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R Interactive Session

R Interactive Session

  • Login to the HPC cluster either by Command Line or the OnDemand Website. For information on how to log into the cluster check out:

Navigate To The Cluster

  • From the login node, load R module and associated modules
module load R/4.0.0 boost/1.63.0-python3 java/1.8.0_60 gsl/2.6

  • Additional modules may need to be loaded, such as sf/R_4.0.0

  • Allocate computing resources. Start an interactive session with your desired number of cores and memory, here we are using 2 cores with 4GB of memory: 

srun -p interactive -n 2 --mem=4g --pty bash

  • The Interactive partition has a default 4-hour time limit.

  • For more information on how to allocate resources on Tufts HPC cluster, check out:

Compute Resources

  • Within the interactive session, you can start R 
R

Installing R packages

  • In R, you can install the packages you need in your home directory with:
install.packages("XXX")
  • You can also use the packages installed in HPC Tools R package repo:
LIB='/cluster/tufts/hpc/tools/R/4.0.0' 
.libPaths(c("",LIB))
  • You can also use packages installed in BioTools R package repo:
LIB='/cluster/tufts/bio/tools/R_libs/4.0.0' 
.libPaths(c("",LIB))

  • If you are having trouble installing the packages you need, please contact tts-research@tufts.edu.

  • To exit from R command line interface:

q()
- To terminate interactive session 

exit

R Package Installation Troubleshooting

Suggestion 1: Try installing the R package from command line instead of RStudio OnDemand

  • The RStudio OnDemand interface is not perfect and can store things like different libPaths between sessions. To be safe, it is always best to install new R package from the command line when on the Tufts HPC.

Suggestion 2: You may need to load more modules

  • On the Tufts HPC you load modules of software that might already be installed on your machine. This is why it can be easier to install R packages on your local machine rather than the Tufts HPC. If you are unsuccessful at installing an R package, try loading the following modules:
module load curl/7.47.1 gcc/7.3.0 hdf5/1.10.4 boost/1.63.0-python3 libpng/1.6.37 java/1.8.0_60 libxml2/2.9.10 libiconv/1.16 fftw/3.3.2 gsl/2.6 R/4.0.0

Suggestion 3: Take a look at the last few lines of the error message

  • The error message will give you a clue as to what is going wrong. For example a common example:
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘Rcpp’
Error: package or namespace load failed for ‘ggplot2’
  • Here you might need to install a dependency beforehand with either:
install.packages("Rcpp")

or:

install.packages("ggplot2",dependencies = TRUE)

Suggestion 4: Install the package from the Repository

  • Dependant on the R module you are loading, you may be working with an older version of a package manager, like BiocManager. As such some of the packages might have dependencies that are deprecated. For example, when installing APAlyzer:
ERROR: dependency ‘DESeq’ is not available for package ‘APAlyzer’
* removing ‘/cluster/home/user/R/x86_64-pc-linux-gnu-library/4.0/APAlyzer’

The downloaded source packages are in
    ‘/tmp/Rtmpraf0Ix/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /opt/shared/R/4.0.0/lib64/R/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS,
    Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'openssl', 'Seurat'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
  installation of package ‘APAlyzer’ had non-zero exit status
  • We can try installing APAlyzer like so:
BiocManager::install('RJWANGbioinfo/APAlyzer')

Suggestion 5: Try updating the packages it asks to update

  • R usually tries to tells you what it needs to proceed. Oftentimes when you install a package, you will be prompted to update the packages you have:
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

 1: All                                           
 2: CRAN packages only                            
 3: None                                          
 4: sitmo        (2.0.1      -> 2.0.2     ) [CRAN]
 5: BH           (1.75.0-0   -> 1.81.0-1  ) [CRAN]
 6: dqrng        (0.2.1      -> 0.3.0     ) [CRAN]
 7: irlba        (2.3.3      -> 2.3.5.1   ) [CRAN]
 ...
 ...
 ...
 Enter one or more numbers, or an empty line to skip updates: 1
  • Some packages require specific/updated versions of the packages you have. Package installation issues can be circumvented when you enter 1 to update all packkages.

Suggestion 6: Restarting R

  • The old IT addage of turning it on and off again is not just all talk. The way you set your libPath or the packages you already have loaded may interrupt your ability to install packages. You can restart R to wipe the proverbial slate clean by going to Session > Restart R. Now try to install your package!