Entering edit mode
Hello, I am trying to install various packages in my hpc, however none of them are getting installed. I have 3 versions of R on the cluster, and in none of them BiocManager or any other tool is installing.
Code should be placed in three backticks as shown below
# include your problematic code here with any corresponding output
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Warning message:
package 'BiocManager' is not available for this version of R
Seurat, liana, none of the packages are available.
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-packages
# please also include the results of running the following in an R session
sessionInfo()
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
Just a thought: does this also happen if you select another mirror (thus not the Uni Munster)? It looks they have an issue with a certificate that expired recently.
Also note that
seurat
andliana
are not Bioconductor packages.Thank you for your response. umm okay, maybe. I will try other mirrors as well. I tried 2-3 of them.
Yes Seurat and liana are not bioconductor packages. I am generally trying to install it for other packages. For liana I get Error: Failed to install 'unknown package' from GitHub: Line starting 'Config/testthat/edit ...' is malformed! this error. So any package I install from GitHub I have this issue.
Have you tried using the more recent version of R?
Switch on and off R (or Rstudio)! Give it a try again. remove also history with
rm(list = ls())