuf/descriptor_database.lo CXX google/protobuf/descriptor.pb.lo CXX google/protobuf/duration.pb.lo CXX google/protobuf/dynamic_message.lo CXX google/protobuf/empty.pb.lo CXX google/protobuf/extension_set_heavy.lo CXX google/protobuf/field_mask.pb.lo CXX google/protobuf/generated_message_reflection.lo CXX google/protobuf/generated_message_table_driven.lo CXX google/protobuf/map_field.lo CXX google/protobuf/message.lo CXX google/protobuf/reflection_ops.lo CXX google/protobuf/service.lo CXX google/protobuf/source_context.pb.lo CXX google/protobuf/struct.pb.lo CXX google/protobuf/stubs/substitute.lo CXX google/protobuf/text_format.lo CXX google/protobuf/timestamp.pb.lo CXX google/protobuf/type.pb.lo CXX google/protobuf/unknown_field_set.lo CXX google/protobuf/wire_format.lo CXX google/protobuf/wrappers.pb.lo CXX google/protobuf/io/gzip_stream.lo CXX google/protobuf/io/printer.lo CXX google/protobuf/io/tokenizer.lo CXX google/protobuf/compiler/importer.lo CXX google/protobuf/compiler/parser.lo CXX google/protobuf/util/delimited_message_util.lo CXX google/protobuf/util/field_comparator.lo CXX google/protobuf/util/field_mask_util.lo CXX google/protobuf/util/internal/datapiece.lo CXX google/protobuf/util/internal/default_value_objectwriter.lo CXX google/protobuf/util/internal/error_listener.lo CXX google/protobuf/util/internal/field_mask_utility.lo CXX google/protobuf/util/internal/json_escaping.lo CXX google/protobuf/util/internal/json_objectwriter.lo CXX google/protobuf/util/internal/json_stream_parser.lo CXX google/protobuf/util/internal/object_writer.lo CXX google/protobuf/util/internal/protostream_objectsource.lo CXX google/protobuf/util/internal/protostream_objectwriter.lo CXX google/protobuf/util/internal/proto_writer.lo CXX google/protobuf/util/internal/type_info.lo CXX google/protobuf/util/internal/type_info_test_helper.lo CXX google/protobuf/util/internal/utility.lo CXX google/protobuf/util/json_util.lo CXX google/protobuf/util/message_differencer.lo CXX google/protobuf/util/time_util.lo CXX google/protobuf/util/type_resolver_util.lo CXXLD libprotobuf.la CXX google/protobuf/compiler/code_generator.lo CXX google/protobuf/compiler/command_line_interface.lo CXX google/protobuf/compiler/plugin.lo CXX google/protobuf/compiler/plugin.pb.lo CXX google/protobuf/compiler/subprocess.lo CXX google/protobuf/compiler/zip_writer.lo CXX google/protobuf/compiler/cpp/cpp_enum.lo CXX google/protobuf/compiler/cpp/cpp_enum_field.lo CXX google/protobuf/compiler/cpp/cpp_extension.lo CXX google/protobuf/compiler/cpp/cpp_field.lo CXX google/protobuf/compiler/cpp/cpp_file.lo CXX google/protobuf/compiler/cpp/cpp_generator.lo CXX google/protobuf/compiler/cpp/cpp_helpers.lo CXX google/protobuf/compiler/cpp/cpp_map_field.lo CXX google/protobuf/compiler/cpp/cpp_message.lo CXX google/protobuf/compiler/cpp/cpp_message_field.lo CXX google/protobuf/compiler/cpp/cpp_padding_optimizer.lo CXX google/protobuf/compiler/cpp/cpp_primitive_field.lo CXX google/protobuf/compiler/cpp/cpp_service.lo CXX google/protobuf/compiler/cpp/cpp_string_field.lo CXX google/protobuf/compiler/java/java_context.lo CXX google/protobuf/compiler/java/java_enum.lo CXX google/protobuf/compiler/java/java_enum_lite.lo CXX google/protobuf/compiler/java/java_enum_field.lo CXX google/protobuf/compiler/java/java_enum_field_lite.lo CXX google/protobuf/compiler/java/java_extension.lo CXX google/protobuf/compiler/java/java_extension_lite.lo CXX google/protobuf/compiler/java/java_field.lo CXX google/protobuf/compiler/java/java_file.lo CXX google/protobuf/compiler/java/java_generator.lo CXX google/protobuf/compiler/java/java_generator_factory.lo CXX google/protobuf/compiler/java/java_helpers.lo CXX google/protobuf/compiler/java/java_map_field.lo CXX google/protobuf/compiler/java/java_map_field_lite.lo CXX google/protobuf/compiler/java/java_message.lo CXX google/protobuf/compiler/java/java_message_lite.lo CXX google/protobuf/compiler/java/java_message_builder.lo CXX google/protobuf/compiler/java/java_message_builder_lite.lo CXX google/protobuf/compiler/java/java_message_field.lo CXX google/protobuf/compiler/java/java_message_field_lite.lo CXX google/protobuf/compiler/java/java_name_resolver.lo CXX google/protobuf/compiler/java/java_primitive_field.lo CXX google/protobuf/compiler/java/java_primitive_field_lite.lo CXX google/protobuf/compiler/java/java_shared_code_generator.lo CXX google/protobuf/compiler/java/java_service.lo CXX google/protobuf/compiler/java/java_string_field.lo CXX google/protobuf/compiler/java/java_string_field_lite.lo CXX google/protobuf/compiler/java/java_doc_comment.lo CXX google/protobuf/compiler/js/js_generator.lo CXX google/protobuf/compiler/js/well_known_types_embed.lo CXX google/protobuf/compiler/objectivec/objectivec_enum.lo CXX google/protobuf/compiler/objectivec/objectivec_enum_field.lo CXX google/protobuf/compiler/objectivec/objectivec_extension.lo CXX google/protobuf/compiler/objectivec/objectivec_field.lo CXX google/protobuf/compiler/objectivec/objectivec_file.lo CXX google/protobuf/compiler/objectivec/objectivec_generator.lo CXX google/protobuf/compiler/objectivec/objectivec_helpers.lo CXX google/protobuf/compiler/objectivec/objectivec_map_field.lo CXX google/protobuf/compiler/objectivec/objectivec_message.lo CXX google/protobuf/compiler/objectivec/objectivec_message_field.lo CXX google/protobuf/compiler/objectivec/objectivec_oneof.lo CXX google/protobuf/compiler/objectivec/objectivec_primitive_field.lo CXX google/protobuf/compiler/php/php_generator.lo CXX google/protobuf/compiler/python/python_generator.lo CXX google/protobuf/compiler/ruby/ruby_generator.lo CXX google/protobuf/compiler/csharp/csharp_doc_comment.lo CXX google/protobuf/compiler/csharp/csharp_enum.lo CXX google/protobuf/compiler/csharp/csharp_enum_field.lo CXX google/protobuf/compiler/csharp/csharp_field_base.lo CXX google/protobuf/compiler/csharp/csharp_generator.lo CXX google/protobuf/compiler/csharp/csharp_helpers.lo CXX google/protobuf/compiler/csharp/csharp_map_field.lo CXX google/protobuf/compiler/csharp/csharp_message.lo CXX google/protobuf/compiler/csharp/csharp_message_field.lo CXX google/protobuf/compiler/csharp/csharp_primitive_field.lo CXX google/protobuf/compiler/csharp/csharp_reflection_class.lo CXX google/protobuf/compiler/csharp/csharp_repeated_enum_field.lo CXX google/protobuf/compiler/csharp/csharp_repeated_message_field.lo CXX google/protobuf/compiler/csharp/csharp_repeated_primitive_field.lo CXX google/protobuf/compiler/csharp/csharp_source_generator_base.lo CXX google/protobuf/compiler/csharp/csharp_wrapper_field.lo CXXLD libprotoc.la CXXLD protoc CXXLD libprotobuf-lite.la make[2]: Entering directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' /bin/bash ../libtool --mode=install /usr/bin/install -c libprotobuf-lite.la libprotobuf.la libprotoc.la '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib' libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.so.24.0.0 /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.so.24.0.0 libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.so.24.0.0 libprotobuf-lite.so.24 || { rm -f libprotobuf-lite.so.24 && ln -s libprotobuf-lite.so.24.0.0 libprotobuf-lite.so.24; }; }) libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.so.24.0.0 libprotobuf-lite.so || { rm -f libprotobuf-lite.so && ln -s libprotobuf-lite.so.24.0.0 libprotobuf-lite.so; }; }) libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.lai /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la libtool: install: /usr/bin/install -c .libs/libprotobuf.so.24.0.0 /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.so.24.0.0 libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf.so.24.0.0 libprotobuf.so.24 || { rm -f libprotobuf.so.24 && ln -s libprotobuf.so.24.0.0 libprotobuf.so.24; }; }) libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf.so.24.0.0 libprotobuf.so || { rm -f libprotobuf.so && ln -s libprotobuf.so.24.0.0 libprotobuf.so; }; }) libtool: install: /usr/bin/install -c .libs/libprotobuf.lai /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf.la libtool: warning: relinking 'libprotoc.la' libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src; /bin/bash "/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/libtool" --silent --tag CXX --mode=relink g++ -std=gnu++14 -pthread -DHAVE_PTHREAD=1 -DHAVE_ZLIB=1 -Wall -Wno-sign-compare -g -O2 -Wall -version-info 24:0:0 -export-dynamic -no-undefined -Wl,--version-script=./libprotoc.map -o libprotoc.la -rpath /home/biocbuild/bbs-3.14-bioc/meat/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 google/protobuf/compiler/java/java_context.lo google/protobuf/compiler/java/java_enum.lo google/protobuf/compiler/java/java_enum_lite.lo google/protobuf/compiler/java/java_enum_field.lo google/protobuf/compiler/java/java_enum_field_lite.lo google/protobuf/compiler/java/java_extension.lo google/protobuf/compiler/java/java_extension_lite.lo google/protobuf/compiler/java/java_field.lo google/protobuf/compiler/java/java_file.lo google/protobuf/compiler/java/java_generator.lo google/protobuf/compiler/java/java_generator_factory.lo google/protobuf/compiler/java/java_helpers.lo google/protobuf/compiler/java/java_map_field.lo google/protobuf/compiler/java/java_map_field_lite.lo google/protobuf/compiler/java/java_message.lo google/protobuf/compiler/java/java_message_lite.lo google/protobuf/compiler/java/java_message_builder.lo google/protobuf/compiler/java/java_message_builder_lite.lo google/protobuf/compiler/java/java_message_field.lo google/protobuf/compiler/java/java_message_field_lite.lo google/protobuf/compiler/java/java_name_resolver.lo google/protobuf/compiler/java/java_primitive_field.lo google/protobuf/compiler/java/java_primitive_field_lite.lo google/protobuf/compiler/java/java_shared_code_generator.lo google/protobuf/compiler/java/java_service.lo google/protobuf/compiler/java/java_string_field.lo google/protobuf/compiler/java/java_string_field_lite.lo google/protobuf/compiler/java/java_doc_comment.lo google/protobuf/compiler/js/js_generator.lo google/protobuf/compiler/js/well_known_types_embed.lo google/protobuf/compiler/objectivec/objectivec_enum.lo google/protobuf/compiler/objectivec/objectivec_enum_field.lo google/protobuf/compiler/objectivec/objectivec_extension.lo google/protobuf/compiler/objectivec/objectivec_field.lo google/protobuf/compiler/objectivec/objectivec_file.lo google/protobuf/compiler/objectivec/objectivec_generator.lo google/protobuf/compiler/objectivec/objectivec_helpers.lo google/protobuf/compiler/objectivec/objectivec_map_field.lo google/protobuf/compiler/objectivec/objectivec_message.lo google/protobuf/compiler/objectivec/objectivec_message_field.lo google/protobuf/compiler/objectivec/objectivec_oneof.lo google/protobuf/compiler/objectivec/objectivec_primitive_field.lo google/protobuf/compiler/php/php_generator.lo google/protobuf/compiler/python/python_generator.lo google/protobuf/compiler/ruby/ruby_generator.lo google/protobuf/compiler/csharp/csharp_doc_comment.lo google/protobuf/compiler/csharp/csharp_enum.lo google/protobuf/compiler/csharp/csharp_enum_field.lo google/protobuf/compiler/csharp/csharp_field_base.lo google/protobuf/compiler/csharp/csharp_generator.lo google/protobuf/compiler/csharp/csharp_helpers.lo google/protobuf/compiler/csharp/csharp_map_field.lo google/protobuf/compiler/csharp/csharp_message.lo google/protobuf/compiler/csharp/csharp_message_field.lo google/protobuf/compiler/csharp/csharp_primitive_field.lo google/protobuf/compiler/csharp/csharp_reflection_class.lo google/protobuf/compiler/csharp/csharp_repeated_enum_field.lo google/protobuf/compiler/csharp/csharp_repeated_message_field.lo google/protobuf/compiler/csharp/csharp_repeated_primitive_field.lo google/protobuf/compiler/csharp/csharp_source_generator_base.lo google/protobuf/compiler/csharp/csharp_wrapper_field.lo libprotobuf.la -lz ) libtool: install: /usr/bin/install -c .libs/libprotoc.so.24.0.0T /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.so.24.0.0 libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotoc.so.24.0.0 libprotoc.so.24 || { rm -f libprotoc.so.24 && ln -s libprotoc.so.24.0.0 libprotoc.so.24; }; }) libtool: install: (cd /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotoc.so.24.0.0 libprotoc.so || { rm -f libprotoc.so && ln -s libprotoc.so.24.0.0 libprotoc.so; }; }) libtool: install: /usr/bin/install -c .libs/libprotoc.lai /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotoc.la libtool: finish: PATH="/home/biocbuild/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/usr/local/ensembl-vep:/sbin" ldconfig -n /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib ---------------------------------------------------------------------- Libraries have been installed in: /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the '-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the 'LD_RUN_PATH' environment variable during linking - use the '-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to '/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c protoc '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/bin' libtool: install: /usr/bin/install -c .libs/protoc /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/bin/protoc /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf' /usr/bin/install -c -m 644 google/protobuf/descriptor.proto google/protobuf/any.proto google/protobuf/api.proto google/protobuf/duration.proto google/protobuf/empty.proto google/protobuf/field_mask.proto google/protobuf/source_context.proto google/protobuf/struct.proto google/protobuf/timestamp.proto google/protobuf/type.proto google/protobuf/wrappers.proto '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler' /usr/bin/install -c -m 644 google/protobuf/compiler/plugin.proto '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf' /usr/bin/install -c -m 644 google/protobuf/any.pb.h google/protobuf/api.pb.h google/protobuf/any.h google/protobuf/arena.h google/protobuf/arena_impl.h google/protobuf/arenastring.h google/protobuf/descriptor_database.h google/protobuf/descriptor.h google/protobuf/descriptor.pb.h google/protobuf/duration.pb.h google/protobuf/dynamic_message.h google/protobuf/empty.pb.h google/protobuf/extension_set.h google/protobuf/extension_set_inl.h google/protobuf/field_mask.pb.h google/protobuf/generated_enum_reflection.h google/protobuf/generated_enum_util.h google/protobuf/generated_message_reflection.h google/protobuf/generated_message_table_driven.h google/protobuf/generated_message_util.h google/protobuf/has_bits.h google/protobuf/implicit_weak_message.h google/protobuf/inlined_string_field.h google/protobuf/map_entry.h google/protobuf/map_entry_lite.h google/protobuf/map_field.h google/protobuf/map_field_inl.h google/protobuf/map_field_lite.h google/protobuf/map.h google/protobuf/map_type_handler.h google/protobuf/message.h google/protobuf/message_lite.h google/protobuf/metadata.h google/protobuf/metadata_lite.h google/protobuf/parse_context.h google/protobuf/port.h google/protobuf/port_def.inc google/protobuf/port_undef.inc google/protobuf/reflection.h google/protobuf/reflection_ops.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/java' /usr/bin/install -c -m 644 google/protobuf/compiler/java/java_generator.h google/protobuf/compiler/java/java_names.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/java' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp' /usr/bin/install -c -m 644 google/protobuf/compiler/cpp/cpp_generator.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/python' /usr/bin/install -c -m 644 google/protobuf/compiler/python/python_generator.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/python' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/js' /usr/bin/install -c -m 644 google/protobuf/compiler/js/js_generator.h google/protobuf/compiler/js/well_known_types_embed.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/js' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf' /usr/bin/install -c -m 644 google/protobuf/repeated_field.h google/protobuf/service.h google/protobuf/source_context.pb.h google/protobuf/struct.pb.h google/protobuf/text_format.h google/protobuf/timestamp.pb.h google/protobuf/type.pb.h google/protobuf/unknown_field_set.h google/protobuf/wire_format.h google/protobuf/wire_format_lite.h google/protobuf/wrappers.pb.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs' /usr/bin/install -c -m 644 google/protobuf/stubs/callback.h google/protobuf/stubs/bytestream.h google/protobuf/stubs/casts.h google/protobuf/stubs/common.h google/protobuf/stubs/fastmem.h google/protobuf/stubs/hash.h google/protobuf/stubs/logging.h google/protobuf/stubs/macros.h google/protobuf/stubs/map_util.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 '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/stubs' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util' /usr/bin/install -c -m 644 google/protobuf/util/type_resolver.h google/protobuf/util/delimited_message_util.h google/protobuf/util/field_comparator.h google/protobuf/util/field_mask_util.h google/protobuf/util/json_util.h google/protobuf/util/time_util.h google/protobuf/util/type_resolver_util.h google/protobuf/util/message_differencer.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/util' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php' /usr/bin/install -c -m 644 google/protobuf/compiler/php/php_generator.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler' /usr/bin/install -c -m 644 google/protobuf/compiler/code_generator.h google/protobuf/compiler/command_line_interface.h google/protobuf/compiler/importer.h google/protobuf/compiler/parser.h google/protobuf/compiler/plugin.h google/protobuf/compiler/plugin.pb.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby' /usr/bin/install -c -m 644 google/protobuf/compiler/ruby/ruby_generator.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io' /usr/bin/install -c -m 644 google/protobuf/io/io_win32.h google/protobuf/io/coded_stream.h google/protobuf/io/gzip_stream.h google/protobuf/io/printer.h google/protobuf/io/strtod.h google/protobuf/io/tokenizer.h google/protobuf/io/zero_copy_stream.h google/protobuf/io/zero_copy_stream_impl.h google/protobuf/io/zero_copy_stream_impl_lite.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/io' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp' /usr/bin/install -c -m 644 google/protobuf/compiler/csharp/csharp_generator.h google/protobuf/compiler/csharp/csharp_names.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp' /usr/bin/mkdir -p '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec' /usr/bin/install -c -m 644 google/protobuf/compiler/objectivec/objectivec_generator.h google/protobuf/compiler/objectivec/objectivec_helpers.h '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec' make[2]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src' make[1]: Leaving directory '/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/protobuf-3.13.0/src' configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -shared -fpic -I../inst/include/ -I/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/ -o GatingSet_pb_lib/libGatingSet.pb.so GatingSet_pb_lib/GatingSet.pb.cc mkdir -p "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include" cp -r /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/google /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/include mkdir -p "/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/" cp /home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/lib/libprotobuf* /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/ cp GatingSet_pb_lib/libGatingSet.pb.so /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib//libGatingSet.pb.so g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I../inst/include/ -I/home/biocbuild/bbs-3.14-bioc/meat/RProtoBufLib/src/pb_build/include/ -I/usr/local/include -fpic -g -O2 -Wall -c dummy.cpp -o dummy.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o RProtoBufLib.so dummy.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RProtoBufLib)