* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’ * installing *source* package ‘hdf5r’ ... ** this is package ‘hdf5r’ version ‘1.3.16’ ** 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... gawk checking for grep that handles long lines and -e... /usr/bin/grep checking for gcc... gcc-16 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 gcc-16 accepts -g... yes checking for gcc-16 option to enable C23 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... /usr/bin/h5cc checking for HDF5 libraries... yes (version 2.2.0) checking for hdf5.h... yes checking for H5Fcreate in -lhdf5... no checking for hdf5_hl.h... yes checking for H5LTpath_valid in -lhdf5_hl... no checking for main in -lhdf5_hl... no checking for matching HDF5 Fortran wrapper... /usr/bin/h5fc Found hdf5 with version: 2.2.0 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 checking for library containing H5TBwrite_fields_index... none required Using variables: HDF5_LIBS= -lhdf5_serial_hl -lhdf5_serial HDF5_CFLAGS= HDF5_CPPFLAGS=-I/usr/include/hdf5/serial configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-16 (Debian 16.2.0-3) 16.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy6W1u1/R.INSTALL24e4ed18c487bc/hdf5r/src' cp 1_12_0/*.c 1_12_0/*.h . if [ "patches/patch_2.0.0" != "" ] && [ -s "patches/patch_2.0.0" ]; then patch -p2 < "patches/patch_2.0.0" || exit $?; fi patching file Wrapper_auto_H5FDfamily.c patching file Wrapper_auto_H5P.c patching file Wrapper_auto_H5P.c patching file Wrapper_auto_H5FDlog.c patching file Wrapper_auto_H5FDsec2.c patching file Wrapper_auto_H5FDstdio.c gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c const_export.c -o const_export.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c datatype_export.c -o datatype_export.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert.c -o convert.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hdf5r_init.c -o hdf5r_init.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5Error.c -o H5Error.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5ls.c -o H5ls.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o gcc-16 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -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 -lhdf5_serial_hl -lhdf5_serial -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpy6W1u1/R.INSTALL24e4ed18c487bc/hdf5r/src' make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy6W1u1/R.INSTALL24e4ed18c487bc/hdf5r/src' cp 1_12_0/*.c 1_12_0/*.h . if [ "patches/patch_2.0.0" != "" ] && [ -s "patches/patch_2.0.0" ]; then patch -p2 < "patches/patch_2.0.0" || exit $?; fi patching file Wrapper_auto_H5FDfamily.c patching file Wrapper_auto_H5P.c patching file Wrapper_auto_H5P.c patching file Wrapper_auto_H5FDlog.c patching file Wrapper_auto_H5FDsec2.c patching file Wrapper_auto_H5FDstdio.c gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c const_export.c -o const_export.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c datatype_export.c -o datatype_export.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert.c -o convert.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hdf5r_init.c -o hdf5r_init.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5Error.c -o H5Error.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5ls.c -o H5ls.o gcc-16 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpy6W1u1/R.INSTALL24e4ed18c487bc/hdf5r/src' installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-hdf5r/00new/hdf5r/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 (hdf5r)