problems installing hdf5r package

[MartaBenegas]

Hi, I'm trying to install the library on an AWS with Linux 4.14.173-137.229.amzn2.x86_64. Following the instructions, I've first typed sudo yum install hdf5-devel on the terminal and the predetermined version of hdf5 installed is 1.8.12-11.el7. Then, inside R whether I try install.packages("hdf5r") or devtools::install_github("hhoeflin/hdf5r") it raises the same error:

Installing package into ‘/home/ec2-user/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)  
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
(I have delete mirror list)
Selection: 45
probando la URL 'https://ftp.cixug.es/CRAN/src/contrib/hdf5r_1.3.2.tar.gz'
Content type 'application/x-gzip' length 2961561 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* 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... 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... /usr/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/bin/h5cc
checking for HDF5 libraries... yes (version 1.8.12)
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... /usr/bin/h5fc
Found hdf5 with version: 1.8.12
configure: error: The version of hdf5 installed on your system is not sufficient. Please ensure that at least version 1.8.13 is installed
ERROR: configuration failed for package ‘hdf5r’
* removing ‘/home/ec2-user/R/x86_64-redhat-linux-gnu-library/3.6/hdf5r’

The downloaded source packages are in
        ‘/tmp/Rtmp8TW6tn/downloaded_packages’
Warning message:
In install.packages("hdf5r") :
  installation of package ‘hdf5r’ had non-zero exit status

How can I update the hdf5 version?

[hanhyebin]

I am having the same issue

[hanhyebin]

@MartaBenegas Were you able to solve this issue?

I realized that R in our university HPCC's has hdf5 as a Linux module. So, I had to load the most recent hdf5, THEN open R, and download hdf5r. Quite the shit show but yea :)