R is a free software environment for statistical computing and graphics.
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A comprehensive list of packages is available in the RStudio singularity images. Click here to view the list and instructions for using them outside RStudio.Â
How to install R packages?
A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory.
Start interactive R session and install package using the command
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install.packages('packagename') |
Alternatively, you can add install.packages('packagename') within your R script. By default, R will try to install packages locally to ${HOME/x86_64-pc-linux-gnu-library. If you wish to use a different directory, then you need to set R_LIBS variable to point to that directory.
If you get an error installing packages locally, then use the command
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install.packages('packagename',lib=Sys.getenv("R_LIBS")) |
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| title | Deprecated CentOS 7.x Software: Use module load cent7 to use the following modules |
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Which versions of R are available?There are four version of R available, 3.3.3, 3.4.2, 3.4.3 and 3.5.3. Of the two 3.5.3 version, one version labelled r-bio contains packages from Bioconductor for Bioinformatics research. Usage| Code Block |
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| module load r-project/3.3.3 |
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| module load r-project/3.4.2 |
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| module load anaconda/python3 |
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| module load r-project/3.5.3 |
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| language | bash |
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| title | r 3.5.3 for Bioinformatics |
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| module load r-bio/3.5.3 |
How to install R packages?A variety of R packages are installed however it is recommended that users install packages (newer and updated versions) in their own home directory. The r-project/3.x.y modules sets up a variable, R_LIBS, to install packages in your home directory. Make sure the R_LIBS directory exists | Code Block |
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| mkdir -p ${R_LIBS} |
Start interactive R session and install package using the command | Code Block |
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| install.packages('packagename') |
Alternatively, you can add install.packages('packagename') within your R script
If you get an error installing packages locally, then use the command | Code Block |
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| install.packages('packagename',lib=Sys.getenv("R_LIBS")) |
Installed PackagesPackage | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | r-bio |
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abind | 1.4-5 | 1.4-5 |
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| 1.4-3 | | acepack |
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| 1.4.1 | | amap |
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| 0.8-16 | | annotate |
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| 1.58.0 | | AnnotationDbi |
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| 1.42.1 | | ape |
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| 5.3 | | argparse |
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| 1.1.1 | askpass | 1.1 | 1.1 |
| 1.1 |
| assertthat | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 | backports | 1.1.2 | 1.1.1 | 1.1.2 | 1.1.3 | 1.1.1 | base | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | base64enc | 0.1-3 | 0.1-3 | 0.1-3 | 0.1-3 | 0.1-3 | BH | 1.65.0-1 | 1.65.0-1 | 1.65.0-1 | 1.69.0-1 | 1.69.0-1 | | BiasedUrn |
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| 1.07 | bindr | 0.1 | 0.1 | 0.1 |
| 0.1.1 | bindrcpp | 0.2 | 0.2 | 0.2 |
| 0.2.2 | | Biobase |
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| 2.40.0 | | BiocGenerics |
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| 0.26.0 | | BiocParallel |
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| 1.14.2 | | biomaRt |
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| 2.36.1 | | Biostrings |
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| 2.48.0 | | bit |
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| 1.1-12 | | bit64 |
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| 0.9-7 | bitops | 1.0-6 | 1.0-6 | 1.0-6 |
| 1.0-6 | | blob |
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| 1.1.0 | boot | 1.3-18 | 1.3-20 | 1.3-20 | 1.3-20 | 1.3-20 | broom | 0.4.3 | 0.4.3 | 0.4.3 | 0.5.1 |
| callr | 3.2.0 | 2.0.1 | 1.0.0 | 3.1.1 | 3.0.0 | car |
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| 2.1-6 |
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| caret |
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| 6.0-78 |
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| caTools | 1.17.1.2 | 1.17.1 | 1.17.1 |
| 1.17.1 | cellranger | 1.1.0 | 1.1.0 | 1.1.0 | 1.1.0 | 1.1.0 | | checkmate |
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| 1.8.4 | chron |
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| 2.3-51 |
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| class | 7.3-14 | 7.3-14 | 7.3-14 | 7.3-15 | 7.3-15 | cli | 1.0.0 | 1.0.0 | 1.0.0 | 1.0.1 | 1.0.1 | clipr | 0.4.0 | 0.5.0 | 0.4.0 | 0.5.0 | 0.4.0 | clisymbols | 1.2.0 | 1.2.0 |
| 1.2.0 |
| cluster | 2.0.5 | 2.0.6 | 2.0.6 | 2.0.7-1 | 2.0.7-1 | codetools | 0.2-15 | 0.2-15 | 0.2-15 | 0.2-16 | 0.2-16 | colorspace | 1.3-2 | 1.3-2 | 1.3-2 | 1.4-0 | 1.3-2 | compiler | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | | covr |
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| 3.0.1 | crayon | 1.3.4 | 1.3.4 | 1.3.4 | 1.3.4 | 1.3.4 | | ctc |
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| 1.54.0 | curl | 3.1 | 3.1 | 3.1 | 3.3 | 3.3 | CVST |
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| 0.2-1 |
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| datasets | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | data.table |
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| 1.10.4-3 |
| 1.11.8 | DBI | 0.7 | 0.7 | 0.7 | 1.0.0 | 0.7 | dbplyr | 1.2.0 | 1.2.0 | 1.1.0 | 1.3.0 | 1.2.2 | ddalpha |
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| 1.3.1 |
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| debugme | 1.1.0 | 1.1.0 |
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| | DelayedArray |
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| 0.6.5 | DEoptimR |
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| 1.0-8 |
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| desc | 1.2.0 | 1.2.0 |
| 1.2.0 |
| devtools | 2.0.1 |
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| 2.0.1 | 1.12.0 | dichromat | 2.0-0 | 2.0-0 | 2.0-0 |
| 2.0-0 | digest | 0.6.14 | 0.6.12 | 0.6.13 | 0.6.18 | 0.6.12 | dimRed |
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| 0.1.0 |
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| dplyr | 0.7.4 | 0.7.4 | 0.7.4 | 0.8.0.1 | 0.7.7 | DRR |
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| 0.0.2 |
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| dygraphs | 1.1.1.6 | 1.1.1.4 |
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| ellipsis | 0.1.0 | 0.1.0 |
| 0.1.0 |
| evaluate | 0.10.1 | 0.10.1 | 0.10.1 | 0.13 | 0.10.1 | fansi | 0.4.0 | 0.4.0 |
| 0.4.0 | 1.1.25 | | fftwtools |
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| 0.9-8 | | findpython |
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| 1.0.3 | flexdashboard | 0.5.1.1 | 0.5.1 |
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| forcats | 0.2.0 | 0.2.0 | 0.2.0 | 0.4.0 | 0.2.0 | foreach |
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| 1.4.4 |
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| foreign | 0.8-67 | 0.8-69 | 0.8-69 | 0.8-71 | 0.8-71 | formatR |
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| 1.5 |
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| fs | 1.2.6 | 1.2.7 |
| 1.2.6 |
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| 1.62.0 | | GenomeInfoDb |
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| 1.16.0 | | GenomeInfoDbData |
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| 1.1.0 | | GenomicRanges |
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| 1.32.6 | generics | 0.0.2 | 0.0.2 |
| 0.0.2 |
| ggplot2 | 2.2.1 | 2.2.1 | 2.2.1 | 3.1.0 | 3.2.0 | gh | 1.0.1 | 1.0.1 |
| 1.0.1 |
| git2r | 0.24.0 | 0.25.2 |
| 0.24.0 | 0.18.0 | glmnet |
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| 2.0-13 |
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| glue | 1.2.0 | 1.2.0 | 1.2.0 | 1.3.1 | 1.2.0 | gower |
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| 0.1.2 |
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| graphics | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | grDevices | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | grid | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | gtable | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 | 0.2.0 | gtools | 3.8.1 | 3.5.0 |
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| 3.5.0 | haven | 1.1.1 | 1.1.1 | 1.1.0 | 2.1.0 | 1.1.0 | hexbin |
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| 1.27.1 |
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| highr | 0.6 | 0.6 | 0.6 | 0.7 | 0.6 | hms | 0.4.0 | 0.4.1 | 0.4.0 | 0.4.2 | 0.3 | htmltools | 0.3.6 | 0.3.6 | 0.3.6 | 0.3.6 | 0.3.6 | htmlwidgets | 1.3 | 0.9 | 0.9 |
| 0.9 | httpuv | 1.5.1 | 1.3.5 | 1.3.5 |
| 1.3.5 | httr | 1.3.1 | 1.3.1 | 1.3.1 | 1.4.0 | 1.3.1 | ini | 0.3.1 | 0.3.1 |
| 0.3.1 |
| ipred |
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| 0.9-6 |
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| IRdisplay |
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| 0.4.4 |
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| IRkernel |
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| 0.8.11 |
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| iterators |
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| 1.0.9 |
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| jsonlite | 1.5 | 1.5 | 1.5 | 1.6 | 1.5 | kernlab |
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| 0.9-25 |
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| KernSmooth | 2.23-15 | 2.23-15 | 2.23-15 | 2.23-15 | 2.23-15 | knitr | 1.18 | 1.19 | 1.18 | 1.22 |
| labeling | 0.3 | 0.3 | 0.3 | 0.3 | 0.3 | later | 0.8.0 |
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| lattice | 0.20-34 | 0.20-35 | 0.20-35 | 0.20-38 | 0.20-38 | lava |
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| 1.5.1 |
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| lazyeval | 0.2.1 | 0.2.0 | 0.2.1 | 0.2.1 | 0.2.0 | lme4 |
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| 1.1-15 |
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| lubridate | 1.7.1 | 1.7.2 | 1.7.1 | 1.7.4 | 1.7.1 | magrittr | 1.5 | 1.5 | 1.5 | 1.5 | 1.5 | maps |
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| 3.2.0 |
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| markdown | 0.8 | 0.8 | 0.8 | 0.9 | 0.8 | MASS | 7.3-45 | 7.3-47 | 7.3-48 | 7.3-51.1 | 7.3-51.1 | Matrix | 1.2-8 | 1.2-11 | 1.2-12 | 1.2-15 | 1.2-15 | MatrixModels |
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| 0.4-1 |
| 0.52.2 | matrixStats | 0.54.0 | 0.53.1 |
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| memoise | 1.1.0 | 1.1.0 |
| 1.1.0 | 1.1.0 | methods | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | mgcv | 1.8-17 | 1.8-20 | 1.8-22 | 1.8-27 | 1.8-27 | mime | 0.5 | 0.5 | 0.5 | 0.6 | 0.5 | minqa |
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| 1.2.4 |
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| mnormt | 1.5-5 | 1.5-5 | 1.5-5 |
| 1.5-5 | ModelMetrics |
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| 1.1.0 |
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| modelr | 0.1.1 | 0.1.1 | 0.1.1 | 0.1.4 |
| munsell | 0.4.3 | 0.4.3 | 0.4.3 | 0.5.0 | 0.4.3 | nlme | 3.1-131 | 3.1-131 | 3.1-131 | 3.1-137 | 3.1-137 | nloptr |
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| 1.0.4 |
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| nnet | 7.3-12 | 7.3-12 | 7.3-12 | 7.3-12 | 7.3-12 | numDeriv |
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| 2016.8-1 |
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| openssl | 0.9.9 | 0.9.9 | 0.9.9 | 1.2.2 | 0.9.7 | | optparse |
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| 1.6.0 | padr | 0.4.1 | 0.4.0 |
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| parallel | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | pbdZMQ |
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| 0.3-0 |
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| pbkrtest |
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| 0.4-7 |
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| | phangorn |
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| 2.5.5 | pillar | 1.1.0 | 1.1.0 | 1.0.1 | 1.3.1 | 1.3.1 | pkgbuild | 1.0.2 | 1.0.3 |
| 1.0.2 |
| pkgconfig | 2.0.1 | 2.0.1 | 2.0.1 | 2.0.2 | 2.0.2 | pkgload | 1.0.2 | 1.0.2 |
| 1.0.2 |
| plogr | 0.1-1 | 0.1-1 | 0.1-1 | 0.2.0 | 0.2.0 | | plot3D |
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| 1.1.1 | plyr | 1.8.4 | 1.8.4 | 1.8.4 | 1.8.4 | 1.8.4 | png | 0.1-7 | 0.1-7 |
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| pracma | 2.2.5 | 2.1.4 |
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| praise | 1.0.0 | 1.0.0 |
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| 1.0.0 | prettyunits | 1.0.2 | 1.0.2 |
| 1.0.2 | 1.0.2 | processx | 3.3.0 | 3.3.0 |
| 3.3.0 | 3.2.0 | prodlim |
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| 1.6.1 |
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| progress | 1.2.0 | 1.2.0 |
| 1.2.0 | 1.1.2 | promises | 1.0.1 |
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| proto |
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| 1.0.0 |
| 1.0.0 | ps | 1.3.0 | 1.3.0 |
| 1.3.0 | 1.1.0 | psych | 1.7.8 | 1.7.8 | 1.7.8 |
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| purrr | 0.2.4 | 0.2.4 | 0.2.4 | 0.3.1 | 0.2.4 | quantmod |
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| 0.4-12 |
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| quantreg |
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| 5.34 |
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| R6 | 2.2.2 | 2.2.2 | 2.2.2 | 2.4.0 | 2.2.2 | randomForest |
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| 4.6-12 |
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| rbokeh |
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| 0.6.3 |
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| rcmdcheck | 1.3.2 | 1.3.2 |
| 1.3.2 |
| RColorBrewer | 1.1-2 | 1.1-2 | 1.1-2 | 1.1-2 |
| Rcpp | 0.12.15 | 0.12.13 | 0.12.14 | 1.0.0 | 1.0.0 | | RcppArmadillo |
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| 0.8.100.1.0 | RcppEigen |
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| 0.3.3.3.1 |
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| RcppRoll |
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| 0.2.2 |
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| | RCurl |
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| 1.95-4.8 | readr | 1.1.1 | 1.1.1 | 1.1.1 | 1.3.1 | 1.1.1 | readxl | 1.0.0 | 1.0.0 | 1.0.0 | 1.3.1 | 1.1.0 | recipes |
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| 0.1.1 |
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| rematch | 1.0.1 | 1.0.1 | 1.0.1 | 1.0.1 | 1.0.1 | remotes | 2.0.2 | 2.0.4 |
| 2.0.2 |
| repr |
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| 0.12.0 |
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| reprex | 0.1.1 | 0.1.2 | 0.1.1 | 0.2.1 |
| reshape2 | 1.4.3 | 1.4.2 | 1.4.3 | 1.4.3 | 1.4.2 | RJSONIO |
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| 1.3-0 |
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| rlang | 0.1.6 | 0.1.6 | 0.1.6 | 0.3.1 | 0.3.1 | rmarkdown | 1.8 | 1.6 | 1.8 | 1.12 |
| R.matlab | 3.6.2 | 3.6.1 |
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| R.methodsS3 | 1.7.1 | 1.7.1 |
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| | Rmpi |
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| 0.6-6 | robustbase |
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| 0.92-8 |
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| R.oo | 1.22.0 | 1.21.0 |
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| rpart | 4.1-10 | 4.1-11 | 4.1-11 | 4.1-13 | 4.1-13 | rprojroot | 1.3-2 | 1.2 | 1.3-1 | 1.3-2 | 1.2 | | Rsamtools |
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| 1.32.2 | | RSQLite |
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| 2.0 | rstudioapi | 0.7 | 0.7 | 0.7 | 0.9.0 | 0.7 | R.utils | 2.8.0 | 2.5.0 |
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| rvest | 0.3.2 | 0.3.2 | 0.3.2 | 0.3.2 | 0.3.2 | rzmq |
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| 0.9.3 |
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| | S4Vectors |
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| 0.18.3 | scales | 0.5.0 | 0.5.0 | 0.5.0 | 1.0.0 | 0.5.0 | selectr | 0.3-1 | 0.3-1 | 0.3-1 | 0.4-1 | 0.3-1 | sessioninfo | 1.1.1 | 1.1.1 |
| 1.1.1 |
| sfsmisc |
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| 1.1-1 |
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| shiny | 1.3.0 | 1.0.5 | 1.0.5 |
| 1.0.5 | | snow |
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| 0.4-2 | sourcetools | 0.1.7 | 0.1.6 | 0.1.6 |
| 0.1.6 | SparseM |
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| 1.77 |
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| spatial | 7.3-11 | 7.3-11 | 7.3-11 | 7.3-11 | 7.3-11 | splines | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | stats | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | stats4 | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | stringi | 1.1.6 | 1.1.5 | 1.1.6 | 1.4.3 | 1.1.5 | stringr | 1.2.0 | 1.2.0 | 1.2.0 | 1.4.0 | 1.2.0 | survival | 2.40-1 | 2.41-3 | 2.41-3 | 2.43-3 | 2.43-3 | sys | 3.1 | 3.1 |
| 3.1 |
| tcltk | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | testthat | 2.0.1 | 2.0.0 |
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| 1.0.2 | tibble | 1.4.1 | 1.4.2 | 1.4.1 | 2.0.1 | 2.0.1 | tidyr | 0.7.2 | 0.8.0 | 0.7.2 | 0.8.3 | 0.7.2 | tidyselect | 0.2.3 | 0.2.3 | 0.2.3 | 0.2.5 | 0.2.3 | tidyverse | 1.2.1 | 1.2.1 | 1.2.1 | 1.2.1 |
| timeDate |
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| 3042.101 |
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| tinytex | 0.11 | 0.11 |
| 0.11 |
| tools | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | TTR |
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| 0.23-2 |
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| usethis | 1.4.0 |
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| 1.4.0 |
| utf8 | 1.1.3 | 1.1.3 | 1.1.2 | 1.1.4 | 1.1.3 | utils | 3.3.3 | 3.4.2 | 3.4.3 | 3.5.3 | 3.5.3 | uuid |
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| 0.1-2 |
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| viridisLite | 0.2.0 | 0.2.0 | 0.2.0 | 0.3.0 | 0.2.0 | whisker | 0.3-2 | 0.3-2 | 0.3-2 | 0.3-2 | 0.3-2 | withr | 2.1.2 | 2.1.2 | 2.1.1 | 2.1.2 | 2.1.2 | xfun | 0.6 | 0.6 |
| 0.5 |
| | XML |
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| 3.98-1.9 | xml2 | 1.1.1 | 1.2.0 | 1.1.1 | 1.2.0 | 1.1.1 | xopen | 1.0.0 | 1.0.0 |
| 1.0.0 |
| xtable | 1.8-3 | 1.8-2 | 1.8-2 |
| 1.8-2 | xts | 0.11-2 | 0.10-1 | 0.10-1 |
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| | XVector |
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| 0.20.0 | yaml | 2.1.16 | 2.1.14 | 2.1.16 | 2.2.0 | 2.1.14 | | zlibbioc |
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| 1.26.0 | zoo | 1.8-5 | 1.8-0 | 1.8-0 |
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