Unable to install hdf5r package - MacOS, R 4.1

[millerkaplanlab]

Hello, I recently upgraded R to version 4.1 and am no longer able to install hdf5r (Warning in install.packages installation of package 'hdf5r' had non-zero exit status). If I install from source, I get the following error: Error: package or namespace load failed for 'hdf5r' in dyn.load. I've also tried to install from brew (Terminal); however, R does not seem to recognize that it is installed. Any help would be appreciated.

[odavalos]

This might help. https://github.com/hhoeflin/hdf5r/issues/171#issuecomment-891367729

On an M1 Mac the comment from above allowed R to find hdf5 but still could not install. :(

  * 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... no
  checking for mawk... no
  checking for nawk... no
  checking for awk... awk
  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 Using provided HDF5 C wrapper... ~/miniforge3/bin/h5cc
  checking for HDF5 libraries... yes (version 1.12.1)
  checking hdf5.h usability... no
  checking hdf5.h presence... yes
  configure: WARNING: hdf5.h: present but cannot be compiled
  configure: WARNING: hdf5.h:     check for missing prerequisite headers?
  configure: WARNING: hdf5.h: see the Autoconf documentation
  configure: WARNING: hdf5.h:     section "Present But Cannot Be Compiled"
  configure: WARNING: hdf5.h: proceeding with the compiler's result
  configure: WARNING:     ## --------------------------------- ##
  configure: WARNING:     ## Report this to [email protected] ##
  configure: WARNING:     ## --------------------------------- ##
  checking for hdf5.h... no
  checking for H5Fcreate in -lhdf5... no
  configure: WARNING: Unable to compile HDF5 test program
  checking for hdf5_hl.h... no
  checking for H5LTpath_valid in -lhdf5_hl... no
  configure: WARNING: Unable to compile HDF5_HL test program
  checking for main in -lhdf5_hl... no
  checking for matching HDF5 Fortran wrapper... no
  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
  configure: creating ./config.status
  config.status: creating src/Makevars

[millerkaplanlab]

I've managed to install hdf5r 1.3.2; however, I am now getting this error. Any ideas on how to fix this?

Error: package or namespace load failed for ‘hdf5r’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/hdf5r/libs/hdf5r.so': dlopen(/Library/Frameworks/R.framework/Versions/4.1/Resources/library/hdf5r/libs/hdf5r.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/hdf5r/libs/hdf5r.so Reason: image not found

[dipterix]

I was wondering if I can get the result of the following scripts?

Open R, run

sessionInfo()
R.version

Then open your terminal, type

h5cc --version

If h5cc is not found, try /opt/homebrew/bin/h5cc --version

Thanks

[odavalos]

https://github.com/hhoeflin/hdf5r/issues/171#issuecomment-891367729 this worked for me after I just upgraded to newest version of R (ARM). Thank you @dipterix !

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1   

> R.version
               _                           
platform       aarch64-apple-darwin20      
arch           aarch64                     
os             darwin20                    
system         aarch64, darwin20           
status                                     
major          4                           
minor          1.1                         
year           2021                        
month          08                          
day            10                          
svn rev        80725                       
language       R                           
version.string R version 4.1.1 (2021-08-10)
nickname       Kick Things  

/opt/homebrew/bin/h5cc --version
Apple clang version 12.0.5 (clang-1205.0.22.11)
Target: arm64-apple-darwin20.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin