* installing *source* package ‘hdf5r’ ... ** package ‘hdf5r’ successfully unpacked and MD5 sums checked ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking for grep that handles long lines and -e... /usr/bin/grep 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 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 h5cc... /opt/R/x86_64/bin/h5cc checking for HDF5 libraries... yes (version 1.12.2) checking for hdf5.h... yes checking for H5Fcreate in -lhdf5... yes checking for hdf5_hl.h... yes checking for H5LTpath_valid in -lhdf5_hl... yes checking for main in -lhdf5_hl... yes checking for matching HDF5 Fortran wrapper... no Found hdf5 with version: 1.12.2 checking for ggrep... /usr/bin/grep checking whether /usr/bin/grep accepts -o... yes checking for ggrep... (cached) /usr/bin/grep checking whether /usr/bin/grep accepts -o... yes Using variables: HDF5_LIBS= -L/opt/R/x86_64/lib -L/opt/R/x86_64/lib -lsz -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm HDF5_CFLAGS= HDF5_CPPFLAGS=-I/opt/R/x86_64/include -I/opt/R/x86_64/include configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using SDK: ‘MacOSX11.3.sdk’ cp 1_12_0/*.c 1_12_0/*.h . if [ "" != "" ]; then patch -p2 < patch_; fi clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c const_export.c -o const_export.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c datatype_export.c -o datatype_export.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c convert.c -o convert.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c hdf5r_init.c -o hdf5r_init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c H5Error.c -o H5Error.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c H5ls.c -o H5ls.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o hdf5r.so const_export.o datatype_export.o Wrapper_auto_H5A.o Wrapper_auto_H5.o Wrapper_auto_H5D.o Wrapper_auto_H5DS.o Wrapper_auto_H5E.o Wrapper_auto_H5F.o Wrapper_auto_H5G.o Wrapper_auto_H5I.o Wrapper_auto_H5IM.o Wrapper_auto_H5L.o Wrapper_auto_H5LT.o Wrapper_auto_H5O.o Wrapper_auto_H5P.o Wrapper_auto_H5R.o Wrapper_auto_H5S.o Wrapper_auto_H5TB.o Wrapper_auto_H5T.o Wrapper_auto_H5Z.o Wrapper_auto_H5FDcore.o Wrapper_auto_H5FDfamily.o Wrapper_auto_H5FDlog.o Wrapper_auto_H5FDsec2.o Wrapper_auto_H5FDstdio.o convert.o hdf5r_init.o H5Error.o H5ls.o Wrapper_manual_H5T.o -L/opt/R/x86_64/lib -L/opt/R/x86_64/lib -lsz -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation cp 1_12_0/*.c 1_12_0/*.h . if [ "" != "" ]; then patch -p2 < patch_; fi clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c const_export.c -o const_export.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c datatype_export.c -o datatype_export.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c convert.c -o convert.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c hdf5r_init.c -o hdf5r_init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c H5Error.c -o H5Error.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c H5ls.c -o H5ls.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -I/opt/R/x86_64/include -I/opt/R/x86_64/include -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fPIC -falign-functions=64 -Wall -g -O2 -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00LOCK-hdf5r/00new/hdf5r/libs ** generating debug symbols (dSYM) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/const_export.o: timestamp mismatch between object file (2024-03-05 01:05:27.495326000) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/datatype_export.o: timestamp mismatch between object file (2024-03-05 01:05:28.490226638) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5A.o: timestamp mismatch between object file (2024-03-05 01:05:27.707308946) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5.o: timestamp mismatch between object file (2024-03-05 01:05:27.486102648) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5D.o: timestamp mismatch between object file (2024-03-05 01:05:27.776861469) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5DS.o: timestamp mismatch between object file (2024-03-05 01:05:27.466533071) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5E.o: timestamp mismatch between object file (2024-03-05 01:05:27.819604016) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5F.o: timestamp mismatch between object file (2024-03-05 01:05:28.142889927) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5G.o: timestamp mismatch between object file (2024-03-05 01:05:27.738286367) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5I.o: timestamp mismatch between object file (2024-03-05 01:05:27.953303618) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5IM.o: timestamp mismatch between object file (2024-03-05 01:05:28.039036919) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5L.o: timestamp mismatch between object file (2024-03-05 01:05:28.096325547) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5LT.o: timestamp mismatch between object file (2024-03-05 01:05:28.412784400) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5O.o: timestamp mismatch between object file (2024-03-05 01:05:28.272667282) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5P.o: timestamp mismatch between object file (2024-03-05 01:05:29.395953809) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5R.o: timestamp mismatch between object file (2024-03-05 01:05:28.320910738) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5S.o: timestamp mismatch between object file (2024-03-05 01:05:28.454496756) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5TB.o: timestamp mismatch between object file (2024-03-05 01:05:28.550286781) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5T.o: timestamp mismatch between object file (2024-03-05 01:05:28.728647164) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5Z.o: timestamp mismatch between object file (2024-03-05 01:05:28.556339073) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDcore.o: timestamp mismatch between object file (2024-03-05 01:05:28.595225251) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDfamily.o: timestamp mismatch between object file (2024-03-05 01:05:28.636401099) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDlog.o: timestamp mismatch between object file (2024-03-05 01:05:28.685297351) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDsec2.o: timestamp mismatch between object file (2024-03-05 01:05:28.689508397) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDstdio.o: timestamp mismatch between object file (2024-03-05 01:05:28.727602381) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/convert.o: timestamp mismatch between object file (2024-03-05 01:05:30.513980497) and debug map (2024-03-05 01:05:26.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/hdf5r_init.o: timestamp mismatch between object file (2024-03-05 01:05:28.847772585) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/H5Error.o: timestamp mismatch between object file (2024-03-05 01:05:28.833857063) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/H5ls.o: timestamp mismatch between object file (2024-03-05 01:05:28.897151379) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_manual_H5T.o: timestamp mismatch between object file (2024-03-05 01:05:28.912474510) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/const_export.o: timestamp mismatch between object file (2024-03-05 01:05:27.495326000) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/datatype_export.o: timestamp mismatch between object file (2024-03-05 01:05:28.490226638) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5A.o: timestamp mismatch between object file (2024-03-05 01:05:27.707308946) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5.o: timestamp mismatch between object file (2024-03-05 01:05:27.486102648) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5D.o: timestamp mismatch between object file (2024-03-05 01:05:27.776861469) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5DS.o: timestamp mismatch between object file (2024-03-05 01:05:27.466533071) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5E.o: timestamp mismatch between object file (2024-03-05 01:05:27.819604016) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5F.o: timestamp mismatch between object file (2024-03-05 01:05:28.142889927) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5G.o: timestamp mismatch between object file (2024-03-05 01:05:27.738286367) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5I.o: timestamp mismatch between object file (2024-03-05 01:05:27.953303618) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5IM.o: timestamp mismatch between object file (2024-03-05 01:05:28.039036919) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5L.o: timestamp mismatch between object file (2024-03-05 01:05:28.096325547) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5LT.o: timestamp mismatch between object file (2024-03-05 01:05:28.412784400) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5O.o: timestamp mismatch between object file (2024-03-05 01:05:28.272667282) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5P.o: timestamp mismatch between object file (2024-03-05 01:05:29.395953809) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5R.o: timestamp mismatch between object file (2024-03-05 01:05:28.320910738) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5S.o: timestamp mismatch between object file (2024-03-05 01:05:28.454496756) and debug map (2024-03-05 01:05:24.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5TB.o: timestamp mismatch between object file (2024-03-05 01:05:28.550286781) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5T.o: timestamp mismatch between object file (2024-03-05 01:05:28.728647164) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5Z.o: timestamp mismatch between object file (2024-03-05 01:05:28.556339073) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDcore.o: timestamp mismatch between object file (2024-03-05 01:05:28.595225251) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDfamily.o: timestamp mismatch between object file (2024-03-05 01:05:28.636401099) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDlog.o: timestamp mismatch between object file (2024-03-05 01:05:28.685297351) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDsec2.o: timestamp mismatch between object file (2024-03-05 01:05:28.689508397) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_auto_H5FDstdio.o: timestamp mismatch between object file (2024-03-05 01:05:28.727602381) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/convert.o: timestamp mismatch between object file (2024-03-05 01:05:30.513980497) and debug map (2024-03-05 01:05:26.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/hdf5r_init.o: timestamp mismatch between object file (2024-03-05 01:05:28.847772585) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/H5Error.o: timestamp mismatch between object file (2024-03-05 01:05:28.833857063) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/H5ls.o: timestamp mismatch between object file (2024-03-05 01:05:28.897151379) and debug map (2024-03-05 01:05:25.000000000) warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.3/hdf5r.Rcheck/00_pkg_src/hdf5r/src/Wrapper_manual_H5T.o: timestamp mismatch between object file (2024-03-05 01:05:28.912474510) and debug map (2024-03-05 01:05:25.000000000) ** 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 (hdf5r)