Installing R packages on Bianca

First check if package is already in R_packages/x.y.z

• On UPPMAX the module R_packages is an omnibus package library containing almost all packages in the CRAN and BioConductor repositories.
  • As of 2023-11-21, there were a total of 23478 R packages installed in R_packages/4.3.1.
    • A total of 23603 packages are available in CRAN and BioConductor
    • 19586 CRAN packages are installed, out of 20044 available
    • 3544 BioConductor-specific packages are installed, out of 3559 available
    • 346 other R packages are installed. These are not in CRAN/BioConductor, are only available in the CRAN/BioConductor archives, or are hosted on github, gitlab or elsewhere

Chances are good the R packages you need are already available once you load this module. You can quickly check by loading it:

$ ml R_packages/4.3.1

Then within R, try loading the package you want:

library(glmnet)

Alternatively, and this is both a longer solution and not our recommended one, you can grep for the package after this module is loaded using the environment variable $R_LIBS_SITE, which contains the locations of all R packages installed within the module.

$ ls -l $R_LIBS_SITE | grep glmnet
drwxrwsr-x  9 douglas sw  4096 May 28 16:59 EBglmnet
drwxrwsr-x 11 douglas sw  4096 May 25 01:22 glmnet
drwxrwsr-x  6 douglas sw  4096 May 25 04:03 glmnetSE
drwxrwsr-x  7 douglas sw  4096 May 25 04:04 glmnetUtils
drwxrwsr-x  8 douglas sw  4096 May 25 04:04 glmnetcr
drwxrwsr-x  7 douglas sw  4096 May 25 10:46 glmnetr

Principles

• Find source files (*.tar.gz)
• Download to Transit and wharf folder with wget
• Install On Bianca

Detailed steps

Use transit!

1. Log in to transit
2. Go to the mounted project folder
3. Download source files with wget
4. Load R_packages of desired version (R is loaded on the fly)
5. Start R session
6. Install from source in R session

Can I use sftp to bianca-sftp.uppmax.uu.se?

• No!
• wget cannot be used within an SFTP session.

Download part

• Use your web browser to find the package in
  • CRAN
  • GitHub page

• Find the version of the package

  • CRAN: go to "old sources/Dowser archive"
  • GitHub: Go to Releases/tags

• Copy link for the package with name similar to <package>_<version>.tar.gz.

• Go to the terminal and and be sure you are in the wharf folder, i.e. the mounted project folder in Transit
• Use the wget <copied link> command in Transit and correct project folder.

wget <package>_<version>.tar.gz

Installation part

• Log in to Bianca and the relevant project
• Load R_packages of desired version

• Start R session, either

  • from the wharf folder where the source files are
  • from other place and note the path to the source files

• Install from source in R session,

• from wharf folder

> install.packages("<filename>", repos = NULL, type="source")

• from other folder

> install.packages("<path-to/filename>", repos = NULL, type="source")

Example with Dowser 2.0.0

dowser on Readthedocs

Info

• Dowser is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq).
• Dowser provides a set of tools for performing phylogenetic analysis on B cell receptor repertoires.
• It supports building and visualising trees using multiple methods, and implements statistical tests for discrete trait analysis of B cell migration, differentiation, and isotype switching.

The version of dowser in R_packages/4.2.1 is 1.1.0. It was updated to version 1.2.0 on 2023-05-30.

• Web page: https://cran.r-project.org/web/packages/dowser/index.html
• just 2.4.0 is listed here
• go to old sources/Dowser archive
• choose 2.0.0.tar.gz
• copy link
• In project folder in Transit

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
...

• Check the used version (look for the dowser ino)

sessionInfo()

How may that look like?

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /sw/apps/R/4.3.1/rackham/lib64/R/lib/libRblas.so
LAPACK: /sw/apps/R/4.3.1/rackham/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       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

time zone: Europe/Stockholm
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] dowser_2.0.0  ggplot2_3.4.3

loaded via a namespace (and not attached):
 [1] ade4_1.7-22                 tidyselect_1.2.0
 [3] dplyr_1.1.3                 Biostrings_2.68.1
 [5] bitops_1.0-7                fastmap_1.1.1
 [7] lazyeval_0.2.2              RCurl_1.98-1.12
 [9] GenomicAlignments_1.36.0    digest_0.6.33
[11] phylotate_1.3               lifecycle_1.0.3
[13] alakazam_1.3.0              tidytree_0.4.5
[15] magrittr_2.0.3              compiler_4.3.1
[17] rlang_1.1.1                 progress_1.2.2
[19] tools_4.3.1                 igraph_1.5.1
[21] utf8_1.2.3                  yaml_2.3.7
[23] phangorn_2.11.1             prettyunits_1.2.0
[25] S4Arrays_1.0.6              DelayedArray_0.26.7
[27] KernSmooth_2.23-21          aplot_0.2.1
[29] abind_1.4-5                 BiocParallel_1.34.2
[31] withr_2.5.1                 purrr_1.0.2
[33] BiocGenerics_0.46.0         grid_4.3.1
[35] stats4_4.3.1                shazam_1.2.0
[37] fansi_1.0.4                 colorspace_2.1-0
[39] iterators_1.0.14            scales_1.2.1
[41] MASS_7.3-60                 SummarizedExperiment_1.30.2
[43] cli_3.6.1                   crayon_1.5.2
[45] treeio_1.24.3               generics_0.1.3
[47] ggtree_3.8.2                tzdb_0.4.0
[49] ape_5.7-1                   cachem_1.0.8
[51] stringr_1.5.0               zlibbioc_1.46.0
[53] parallel_4.3.1              ggplotify_0.1.2
[55] XVector_0.40.0              matrixStats_1.0.0
[57] yulab.utils_0.1.0           vctrs_0.6.3
[59] Matrix_1.6-1.1              jsonlite_1.8.7
[61] gridGraphics_0.5-1          IRanges_2.34.1
[63] hms_1.1.3                   patchwork_1.1.3
[65] S4Vectors_0.38.2            seqinr_4.2-30
[67] foreach_1.5.2               diptest_0.76-0
[69] tidyr_1.3.0                 glue_1.6.2
[71] codetools_0.2-19            stringi_1.7.12
[73] gtable_0.3.4                GenomeInfoDb_1.36.3
[75] quadprog_1.5-8              GenomicRanges_1.52.0
[77] munsell_0.5.0               tibble_3.2.1
[79] pillar_1.9.0                GenomeInfoDbData_1.2.10
[81] R6_2.5.1                    airr_1.5.0
[83] doParallel_1.0.17           lattice_0.21-8
[85] Biobase_2.60.0              markdown_1.9
[87] readr_2.1.4                 Rsamtools_2.16.0
[89] memoise_2.0.1               ggfun_0.1.3
[91] Rcpp_1.0.11                 fastmatch_1.1-4
[93] gridExtra_2.3               nlme_3.1-162
[95] fs_1.6.3                    MatrixGenerics_1.12.3
[97] pkgconfig_2.0.3
>

• You should see: dowser_2.0.0
• This confirms that you are using version 2.0.0!
• You can now remove the source file from the wharf folder.