Installation of R packages binaries not supported

Locales: Data Centers & Campus RC Yale
1

Hi,

I’m trying to install some R packages, using the R install on the McCleary cluster(module load R/4.3.0-foss-2020b).

I noticed that all packages were installed from source. I tried to switch to binary but got this:

> options(pkgType = "binary")
> install.packages("BiocManager")
Error in install.packages("BiocManager") : 
  type 'binary' is not supported on this platform

This is an example, I tried a few other packages and got the same error.

Is this an intended behaviour? It gets really time consuming when packages have lots of dependencies to install everything from source. I was wondering if there’s a way to use binaries on main repositories like CRAN and bioconductor.

Thanks,
Pierre-Paul

2

This may be because you cannot write to the default lib directory. You should define your own R_LIBS directory and try installing to there.

export R_LIBS=/path/to/your/directory:$R_LIBS

mkdir your /path/to/your/directory

then run the install command:

install.packages(“BiocManager”, lib="/path/to/your/directory, repos=“http://cran.r-project.org”)

2 Likes
3

Hi,

I am one of the YCRC support staff at Yale and our modules don’t really support binary installation. However, I think you would be interested to know that we have just installed some new R modules that come with many of these R packages preinstalled. You can find over 1150 different cran packages in this R module:

R-bundle-CRAN/2023.12-foss-2022b

And over 400 Bioconductor packages, such as biocmanager in this module:

 R-bundle-Bioconductor/3.18-foss-2022b-R-4.3.2

Both of these modules can be loaded simultaneously with the new R/4.3.2 module.

If you require further assistance, we at the YCRC would be happy to provide further support and you can reach us at HPC@yale.edu.

Best of luck with your research!

4

Sounds like someone who has “been there” Jeff. That’s what I tell folks to do on our system when they use the centralized structure.

Note: Be careful with binary installs - sometimes you can run into GLIBC issues because the system they were compiled have incompatible base libraries.

5

Thanks for all the answers! @nucci I had set a user specific location for library installs to no avail. I will definitely check those bundles that seems very useful. In the meantime I’ve installed some packages from source without any problems.