* installing to library ‘/home/hornik/tmp/R.check/r-release-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-14
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-14 accepts -g... yes
checking for gcc-14 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 1.14.5)
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: 1.14.5
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-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpAWGPnt/R.INSTALL146b1265c10231/hdf5r/src'
cp 1_12_0/*.c 1_12_0/*.h .
if [ "" != "" ]; then patch -p2 < patch_; fi
gcc-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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
H5ls.c: In function ‘H5Dget_info’:
H5ls.c:79:97: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
79 | dims_char_written += snprintf(dataset_info->dims + dims_char_written, alloc_size, "%llu", dims[i]);
| ~~~^ ~~~~~~~
| | |
| | hsize_t {aka long unsigned int}
| long long unsigned int
| %lu
H5ls.c:89:108: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
89 | maxdims_char_written += snprintf(dataset_info->maxdims + maxdims_char_written, alloc_size, "%llu", maxdims[i]);
| ~~~^ ~~~~~~~~~~
| | |
| | hsize_t {aka long unsigned int}
| long long unsigned int
| %lu
gcc-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -shared -L/home/hornik/tmp/R.check/r-release-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-release-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpAWGPnt/R.INSTALL146b1265c10231/hdf5r/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpAWGPnt/R.INSTALL146b1265c10231/hdf5r/src'
cp 1_12_0/*.c 1_12_0/*.h .
if [ "" != "" ]; then patch -p2 < patch_; fi
gcc-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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-14 -I"/home/hornik/tmp/R.check/r-release-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
H5ls.c: In function ‘H5Dget_info’:
H5ls.c:79:97: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
79 | dims_char_written += snprintf(dataset_info->dims + dims_char_written, alloc_size, "%llu", dims[i]);
| ~~~^ ~~~~~~~
| | |
| | hsize_t {aka long unsigned int}
| long long unsigned int
| %lu
H5ls.c:89:108: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘hsize_t’ {aka ‘long unsigned int’} [-Wformat=]
89 | maxdims_char_written += snprintf(dataset_info->maxdims + maxdims_char_written, alloc_size, "%llu", maxdims[i]);
| ~~~^ ~~~~~~~~~~
| | |
| | hsize_t {aka long unsigned int}
| long long unsigned int
| %lu
gcc-14 -I"/home/hornik/tmp/R.check/r-release-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/RtmpAWGPnt/R.INSTALL146b1265c10231/hdf5r/src'
installing to /home/hornik/tmp/R.check/r-release-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)