############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhdf5lib ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘Rhdf5lib’ ... ** 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 the compiler supports GNU C... yes checking whether clang -arch x86_64 accepts -g... yes checking for clang -arch x86_64 option to enable C11 features... none needed checking whether the compiler supports GNU C++... yes checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... none needed COMPILER = clang checking whether C compiler accepts -w... yes checking whether to use -Wl,-rpath setting... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes checking for szlib.h... no checking for libaec.h... no checking for curl/curl.h... yes checking for openssl/evp.h... yes checking for openssl/hmac.h... yes checking for openssl/sha.h... yes checking for curl_global_init in -lcurl... yes checking for EVP_sha256 in -lcrypto... yes S3_VFD=--enable-ros3-vfd 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 SDK: ‘MacOSX11.3.sdk’ gunzip -dc hdf5small_cxx_hl_1.10.7.tar.gz | tar xf -; cd hdf5/libaec-1.0.4/build; \ ../configure --with-pic --enable-shared=no --prefix=/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \ CC='clang -arch x86_64' CXX='clang++ -arch x86_64 -std=gnu++17' \ CPPFLAGS='-I/opt/R/x86_64/include' \ CFLAGS='-falign-functions=64 -Wall -g -O2 -w -fPIC' \ AR='ar' RANLIB='ranlib'; \ make; \ make install checking build system type... x86_64-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking how to print strings... printf 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 for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by clang -arch x86_64... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... rm: conftest.dSYM: is a directory BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... rm: conftest.dSYM: is a directory no checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking command to parse /usr/bin/nm -B output from clang -arch x86_64 object... rm: conftest.dSYM: is a directory ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... clang -arch x86_64 -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if clang -arch x86_64 supports -fno-rtti -fno-exceptions... yes checking for clang -arch x86_64 option to produce PIC... -fno-common -DPIC checking if clang -arch x86_64 PIC flag -fno-common -DPIC works... yes checking if clang -arch x86_64 static flag -static works... no checking if clang -arch x86_64 supports -c -o file.o... yes checking if clang -arch x86_64 supports -c -o file.o... (cached) yes checking whether the clang -arch x86_64 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking whether the -Werror option is usable... yes checking for simple visibility declarations... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ../config/install-sh -c -d checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of clang -arch x86_64... gcc3 checking whether to enable maintainer-specific portions of Makefiles... yes checking for clang -arch x86_64 option to accept ISO C99... none needed checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for inline... inline checking for int64_t... yes checking for size_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for inline... (cached) inline checking for C/C++ restrict keyword... __restrict checking for memset... yes checking for strstr... yes checking for snprintf... yes checking whether __builtin_clzll is declared... no 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 config/config.h config.status: executing libtool commands config.status: executing depfiles commands Making all in src clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT aec.o -MD -MP -MF .deps/aec.Tpo -c -o aec.o ../../src/aec.c mv -f .deps/aec.Tpo .deps/aec.Po /bin/sh ../libtool --tag=CC --mode=compile clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c -o encode.lo ../../src/encode.c libtool: compile: clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c ../../src/encode.c -fno-common -DPIC -o encode.o mv -f .deps/encode.Tpo .deps/encode.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c -o encode_accessors.lo ../../src/encode_accessors.c libtool: compile: clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c ../../src/encode_accessors.c -fno-common -DPIC -o encode_accessors.o mv -f .deps/encode_accessors.Tpo .deps/encode_accessors.Plo /bin/sh ../libtool --tag=CC --mode=compile clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c -o decode.lo ../../src/decode.c libtool: compile: clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c ../../src/decode.c -fno-common -DPIC -o decode.o mv -f .deps/decode.Tpo .deps/decode.Plo /bin/sh ../libtool --tag=CC --mode=link clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -version-info 0:10:0 -no-undefined -o libaec.la -rpath /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib encode.lo encode_accessors.lo decode.lo libtool: link: ar cr .libs/libaec.a encode.o encode_accessors.o decode.o libtool: link: ranlib .libs/libaec.a libtool: link: ( cd ".libs" && rm -f "libaec.la" && ln -s "../libaec.la" "libaec.la" ) /bin/sh ../libtool --tag=CC --mode=link clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o aec aec.o libaec.la libtool: link: clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o aec aec.o ./.libs/libaec.a clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT utime.o -MD -MP -MF .deps/utime.Tpo -c -o utime.o ../../src/utime.c mv -f .deps/utime.Tpo .deps/utime.Po /bin/sh ../libtool --tag=CC --mode=link clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o utime utime.o libtool: link: clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -o utime utime.o /bin/sh ../libtool --tag=CC --mode=compile clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c -o sz_compat.lo ../../src/sz_compat.c libtool: compile: clang -arch x86_64 -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -I/opt/R/x86_64/include -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c ../../src/sz_compat.c -fno-common -DPIC -o sz_compat.o mv -f .deps/sz_compat.Tpo .deps/sz_compat.Plo /bin/sh ../libtool --tag=CC --mode=link clang -arch x86_64 -fvisibility=hidden -falign-functions=64 -Wall -g -O2 -w -fPIC -version-info 2:1:0 -no-undefined -o libsz.la -rpath /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib sz_compat.lo libaec.la libtool: link: ar cr .libs/libsz.a sz_compat.o libtool: link: ranlib .libs/libsz.a libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" ) make[2]: Nothing to be done for `all-am'. Making install in src ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c libaec.la libsz.la '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' libtool: install: /usr/bin/install -c .libs/libaec.lai /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.la libtool: install: /usr/bin/install -c .libs/libsz.lai /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.la libtool: install: /usr/bin/install -c .libs/libaec.a /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: chmod 644 /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: ranlib /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: /usr/bin/install -c .libs/libsz.a /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: chmod 644 /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: ranlib /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c aec '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' libtool: install: /usr/bin/install -c aec /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' ../../config/install-sh -c -d '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' /usr/bin/install -c -m 644 ../../src/aec.1 '/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. cd hdf5; \ ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \ --enable-tests=no --enable-tools=no \ --with-szlib=/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \ --enable-ros3-vfd \ --enable-sharedlib-rpath \ CC='clang -arch x86_64' CXX='clang++ -arch x86_64 -std=gnu++17' \ CPPFLAGS='-I/opt/R/x86_64/include' \ CFLAGS='-falign-functions=64 -Wall -g -O2 -w -fPIC' \ CXXFLAGS='-w -falign-functions=64 -Wall -g -O2 -fPIC' \ AR='ar' RANLIB='ranlib' \ LDFLAGS='-L/opt/R/x86_64/lib'; \ make lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... bin/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 make supports nested variables... (cached) yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-apple-darwin21.6.0 checking host system type... x86_64-apple-darwin21.6.0 checking shell variables initial values... done checking if basename works... yes checking if xargs works... yes checking for cached host... none checking for config x86_64-apple-darwin21.6.0... no checking for config x86_64-apple-darwin21.6.0... no checking for config apple-darwin21.6.0... no checking for config apple-darwin21.6.0... no checking for config x86_64-darwin21.6.0... no checking for config x86_64-darwin21.6.0... no checking for config x86_64-apple... no checking for config darwin21.6.0... no checking for config darwin21.6.0... no checking for config apple... found compiler 'clang -arch x86_64' is clang-14.0.0 No match to get cc_version_info for clang -arch x86_64 compiler 'gfortran' is GNU gfortran-12.2.0 checking for config ./config/site-specific/host-merida1... no checking for clang sanitizer checks... none checking build mode... production 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 if unsupported combinations of configure options are allowed... no checking how to run the C preprocessor... clang -arch x86_64 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for off_t... yes checking for size_t... yes checking for ssize_t... yes checking for ptrdiff_t... yes checking whether byte ordering is bigendian... no checking size of char... 1 checking size of short... 2 checking size of int... 4 checking size of unsigned... 4 checking size of long... 8 checking size of long long... 8 checking size of __int64... 0 checking size of float... 4 checking size of double... 8 checking size of long double... 16 checking size of __float128... 0 checking size of _Quad... 0 checking quadmath.h usability... no checking quadmath.h presence... no checking for quadmath.h... no checking maximum decimal precision for C... 21 checking if Fortran interface enabled... no 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 -std=gnu++17 -E checking if c++ interface enabled... yes checking if clang++ -arch x86_64 -std=gnu++17 needs old style header files in includes... no checking if clang++ -arch x86_64 -std=gnu++17 can handle namespaces... yes checking if clang++ -arch x86_64 -std=gnu++17 can handle static cast... yes checking if clang++ -arch x86_64 -std=gnu++17 has offsetof extension... yes checking if the high-level library is enabled... yes checking whether make sets $(MAKE)... (cached) yes checking for tr... /usr/bin/tr checking if srcdir= and time commands work together... yes checking if Java JNI interface enabled... no checking if building tests is disabled... Building HDF5 tests is disabled checking if building tools is disabled... Building HDF5 tools is disabled 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 clang -arch x86_64... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin21.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from clang -arch x86_64 object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if clang -arch x86_64 supports -fno-rtti -fno-exceptions... yes checking for clang -arch x86_64 option to produce PIC... -fno-common -DPIC checking if clang -arch x86_64 PIC flag -fno-common -DPIC works... yes checking if clang -arch x86_64 static flag -static works... no checking if clang -arch x86_64 supports -c -o file.o... yes checking if clang -arch x86_64 supports -c -o file.o... (cached) yes checking whether the clang -arch x86_64 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld checking how to hardcode library paths into programs... immediate checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... yes checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++17 -E checking for ld used by clang++ -arch x86_64 -std=gnu++17... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the clang++ -arch x86_64 -std=gnu++17 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for clang++ -arch x86_64 -std=gnu++17 option to produce PIC... -fno-common -DPIC checking if clang++ -arch x86_64 -std=gnu++17 PIC flag -fno-common -DPIC works... yes checking if clang++ -arch x86_64 -std=gnu++17 static flag -static works... no checking if clang++ -arch x86_64 -std=gnu++17 supports -c -o file.o... yes checking if clang++ -arch x86_64 -std=gnu++17 supports -c -o file.o... (cached) yes checking whether the clang++ -arch x86_64 -std=gnu++17 linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.6.0 dyld checking how to hardcode library paths into programs... immediate checking if we should install only statically linked executables... no checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes checking for ceil in -lm... yes checking for dlopen in -ldl... (cached) yes checking for ANSI C header files... (cached) yes checking whether time.h and sys/time.h may both be included... yes checking sys/resource.h usability... yes checking sys/resource.h presence... yes checking for sys/resource.h... yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking sys/ioctl.h usability... yes checking sys/ioctl.h presence... yes checking for sys/ioctl.h... yes checking for sys/stat.h... (cached) yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for sys/types.h... (cached) yes checking sys/file.h usability... yes checking sys/file.h presence... yes checking for sys/file.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking setjmp.h usability... yes checking setjmp.h presence... yes checking for setjmp.h... yes checking features.h usability... no checking features.h presence... no checking for features.h... no checking dirent.h usability... yes checking dirent.h presence... yes checking for dirent.h... yes checking for stdint.h... (cached) yes checking stdbool.h usability... yes checking stdbool.h presence... yes checking for stdbool.h... yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking io.h usability... no checking io.h presence... no checking for io.h... no checking winsock2.h usability... no checking winsock2.h presence... no checking for winsock2.h... no checking sys/timeb.h usability... yes checking sys/timeb.h presence... yes checking for sys/timeb.h... yes checking for _FILE_OFFSET_BITS value needed for large files... no checking size of int8_t... 1 checking size of uint8_t... 1 checking size of int_least8_t... 1 checking size of uint_least8_t... 1 checking size of int_fast8_t... 1 checking size of uint_fast8_t... 1 checking size of int16_t... 2 checking size of uint16_t... 2 checking size of int_least16_t... 2 checking size of uint_least16_t... 2 checking size of int_fast16_t... 2 checking size of uint_fast16_t... 2 checking size of int32_t... 4 checking size of uint32_t... 4 checking size of int_least32_t... 4 checking size of uint_least32_t... 4 checking size of int_fast32_t... 4 checking size of uint_fast32_t... 4 checking size of int64_t... 8 checking size of uint64_t... 8 checking size of int_least64_t... 8 checking size of uint_least64_t... 8 checking size of int_fast64_t... 8 checking size of uint_fast64_t... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of off_t... 8 checking size of bool... 1 checking size of time_t... 8 checking if dev_t is scalar... yes checking for dmalloc library... suppressed checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for compress2 in -lz... yes checking for compress2... yes configure: testing for aec and szip checking for aec_encode in -laec... yes checking for SZ_BufftoBuffCompress in -lsz... yes checking libaec.h usability... yes checking libaec.h presence... yes checking for libaec.h... yes checking szlib.h usability... yes checking szlib.h presence... yes checking for szlib.h... yes checking for szlib encoder... yes checking for thread safe support... no checking whether CLOCK_MONOTONIC is declared... yes checking for tm_gmtoff in struct tm... yes checking for global timezone variable... yes checking for st_blocks in struct stat... no checking for _getvideoconfig... no checking for gettextinfo... no checking for GetConsoleScreenBufferInfo... no checking for getpwuid... yes checking for _scrsize... no checking for ioctl... yes checking for struct videoconfig... no checking for struct text_info... no checking for TIOCGWINSZ... yes checking for TIOCGETD... yes checking for library containing clock_gettime... none required checking for alarm... yes checking for clock_gettime... yes checking for difftime... yes checking for fcntl... yes checking for flock... yes checking for fork... yes checking for frexpf... yes checking for frexpl... yes checking for gethostname... yes checking for getrusage... yes checking for gettimeofday... yes checking for lstat... yes checking for rand_r... yes checking for random... yes checking for setsysinfo... no checking for signal... yes checking for longjmp... yes checking for setjmp... yes checking for siglongjmp... yes checking for sigsetjmp... yes checking for sigprocmask... yes checking for snprintf... yes checking for srandom... yes checking for strdup... yes checking for symlink... yes checking for system... yes checking for strtoll... yes checking for strtoull... yes checking for tmpfile... yes checking for asprintf... yes checking for vasprintf... yes checking for vsnprintf... yes checking for waitpid... yes checking for roundf... yes checking for lroundf... yes checking for llroundf... yes checking for round... yes checking for lround... yes checking for llround... yes checking for an ANSI C-conforming const... yes checking if the compiler understands __inline__... yes checking if the compiler understands __inline... yes checking if the compiler understands inline... yes checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking enable debugging symbols... no checking enable asserts... no checking enable developer warnings... no checking profiling... no checking optimization level... high checking enable file locking... best-effort checking for internal debug output... none checking whether function stack tracking is enabled... no checking for API tracing... no checking whether a memory checking tool will be used... no checking whether internal memory allocation sanity checking is used... no checking for parallel support files... skipped checking whether O_DIRECT is declared... no checking for posix_memalign... yes checking if the direct I/O virtual file driver (VFD) is enabled... no checking if the Mirror virtual file driver (VFD) is enabled... no checking curl/curl.h usability... yes checking curl/curl.h presence... yes checking for curl/curl.h... yes checking openssl/evp.h usability... yes checking openssl/evp.h presence... yes checking for openssl/evp.h... yes checking openssl/hmac.h usability... yes checking openssl/hmac.h presence... yes checking for openssl/hmac.h... yes checking openssl/sha.h usability... yes checking openssl/sha.h presence... yes checking for openssl/sha.h... yes checking for curl_global_init in -lcurl... yes checking for EVP_sha256 in -lcrypto... yes checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes checking for libhdfs... suppressed checking for custom examples path definition... ${prefix}/share/hdf5_examples checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin checking whether exception handling functions is checked during data conversions... yes checking whether data accuracy is guaranteed during data conversions... yes checking if the machine has window style path name... no checking if using special algorithm to convert long double to (unsigned) long values... no checking if using special algorithm to convert (unsigned) long to long double values... no checking if correctly converting long double to (unsigned) long long values... yes checking if correctly converting (unsigned) long long to long double values... yes checking if the system is IBM ppc64le and cannot correctly convert some long double values... no checking additional programs should be built... no checking if deprecated public symbols are available... yes checking which version of public symbols to use by default... v110 checking whether to perform strict file format checks... no checking for pread... yes checking for pwrite... yes checking whether to use pread/pwrite instead of read/write in certain VFDs... yes checking whether to have library information embedded in the executables... yes checking if alignment restrictions are strictly enforced... no configure: creating ./config.lt config.lt: creating libtool checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating src/libhdf5.settings config.status: creating Makefile config.status: creating src/Makefile config.status: creating utils/Makefile config.status: creating utils/mirror_vfd/Makefile config.status: creating bin/h5cc config.status: creating bin/Makefile config.status: creating c++/Makefile config.status: creating c++/src/Makefile config.status: creating c++/src/h5c++ config.status: creating hl/Makefile config.status: creating hl/src/Makefile config.status: creating hl/c++/Makefile config.status: creating hl/c++/src/Makefile config.status: creating src/H5config.h config.status: executing pubconf commands creating src/H5pubconf.h Post process src/libhdf5.settings config.status: executing depfiles commands config.status: executing libtool commands config.status: executing .classes commands sed: -I or -i may not be used with stdin SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.7 Configured on: Sun Oct 15 15:05:54 EDT 2023 Configured by: biocbuild@merida1 Host system: x86_64-apple-darwin21.6.0 Uname information: Darwin merida1 21.6.0 Darwin Kernel Version 21.6.0: Thu Mar 9 20:08:59 PST 2023; root:xnu-8020.240.18.700.8~1/RELEASE_X86_64 x86_64 Byte sex: little-endian Installation point: /Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/hdf5 Compiling Options: ------------------ Build Mode: production Debugging Symbols: no Asserts: no Profiling: no Optimization Level: high Linking Options: ---------------- Libraries: static Statically Linked Executables: LDFLAGS: -L/opt/R/x86_64/lib H5_LDFLAGS: AM_LDFLAGS: -L/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib Extra libraries: -lcrypto -lcurl -lsz -laec -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib Languages: ---------- C: yes C Compiler: /usr/bin/clang -arch x86_64 CPPFLAGS: -I/opt/R/x86_64/include H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: -I/Users/biocbuild/bbs-3.17-bioc/meat/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include C Flags: -falign-functions=64 -Wall -g -O2 -w -fPIC H5 C Flags: -std=c99 -Warray-bounds -Wcast-qual -Wconversion -Wdouble-promotion -Wformat=2 -Wframe-larger-than=16384 -Wimplicit-fallthrough -Wno-c++-compat -Wno-format-nonliteral -Wnull-dereference -Wunused-const-variable -Wwrite-strings -Wvolatile-register-var -Wno-self-assign-overloaded -Wno-unknown-warning-option -Wno-missing-noreturn -O3 -Werror=bad-function-cast -Werror=implicit-function-declaration -Werror=incompatible-pointer-types -Werror=missing-declarations -Werror=packed -Werror=shadow -Werror=switch -Wno-error=incompatible-pointer-types-discards-qualifiers -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wformat AM C Flags: Shared C Library: no Static C Library: yes Fortran: no C++: yes C++ Compiler: /usr/bin/clang++ -arch x86_64 -std=gnu++17 C++ Flags: -w -falign-functions=64 -Wall -g -O2 -fPIC H5 C++ Flags: AM C++ Flags: Shared C++ Library: no Static C++ Library: yes Java: no Features: --------- Parallel HDF5: no Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Build HDF5 Tests: no Build HDF5 Tools: no Threadsafety: no Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib),szip(encoder) MPE: no Direct VFD: no Mirror VFD: no (Read-Only) S3 VFD: yes (Read-Only) HDFS VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no for d in src . c++ hl; do \ if test $d != .; then \ (cd $d && make lib) || exit 1; \ fi; \ done CC H5.lo CC H5checksum.lo CC H5dbg.lo CC H5system.lo CC H5timer.lo CC H5trace.lo CC H5A.lo CC H5Abtree2.lo CC H5Adense.lo CC H5Adeprec.lo CC H5Aint.lo CC H5Atest.lo CC H5AC.lo CC H5ACdbg.lo CC H5ACproxy_entry.lo CC H5B.lo CC H5Bcache.lo CC H5Bdbg.lo CC H5B2.lo CC H5B2cache.lo CC H5B2dbg.lo CC H5B2hdr.lo CC H5B2int.lo CC H5B2internal.lo CC H5B2leaf.lo CC H5B2stat.lo CC H5B2test.lo CC H5C.lo CC H5Cdbg.lo CC H5Cepoch.lo CC H5Cimage.lo CC H5Clog.lo CC H5Clog_json.lo CC H5Clog_trace.lo CC H5Cprefetched.lo CC H5Cquery.lo CC H5Ctag.lo CC H5Ctest.lo CC H5CS.lo CC H5CX.lo CC H5D.lo CC H5Dbtree.lo CC H5Dbtree2.lo CC H5Dchunk.lo CC H5Dcompact.lo CC H5Dcontig.lo CC H5Ddbg.lo CC H5Ddeprec.lo CC H5Dearray.lo CC H5Defl.lo CC H5Dfarray.lo CC H5Dfill.lo CC H5Dint.lo CC H5Dio.lo CC H5Dlayout.lo CC H5Dnone.lo CC H5Doh.lo CC H5Dscatgath.lo CC H5Dselect.lo CC H5Dsingle.lo CC H5Dtest.lo CC H5Dvirtual.lo CC H5E.lo CC H5Edeprec.lo CC H5Eint.lo CC H5EA.lo CC H5EAcache.lo CC H5EAdbg.lo CC H5EAdblkpage.lo CC H5EAdblock.lo CC H5EAhdr.lo CC H5EAiblock.lo CC H5EAint.lo CC H5EAsblock.lo CC H5EAstat.lo CC H5EAtest.lo CC H5F.lo CC H5Faccum.lo CC H5Fcwfs.lo CC H5Fdbg.lo CC H5Fdeprec.lo CC H5Fefc.lo CC H5Ffake.lo CC H5Fint.lo CC H5Fio.lo CC H5Fmount.lo CC H5Fquery.lo CC H5Fsfile.lo CC H5Fspace.lo CC H5Fsuper.lo CC H5Fsuper_cache.lo CC H5Ftest.lo CC H5FA.lo CC H5FAcache.lo CC H5FAdbg.lo CC H5FAdblock.lo CC H5FAdblkpage.lo CC H5FAhdr.lo CC H5FAint.lo CC H5FAstat.lo CC H5FAtest.lo CC H5FD.lo CC H5FDcore.lo CC H5FDfamily.lo CC H5FDhdfs.lo CC H5FDint.lo CC H5FDlog.lo CC H5FDmulti.lo CC H5FDsec2.lo CC H5FDspace.lo CC H5FDsplitter.lo CC H5FDstdio.lo CC H5FDtest.lo CC H5FL.lo CC H5FO.lo CC H5FS.lo CC H5FScache.lo CC H5FSdbg.lo CC H5FSint.lo CC H5FSsection.lo CC H5FSstat.lo CC H5FStest.lo CC H5G.lo CC H5Gbtree2.lo CC H5Gcache.lo CC H5Gcompact.lo CC H5Gdense.lo CC H5Gdeprec.lo CC H5Gent.lo CC H5Gint.lo CC H5Glink.lo CC H5Gloc.lo CC H5Gname.lo CC H5Gnode.lo CC H5Gobj.lo CC H5Goh.lo CC H5Groot.lo CC H5Gstab.lo CC H5Gtest.lo CC H5Gtraverse.lo CC H5HF.lo CC H5HFbtree2.lo CC H5HFcache.lo CC H5HFdbg.lo CC H5HFdblock.lo CC H5HFdtable.lo CC H5HFhdr.lo CC H5HFhuge.lo CC H5HFiblock.lo CC H5HFiter.lo CC H5HFman.lo CC H5HFsection.lo CC H5HFspace.lo CC H5HFstat.lo CC H5HFtest.lo CC H5HFtiny.lo CC H5HG.lo CC H5HGcache.lo CC H5HGdbg.lo CC H5HGquery.lo CC H5HL.lo CC H5HLcache.lo CC H5HLdbg.lo CC H5HLint.lo CC H5HLprfx.lo CC H5HLdblk.lo CC H5HP.lo CC H5I.lo CC H5Itest.lo CC H5L.lo CC H5Lexternal.lo CC H5make_libsettings.o CCLD H5make_libsettings LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/opt/R/x86_64/lib | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5make_libsettings > H5lib_settings.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) CC H5lib_settings.lo CC H5MF.lo CC H5MFaggr.lo CC H5MFdbg.lo CC H5MFsection.lo CC H5MM.lo CC H5MP.lo CC H5MPtest.lo CC H5O.lo CC H5Odeprec.lo CC H5Oainfo.lo CC H5Oalloc.lo CC H5Oattr.lo CC H5Oattribute.lo CC H5Obogus.lo CC H5Obtreek.lo CC H5Ocache.lo CC H5Ocache_image.lo CC H5Ochunk.lo CC H5Ocont.lo CC H5Ocopy.lo CC H5Odbg.lo CC H5Odrvinfo.lo CC H5Odtype.lo CC H5Oefl.lo CC H5Ofill.lo CC H5Oflush.lo CC H5Ofsinfo.lo CC H5Oginfo.lo CC H5Oint.lo CC H5Olayout.lo CC H5Olinfo.lo CC H5Olink.lo CC H5Omessage.lo CC H5Omtime.lo CC H5Oname.lo CC H5Onull.lo CC H5Opline.lo CC H5Orefcount.lo CC H5Osdspace.lo CC H5Oshared.lo CC H5Oshmesg.lo CC H5Ostab.lo CC H5Otest.lo CC H5Ounknown.lo CC H5P.lo CC H5Pacpl.lo CC H5Pdapl.lo CC H5Pdcpl.lo CC H5Pdeprec.lo CC H5Pdxpl.lo CC H5Pencdec.lo CC H5Pfapl.lo CC H5Pfcpl.lo CC H5Pfmpl.lo CC H5Pgcpl.lo CC H5Pint.lo CC H5Plapl.lo CC H5Plcpl.lo CC H5Pocpl.lo CC H5Pocpypl.lo CC H5Pstrcpl.lo CC H5Ptest.lo CC H5PB.lo CC H5PL.lo CC H5PLint.lo CC H5PLpath.lo CC H5PLplugin_cache.lo CC H5R.lo CC H5Rint.lo CC H5Rdeprec.lo CC H5UC.lo CC H5RS.lo CC H5S.lo CC H5Sall.lo CC H5Sdbg.lo CC H5Shyper.lo CC H5Snone.lo CC H5Spoint.lo CC H5Sselect.lo CC H5Stest.lo CC H5SL.lo CC H5SM.lo CC H5SMbtree2.lo CC H5SMcache.lo CC H5SMmessage.lo CC H5SMtest.lo CC H5ST.lo CC H5T.lo CC H5Tarray.lo CC H5Tbit.lo CC H5Tcommit.lo CC H5Tcompound.lo CC H5Tconv.lo CC H5Tcset.lo CC H5Tdbg.lo CC H5Tdeprec.lo CC H5Tenum.lo CC H5Tfields.lo CC H5Tfixed.lo CC H5Tfloat.lo CC H5detect.o CCLD H5detect LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -L/opt/R/x86_64/lib | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5detect > H5Tinit.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5Tinit.c ; exit 1) CC H5Tinit.lo CC H5Tnative.lo CC H5Toffset.lo CC H5Toh.lo CC H5Topaque.lo CC H5Torder.lo CC H5Tpad.lo CC H5Tprecis.lo CC H5Tstrpad.lo CC H5Tvisit.lo CC H5Tvlen.lo CC H5TS.lo CC H5VM.lo CC H5WB.lo CC H5Z.lo CC H5Zdeflate.lo CC H5Zfletcher32.lo CC H5Znbit.lo CC H5Zshuffle.lo CC H5Zscaleoffset.lo CC H5Zszip.lo CC H5Ztrans.lo CC H5FDros3.lo CC H5FDs3comms.lo CCLD libhdf5.la /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5CS.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5Obogus.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libhdf5.a(H5TS.o) has no symbols make[3]: Nothing to be done for `build-lib'. + cd src + make lib CXX H5Exception.lo CXX H5IdComponent.lo CXX H5DataSpace.lo CXX H5PropList.lo CXX H5Library.lo CXX H5FaccProp.lo CXX H5FcreatProp.lo CXX H5LcreatProp.lo CXX H5LaccProp.lo CXX H5DaccProp.lo CXX H5DxferProp.lo CXX H5DcreatProp.lo CXX H5Location.lo CXX H5AbstractDs.lo CXX H5Attribute.lo CXX H5Object.lo CXX H5OcreatProp.lo CXX H5DataType.lo CXX H5AtomType.lo CXX H5PredType.lo CXX H5EnumType.lo CXX H5IntType.lo CXX H5FloatType.lo CXX H5StrType.lo CXX H5ArrayType.lo CXX H5VarLenType.lo CXX H5CompType.lo CXX H5DataSet.lo CXX H5CommonFG.lo CXX H5Group.lo CXX H5File.lo CXXLD libhdf5_cpp.la make[3]: Nothing to be done for `build-lib'. + cd src + make lib CC H5DO.lo CC H5DS.lo CC H5IM.lo CC H5LT.lo CC H5LTanalyze.lo CC H5LTparse.lo CC H5PT.lo CC H5TB.lo CC H5LD.lo CCLD libhdf5_hl.la + cd c++ + make lib make[4]: Nothing to be done for `build-lib'. + cd src + make lib CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.la mkdir -p "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src"/*.h "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/libhdf5.settings "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/include -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rhdf5lib.c -o Rhdf5lib.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o Rhdf5lib.so Rhdf5lib.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libaec.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (Rhdf5lib)