Install log for 'hdf5r'

* 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... /usr/local/clang19/bin/clang
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 /usr/local/clang19/bin/clang accepts -g... yes
checking for /usr/local/clang19/bin/clang 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 1.12.1)
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: 1.12.1
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/lib64  -lhdf5_hl  -lhdf5  -L. -lhdf5_hl -lhdf5 -lz -lm
HDF5_CFLAGS=
HDF5_CPPFLAGS=-I/usr/include 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hdf5r/src'
cp 1_12_0/*.c 1_12_0/*.h .
if [ "" != "" ]; then patch -p2 < patch_; fi
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c const_export.c -o const_export.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c datatype_export.c -o datatype_export.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c convert.c -o convert.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hdf5r_init.c -o hdf5r_init.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c H5Error.c -o H5Error.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c H5ls.c -o H5ls.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o
/usr/local/clang19/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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/lib64 -lhdf5_hl -lhdf5 -L. -lhdf5_hl -lhdf5 -lz -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hdf5r/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/hdf5r/src'
cp 1_12_0/*.c 1_12_0/*.h .
if [ "" != "" ]; then patch -p2 < patch_; fi
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c const_export.c -o const_export.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c datatype_export.c -o datatype_export.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5A.c -o Wrapper_auto_H5A.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5.c -o Wrapper_auto_H5.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5D.c -o Wrapper_auto_H5D.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5DS.c -o Wrapper_auto_H5DS.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5E.c -o Wrapper_auto_H5E.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5F.c -o Wrapper_auto_H5F.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5G.c -o Wrapper_auto_H5G.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5I.c -o Wrapper_auto_H5I.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5IM.c -o Wrapper_auto_H5IM.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5L.c -o Wrapper_auto_H5L.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5LT.c -o Wrapper_auto_H5LT.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5O.c -o Wrapper_auto_H5O.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5P.c -o Wrapper_auto_H5P.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5R.c -o Wrapper_auto_H5R.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5S.c -o Wrapper_auto_H5S.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5TB.c -o Wrapper_auto_H5TB.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5T.c -o Wrapper_auto_H5T.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5Z.c -o Wrapper_auto_H5Z.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDcore.c -o Wrapper_auto_H5FDcore.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDfamily.c -o Wrapper_auto_H5FDfamily.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDlog.c -o Wrapper_auto_H5FDlog.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDsec2.c -o Wrapper_auto_H5FDsec2.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_auto_H5FDstdio.c -o Wrapper_auto_H5FDstdio.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c convert.c -o convert.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c hdf5r_init.c -o hdf5r_init.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c H5Error.c -o H5Error.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c H5ls.c -o H5ls.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I/usr/include   -isystem /usr/local/clang19/include -I/usr/local/clang/include   -D__USE_MINGW_ANSI_STDIO -DH5_USE_110_API -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c Wrapper_manual_H5T.c -o Wrapper_manual_H5T.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/hdf5r/src'
installing to /data/gannet/ripley/R/packages/tests-clang/hdf5r.Rcheck/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)