* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/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... clang-22 -std=gnu23
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-22 -std=gnu23 accepts -g... yes
checking for clang-22 -std=gnu23 option to enable C11 features... -std=gnu11
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: ‘Debian clang version 22.1.8 (1+b2)’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpIKQQ0U/R.INSTALL13f29818a0be36/hdf5r/src'
cp 1_12_0/*.c 1_12_0/*.h .
if [ "" != "" ]; then patch -p2 < patch_; fi
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c const_export.c -o const_export.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c datatype_export.c -o datatype_export.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o
clang-22 -std=gnu23 -I"/home/hornik/tmp/R.check/r-devel-clang/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 -O3 -Wall -pedantic -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o
Wrapper_auto_H5FDfamily.c:23:22: error: use of undeclared identifier 'H5FD_family_init'; did you mean 'R_H5FD_family_init'?
23 | hid_t return_val = H5FD_family_init();
| ^~~~~~~~~~~~~~~~
| R_H5FD_family_init
Wrapper_auto_H5FDfamily.c:21:6: note: 'R_H5FD_family_init' declared here
21 | SEXP R_H5FD_family_init(void){
| ^
Wrapper_auto_H5FDfamily.c:23:9: error: incompatible pointer to integer conversion initializing 'hid_t' (aka 'long') with an expression of type 'SEXP' (aka 'struct SEXPREC *') [-Wint-conversion]
23 | hid_t return_val = H5FD_family_init();
| ^ ~~~~~~~~~~~~~~~~~~
2 errors generated.
make[1]: *** [/home/hornik/tmp/R.check/r-devel-clang/Work/build/etc/Makeconf:190: Wrapper_auto_H5FDfamily.o] Error 1
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpIKQQ0U/R.INSTALL13f29818a0be36/hdf5r/src'
ERROR: compilation failed for package ‘hdf5r’
* removing ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/hdf5r’