* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* 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... gawk
checking for grep that handles long lines and -e... /usr/bin/grep
checking for gcc... gcc-13
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-13 accepts -g... yes
checking for gcc-13 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... /usr/bin/h5cc
checking for HDF5 libraries... yes (version 1.10.10)
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... /usr/bin/h5fc
Found hdf5 with version: 1.10.10
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/usr/lib/x86_64-linux-gnu/hdf5/serial -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm
HDF5_CFLAGS=
HDF5_CPPFLAGS=-I/usr/include/hdf5/serial
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpSMLXjD/R.INSTALL3e55a30f78a22/hdf5r/src'
cp 1_10_3/*.c 1_10_3/*.h .
if [ "1.10.6" != "" ]; then patch -p2 < patch_1.10.6; fi
patching file datatype_export.c
Hunk #1 succeeded at 1901 (offset 1 line).
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c const_export.c -o const_export.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c datatype_export.c -o datatype_export.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert.c -o convert.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hdf5r_init.c -o hdf5r_init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5Error.c -o H5Error.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5ls.c -o H5ls.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-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 -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -L. -lhdf5_hl -lhdf5 -lz -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpSMLXjD/R.INSTALL3e55a30f78a22/hdf5r/src'
make[1]: Entering directory '/tmp/RtmpSMLXjD/R.INSTALL3e55a30f78a22/hdf5r/src'
cp 1_10_3/*.c 1_10_3/*.h .
if [ "1.10.6" != "" ]; then patch -p2 < patch_1.10.6; fi
patching file datatype_export.c
Hunk #1 succeeded at 1901 (offset 1 line).
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c const_export.c -o const_export.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c datatype_export.c -o datatype_export.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c convert.c -o convert.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hdf5r_init.c -o hdf5r_init.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5Error.c -o H5Error.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c H5ls.c -o H5ls.o
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I/usr/include/hdf5/serial -I/usr/local/include -D_FORTIFY_SOURCE=3 -D__USE_MINGW_ANSI_STDIO -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o
make[1]: Leaving directory '/tmp/RtmpSMLXjD/R.INSTALL3e55a30f78a22/hdf5r/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-hdf5r/00new/hdf5r/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘hdf5r’
finding HTML links ... done
H5A-class html
H5D-class html
H5File-class html
H5File.open html
H5GTD_factory html
H5Group-class html
H5Group_access html
H5P-class html
H5P_ATTRIBUTE_CREATE-class html
H5P_CLASS-class html
H5P_DATASET_ACCESS-class html
H5P_DATASET_CREATE-class html
H5P_DATASET_XFER-class html
H5P_DEFAULT-class html
H5P_FILE_ACCESS-class html
H5P_FILE_CREATE-class html
H5P_LINK_ACCESS-class html
H5P_LINK_CREATE-class html
H5P_OBJECT_COPY-class html
H5P_OBJECT_CREATE-class html
H5P_factory html
H5R-class html
H5R_DATASET_REGION-class html
H5R_OBJECT-class html
H5R_functions html
H5RefClass-class html
H5S-class html
H5S_ALL-class html
H5S_H5D_subset_assign html
H5T-class html
H5T_ARRAY-class html
H5T_COMPLEX-class html
H5T_COMPOUND-class html
H5T_ENUM-class html
H5T_FLOAT-class html
H5T_INTEGER-class html
H5T_LOGICAL-class html
H5T_STRING-class html
H5T_VLEN-class html
H5T_extractID html
H5T_factory html
H5_close_any html
RToH5 html
apply_selection html
are_args_scalar html
args_regularity_evaluation html
array_counter html
array_reorder html
as_hex html
check_arg_for_hyperslab_func html
clean_ls_df html
convertRoundTrip html
create_empty html
do_reshuffle html
equal_id_check html
expand_point_grid html
extract_dim html
factor_ext html
factor_ext_functions html
flatten_df html
get_id html
guess_chunks html
guess_dtype html
guess_space html
h5-wrapper html
h5attributes html
h5const html
h5garbage_collect html
h5types html
h5version html
hdf5r-package html
hyperslab_to_points html
is_hdf5 html
list-groups-datasets html
match.call.withDef html
names.H5Group html
print.data.frame_ext html
print_attributes html
print_class_id html
print_listing html
regularity_eval_to_selection html
standalone_H5D_get_type html
standalone_H5S_select_multiple_hyperslab
html
text_to_dtype html
types_env_access html
** 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)