* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘hdf5r’ ...
** this is package ‘hdf5r’ version ‘1.3.12’
** 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 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 2.1.0)
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: 2.1.0
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
Using variables:
HDF5_LIBS= -lhdf5_serial_hl -lhdf5_serial -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-16 (Debian 16.1.0-3) 16.1.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgDWbGz/R.INSTALL37946e72dc15dd/hdf5r/src'
cp 1_12_0/*.c 1_12_0/*.h .
if [ "" != "" ]; then patch -p2 < patch_; fi
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
Wrapper_auto_H5FDfamily.c: In function ‘R_H5FD_family_init’:
Wrapper_auto_H5FDfamily.c:23:22: error: implicit declaration of function ‘H5FD_family_init’; did you mean ‘R_H5FD_family_init’? [-Wimplicit-function-declaration]
23 | hid_t return_val = H5FD_family_init();
| ^~~~~~~~~~~~~~~~
| R_H5FD_family_init
make[1]: *** [/home/hornik/tmp/R.check/r-devel-gcc/Work/build/etc/Makeconf:190: Wrapper_auto_H5FDfamily.o] Error 1
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgDWbGz/R.INSTALL37946e72dc15dd/hdf5r/src'
ERROR: compilation failed for package ‘hdf5r’
* removing ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/hdf5r’