Issue in installing any package in R
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.
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contact the HPC support team
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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.
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!