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Installing R packages on Bianca

Read through the content of R packages on Bianca in our documentation
Can't you find it?

https://docs.uppmax.uu.se/software/r_packages_bianca/

Exercise

Example with Dowser 2.0.0

wget https://cran.r-project.org/src/contrib/Archive/dowser/dowser_2.0.0.tar.gz

  • In Bianca session (right project!) and in wharf folder load R_packages and start R session

  • Ex: cd /proj/nobackup/sens2025560/wharf/bjornc/bjornc-sens2025560

ml R_packages/4.3.1
R

In R session:

> install.packages("dowser_2.0.0.tar.gz", repos = NULL, type="source")
  • Type yes when asked about using a personal library.
Output 
Warning in install.packages("dowser_2.0.0.tar.gz", repos = NULL, type = "source") :
  'lib = "/sw/apps/R/4.3.1/rackham/lib64/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘/castor/project/home/bjornc/R/x86_64-pc-linux-gnu-library/4.3’
to install packages into? (yes/No/cancel) yes
Installing package into ‘/castor/project/home/bjornc/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package ‘dowser’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dowser)
>
  • Test it!
> library(dowser)
Loading required package: ggplot2
Registered S3 methods overwritten by 'treeio':
  method              from
  MRCA.phylo          tidytree
  MRCA.treedata       tidytree
  Nnode.treedata      tidytree
...