Issue in installing any package in R

Question

[sidrah.maryam]

Hello everyone! I am facing a very weird issue. I am working on hpc where R is preinstalled. As I am trying to install any package, I am getting this error:

**Warning message:
package 'BiocManager' is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-package**s 

with any package.

Or if I install anything from GitHub, I get this error: Error: Failed to install 'unknown package' from GitHub: Line starting 'Config/testthat/edit ...' is malformed!

I have tried to completely remove R from my environment and then again install packages, but nothing works.

The sessionInfo() is:
*R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.7 (Green Obsidian)
Matrix products: default
BLAS:   /cm/shared/apps/R4.1.2/lib64/R/lib/libRblas.so
LAPACK: /cm/shared/apps/R4.1.2/lib64/R/lib/libRlapack.so
locale:
 [1] LC_CTYPE=C                 LC_NUMERIC=C              
 [3] LC_TIME=en_US.utf-8        LC_COLLATE=en_US.utf-8    
 [5] LC_MONETARY=en_US.utf-8    LC_MESSAGES=en_US.utf-8   
 [7] LC_PAPER=en_US.utf-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.utf-8 LC_IDENTIFICATION=C       
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
loaded via a namespace (and not attached):
[1] compiler_4.1.2 tools_4.1.2*   

I am not able to do anything here. Can anyone please help me with this.

[ATpoint]

What command did you run exactly. Could this be some sort of firewall issue? Try also the cran cloud mirrow. What I personally like rather than ever using HPC software itself is to put together a docker or singularity container depending on what your HPC supports. Seurat and packages like that are also quite meant for interactive analysis, do you really want to do that on a HPC, that is usually clunky.

[sidrah.maryam]

I used install.packages("BiocManager") Thank you so much for the suggestion. I think that too. Because it works fine on my laptop, issue is only when I run on HPC. Thanks a lot!

Answer 1

[jv]

contact the HPC support team