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The-Bioinformatics-Group / Albiorix

Code used for configuration and administration of the bioinformatics computer cluster Albiorix at the Department of Biological and Environmental Sciences and Marine sciences, University of Gothenburg.
http://albiorix.bioenv.gu.se/
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Install R-package "rbrothers" #93

Closed Patrulk closed 6 years ago

Patrulk commented 7 years ago

Tried installing rbrothers as a local library but it is not in the CRAN archive and requires the packages "git2r" and "devtools" for installation, which it seems I cannot install either. Any ideas on how to solve this or can someone make a general installation of the package on the cluster?

mtop commented 7 years ago

Hi @Patrulk. I can install the package globally. Which version of R are you using?

Patrulk commented 7 years ago

Hi @mtop, Great, I am using R v.3.2.3. Thanks!

mtop commented 7 years ago

Hi @Patrulk. It was quite difficult to install this package under version 3.2.3 of R, as some of the dependencies where not available. I have therefore installed the latest version of R and then installed "rbrothers" there instead. This version is available using the command "module load R/v.3.3.2". Hope this is OK.

Patrulk commented 7 years ago

Hi @mtop. No problem at all, that works great. Thank you for fixing this and putting in the extra effort with the installation!

Patrulk commented 7 years ago

Hi @mtop. I had some problems trying to run the rbrothers package, do I need to use any specific node?

On the main node there seems to be missing a library and return the message: "/usr/local/packages/R-3.3.2/lib64/R/bin/exec/R: error while loading shared libraries: liblzma.so.5: cannot open shared object file: No such file or directory"

On the other nodes it fails to load the rJava library.

Is there some other action I need to take Before running it?

mtop commented 7 years ago

Hi @Patrulk Has this problem been resolved?