Programming/R
From HPC
Contents
Programming Details
R is a programming language and software environment for statistical analysis, graphics representation, and reporting.
R is freely available under the GNU General Public License and can be loaded as a module on Viper (with Linux), Windows (PC), and Mac.
- R has versions 3.5.1 and R/4.0.2. (Earlier versions will be retired)
R-Studio is also provided as an interactive session on Viper for R-Studio.
Programming example
x <- c(151, 174, 138, 186, 128, 136, 179, 163, 152, 131) y <- c(63, 81, 56, 91, 47, 57, 76, 72, 62, 48) # Apply the lm() function. relation <- lm(y~x) print(relation)
Modules Available
The following modules are available:
- module add R/3.4.1
Batch Mode
The SLURM batch file would typically look like the one below, in this case, it would be named 'rscript.job'.
#!/bin/bash #SBATCH -J compute-single-node #SBATCH -N 1 #SBATCH --ntasks-per-node 1 #SBATCH -D /home/pysdlb/CODE_SAMPLES/R #SBATCH -o %N.%j.%a.out #SBATCH -e %N.%j.%a.err #SBATCH -p compute #SBATCH --mail-user= your email address here echo $SLURM_JOB_NODELIST module purge module add R/3.4.1 export I_MPI_DEBUG=5 export I_MPI_FABRICS=shm:tmi export I_MPI_FALLBACK=no Rscript r.rsc
To run this on the cluster you would need to invoke the command sbatch rscript.job
Interactive Mode
The program is interpreted by the R runtime program, so compilation does not apply here.
[pysdlb@login01 ~]$ interactive salloc: Granted job allocation 3039458 Job ID 3039458 connecting to c120, please wait... [pysdlb@c120 ~]$ module load R/4.0.2 [pysdlb@c120 ~]$ R R version 4.0.2 (2020-06-22) -- "Taking Off Again" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] >
Libraries
To show the libraries included type ( within R ) the command : library()
Packages in library '/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library':
AnnotationDbi Manipulation of SQLite-based annotations in
Bioconductor
BH Boost C++ Header Files
Biobase Biobase: Base functions for Bioconductor
BiocFileCache Manage Files Across Sessions
BiocGenerics S4 generic functions used in Bioconductor
BiocManager Access the Bioconductor Project Package
Repository
BiocParallel Bioconductor facilities for parallel evaluation
BiocStyle Standard styles for vignettes and other
Bioconductor documents
BiocVersion Set the appropriate version of Bioconductor
packages
Biostrings Efficient manipulation of biological strings
DBI R Database Interface
DelayedArray A unified framework for working transparently
with on-disk and in-memory array-like datasets
GenomeInfoDb Utilities for manipulating chromosome names,
including modifying them to follow a particular
naming style
GenomeInfoDbData Species and taxonomy ID lookup tables used by
GenomeInfoDb
GenomicAlignments Representation and manipulation of short
genomic alignments
GenomicFeatures Conveniently import and query gene models
GenomicRanges Representation and manipulation of genomic
intervals
IRanges Foundation of integer range manipulation in
Bioconductor
KEGG.db A set of annotation maps for KEGG
KernSmooth Functions for Kernel Smoothing Supporting Wand
& Jones (1995)
MASS Support Functions and Datasets for Venables and
Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
R6 Encapsulated Classes with Reference Semantics
RColorBrewer ColorBrewer Palettes
RCurl General Network (HTTP/FTP/...) Client Interface
for R
RNAseqData.HNRNPC.bam.chr14
Aligned reads from RNAseq experiment:
Transcription profiling by high throughput
sequencing of HNRNPC knockdown and control HeLa
cells
RSQLite 'SQLite' Interface for R
RUnit R Unit Test Framework
Rcpp Seamless R and C++ Integration
Rhtslib HTSlib high-throughput sequencing library as an
R package
Rsamtools Binary alignment (BAM), FASTA, variant calling
(BCF), and tabix file import
S4Vectors Foundation of vector-like and list-like
containers in Bioconductor
SummarizedExperiment SummarizedExperiment container
XML Tools for Parsing and Generating XML Within R
and S-Plus
XVector Foundation of external vector representation
and manipulation in Bioconductor
askpass Safe Password Entry for R, Git, and SSH
assertthat Easy Pre and Post Assertions
:
Installing Additional Libraries
If you need an additional library installed that would be used by more than just yourself, contact the Viper team by raising a support ticket with the details of the library and the version of R you require it for.
Alternatively, you can install an R library into your library. Within R run the install.packages command with the package you wish to install.
> install.packages("R.matlab")
Warning in install.packages("R.matlab") :
'lib = "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"' is not writable
Would you like to use a personal library instead? (y/n) y
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/3.3
to install packages into? (y/n) y
--- Please select a CRAN mirror for use in this session ---
HTTPS CRAN mirror
1: 0-Cloud [https] 2: Algeria [https]
3: Australia (Canberra) [https] 4: Australia (Melbourne) [https]
5: Australia (Perth) [https] 6: Austria [https]
7: Belgium (Ghent) [https] 8: Brazil (RJ) [https]
9: Brazil (SP 1) [https] 10: Bulgaria [https]
11: Canada (MB) [https] 12: Chile 1 [https]
13: Chile 2 [https] 14: China (Beijing) [https]
15: China (Hefei) [https] 16: China (Lanzhou) [https]
17: Colombia (Cali) [https] 18: Czech Republic [https]
19: Denmark [https] 20: France (Lyon 1) [https]
21: France (Lyon 2) [https] 22: France (Marseille) [https]
23: France (Montpellier) [https] 24: France (Paris 2) [https]
25: Germany (Münster) [https] 26: Iceland [https]
27: India [https] 28: Indonesia (Jakarta) [https]
29: Ireland [https] 30: Italy (Padua) [https]
31: Japan (Tokyo) [https] 32: Malaysia [https]
33: Mexico (Mexico City) [https] 34: New Zealand [https]
35: Norway [https] 36: Philippines [https]
37: Russia (Moscow) [https] 38: Serbia [https]
39: Spain (A Coruña) [https] 40: Spain (Madrid) [https]
41: Sweden [https] 42: Switzerland [https]
43: Taiwan (Chungli) [https] 44: Turkey (Denizli) [https]
45: Turkey (Mersin) [https] 46: UK (Bristol) [https]
47: UK (Cambridge) [https] 48: UK (London 1) [https]
49: USA (CA 1) [https] 50: USA (IA) [https]
51: USA (IN) [https] 52: USA (KS) [https]
53: USA (MI 1) [https] 54: USA (OR) [https]
55: USA (TN) [https] 56: USA (TX 1) [https]
57: USA (TX 2) [https] 58: (HTTP mirrors)
Selection: 48
also installing the dependencies ‘R.methodsS3’, ‘R.oo’, ‘R.utils’
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.methodsS3_1.7.1.tar.gz'
Content type 'unknown' length 25731 bytes (25 KB)
==================================================
downloaded 25 KB
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.oo_1.21.0.tar.gz'
Content type 'unknown' length 403410 bytes (393 KB)
==================================================
downloaded 393 KB
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.utils_2.5.0.tar.gz'
Content type 'unknown' length 389402 bytes (380 KB)
==================================================
downloaded 380 KB
trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.matlab_3.6.1.tar.gz'
Content type 'unknown' length 109818 bytes (107 KB)
==================================================
downloaded 107 KB
* installing *source* package ‘R.methodsS3’ ...
** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.methodsS3)
* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.oo)
* installing *source* package ‘R.utils’ ...
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, :
Renamed the preexisting function warnings to warnings.default, which was defined in environment base.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.utils)
* installing *source* package ‘R.matlab’ ...
** package ‘R.matlab’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.matlab)
The downloaded source packages are in
‘/tmp/RtmpO7iqto/downloaded_packages’
Listing packages installed
If you need a package that will be frequently used raise a support ticket with your request.
To view those already installed within R.
> installed.packages() AnnotationDbi "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BH "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" Biobase "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BiocFileCache "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BiocGenerics "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BiocManager "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BiocParallel "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BiocStyle "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" BiocVersion "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" Biostrings "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" DBI "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" DelayedArray "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" GenomeInfoDb "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" GenomeInfoDbData "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" GenomicAlignments "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" GenomicFeatures "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" GenomicRanges "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" IRanges "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" KEGG.db "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" KernSmooth "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" MASS "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" Matrix "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" R6 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" RColorBrewer "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" RCurl "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" RNAseqData.HNRNPC.bam.chr14 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" RSQLite "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" RUnit "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" Rcpp "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library" ....