failed to install hdf5r from rstudio on unix

[zpingfeng]

install.packages("hdf5r") ### :-() Installing package into ‘/usr/local/Rlibs’ (as ‘lib’ is unspecified) % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1585k 100 1585k 0 0 538k 0 0:00:02 0:00:02 --:--:-- 538k

• installing source package ‘hdf5r’ ... ** package ‘hdf5r’ successfully unpacked and MD5 sums checked checking for a sed that does not truncate output... /bin/sed checking for gawk... gawk checking for grep that handles long lines and -e... /bin/grep checking for gcc... /usr/local/bin/gcc 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 we are using the GNU C compiler... yes checking whether /usr/local/bin/gcc accepts -g... yes checking for /usr/local/bin/gcc option to accept ISO C89... none needed checking how to run the C preprocessor... /usr/local/bin/gcc -E checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for h5cc... /usr/local/bin/h5cc checking for HDF5 libraries... yes (version 1.9.224) checking hdf5.h usability... yes checking hdf5.h presence... yes 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... no Found hdf5 with version: 1.9.224 checking for ggrep... /bin/grep checking whether /bin/grep accepts -o... yes checking for ggrep... (cached) /bin/grep checking whether /bin/grep accepts -o... yes configure: creating ./config.status config.status: creating src/Makevars ** libs cp 1_8_16/.c 1_8_16/.h . x86_64-conda_cos6-linux-gnu-cc -I/home/ping/miniconda3/lib/R/include -DNDEBUG -I/usr/local/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/ping/miniconda3/include -I/home/ping/miniconda3/include -D_DEFINE_H5FREE_MEMORY_=0 -D__USE_MINGW_ANSI_STDIO -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/ping/miniconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c const_export.c -o const_export.o x86_64-conda_cos6-linux-gnu-cc -I/home/ping/miniconda3/lib/R/include -DNDEBUG -I/usr/local/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/ping/miniconda3/include -I/home/ping/miniconda3/include -D_DEFINE_H5FREE_MEMORY_=0 -D__USE_MINGW_ANSI_STDIO -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/ping/miniconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c datatype_export.c -o datatype_export.o datatype_export.c: In function 'create_DT_H5D_chunk_index_t': datatype_export.c:1370:12: error: 'H5D_CHUNK_BTREE' undeclared (first use in this function); did you mean 'H5D_CHUNK_IDX_BTREE'? myenum = H5D_CHUNK_BTREE; ^~~~~~~~~~~~~~~ H5D_CHUNK_IDX_BTREE datatype_export.c:1370:12: note: each undeclared identifier is reported only once for each function it appears in In file included from /home/ping/miniconda3/x86_64-conda_cos6-linux-gnu/sysroot/usr/include/string.h:34:0, from /home/ping/miniconda3/lib/R/include/R_ext/RS.h:34, from /home/ping/miniconda3/lib/R/include/R.h:91, from global.h:27, from datatype_export.h:23, from datatype_export.c:20: datatype_export.c: In function 'create_DT_H5F_info_t': /usr/local/include/H5Tpublic.h:26:26: error: 'H5F_info2_t {aka struct H5F_info2_t}' has no member named 'super_ext_size' #define HOFFSET(S,M) (offsetof(S,M)) ^ datatype_export.c:2291:41: note: in expansion of macro 'HOFFSET' H5Tinsert(dtype_id, "super_ext_size", HOFFSET(H5F_info_t, super_ext_size), h5_datatype[DT_hsize_t]); ^~~~~~~ make: *** [/home/ping/miniconda3/lib/R/etc/Makeconf:160: datatype_export.o] Error 1 ERROR: compilation failed for package ‘hdf5r’
• removing ‘/usr/local/Rlibs/hdf5r’ Warning in install.packages : installation of package ‘hdf5r’ had non-zero exit status

The downloaded source packages are in ‘/home/tmp/RtmpQo81aQ/downloaded_packages’

[mannau]

The problem seems to be the version of miniconda you are linking to, see also #113.