Compilation error on AWS

[elenichri]

Hello. I am trying to install hdf5r on AWS. The installed R version is 3.6.1. I have already successfully ran sudo apt-get install libhdf5-dev

When I try to install the hdfr5 library here is what happens:

install.packages("hdf5r")
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1585k  100 1585k    0     0   740k      0  0:00:02  0:00:02 --:--:--  740k
* 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... 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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... 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... /home/ubuntu/anaconda3/bin//h5cc
checking for HDF5 libraries... yes (version 1.10.2)
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... /home/ubuntu/anaconda3/bin//h5fc
Found hdf5 with version: 1.10.2
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_10_0/*.c 1_10_0/*.h .
x86_64-conda_cos6-linux-gnu-cc -I/home/ubuntu/anaconda3/lib/R/include -DNDEBUG -I/home/ubuntu/anaconda3/include -I/home/ubuntu/anaconda3/include -I/home/ubuntu/anaconda3/include   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/ubuntu/anaconda3/include -I/home/ubuntu/anaconda3/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/ubuntu/anaconda3/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/ubuntu/anaconda3/lib/R/include -DNDEBUG -I/home/ubuntu/anaconda3/include -I/home/ubuntu/anaconda3/include -I/home/ubuntu/anaconda3/include   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/ubuntu/anaconda3/include -I/home/ubuntu/anaconda3/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/ubuntu/anaconda3/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_mpio_no_collective_cause_t':
datatype_export.c:1496:12: error: 'H5D_MPIO_FILTERS' undeclared (first use in this function); did you mean 'H5Z_MAX_NFILTERS'?
   myenum = H5D_MPIO_FILTERS;
            ^~~~~~~~~~~~~~~~
            H5Z_MAX_NFILTERS
datatype_export.c:1496:12: note: each undeclared identifier is reported only once for each function it appears in
make: *** [/home/ubuntu/anaconda3/lib/R/etc/Makeconf:160: datatype_export.o] Error 1
ERROR: compilation failed for package ‘hdf5r’
* removing ‘/home/ubuntu/anaconda3/lib/R/library/hdf5r’

The downloaded source packages are in
	‘/tmp/RtmpLHbxOK/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("hdf5r") :
  installation of package ‘hdf5r’ had non-zero exit status

Could you please help?