R is a free software environment for statistical computing and graphics.
| Version | module name | build | notes |
|---|
| 4.0.3 | r/4.0.3 | SPACK using gcc 8.3.1 | optimized for avx, avx2 and avx512 |
| 4.0.3 | conda/r | Conda packages | Load anaconda3/2020.07 first |
| 4.1.1 | conda/spark | Conda packages | Load anaconda3/2020.07 first.
For use with Apache Spark |
Seminar Slides
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R packages are built using SPACK optimized for the underlying CPU architecture or binary installs using Conda. Applications built by RC staff that are dependent on R use the SPACK built R packages.
| Info |
|---|
See Apache Spark for list of packages in the spark module. |
| Expand |
|---|
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Package | 4.0.3 SPACK | 4.0.3 Conda |
|---|
acepack | 1.4.1 |
| amap | 0.8-17 |
| animation | 2.6 |
| annotate | 1.62.0 |
| AnnotationDbi | 1.46.1 |
| ape | 5.3 |
| argparse | 2.0.1 |
| askpass | 1.1 | 1.1 | assertthat | 0.2.1 | 0.2.1 | backports | 1.1.4 | 1.2.0 | base | 4.0.3 | 4.0.3 | base64enc | 0.1-3 | 0.1-3 | BBmisc | 1.11 |
| BH | 1.69.0-1 |
| BiasedUrn | 1.07 |
| bibtex | 0.4.2 |
| bigmemory | 4.5.36 |
| bigmemory.sri | 0.1.3 |
| Biobase | 2.44.0 |
| BiocGenerics | 0.34.0 |
| BiocManager | 1.30.10 |
| BiocParallel | 1.18.1 |
| biomaRt | 2.40.5 |
| Biostrings | 2.52.0 |
| bit | 1.1-14 |
| bit64 | 0.9-7 |
| bitops | 1.0-6 |
| blob | 1.2.0 | 1.2.1 | boot | 1.3-23 | 1.3-25 | boot | 1.3-27 | 1.3-25 | brew | 1.0-6 |
| brio |
| 1.1.0 | broom | 0.5.2 | 0.7.2 | callr | 3.4.3 | 3.5.1 | caret | 6.0-84 | 6.0-86 | caTools | 1.17.1.2 |
| cellranger | 1.1.0 | 1.1.0 | checkmate | 1.9.4 |
| chron | 2.3-53 |
| class | 7.3-15 | 7.3-17 | cli | 2.0.2 | 2.2.0 | clipr | 0.7.0 | 0.7.1 | cluster | 2.1.0 | 2.1.0 | cluster | 2.1.1 | 2.1.0 | clusterGeneration | 1.3.4 |
| coda | 0.19-3 |
| codetools | 0.2-16 | 0.2-18 | codetools | 0.2-18 | 0.2-18 | colorspace | 1.4-1 | 2.0-0 | combinat | 0.0-8 |
| commonmark | 1.7 | 1.7 | compiler | 4.0.3 | 4.0.3 | covr | 3.5.0 |
| cowplot | 1.0.0 |
| cpp11 |
| 0.2.4 | crayon | 1.3.4 | 1.3.4 | crosstalk | 1.0.0 | 1.1.0.1 | crul |
| 1.0.0 | ctc | 1.58.0 |
| curl | 4.3 | 4.3 | data.table | 1.12.8 | 1.13.2 | datasets | 4.0.3 | 4.0.3 | DBI | 1.1.0 | 1.1.0 | dbplyr | 1.4.2 | 2.0.0 | DelayedArray | 0.10.0 |
| dendextend | 1.12.0 |
| desc | 1.2.0 | 1.2.0 | DESeq2 | 1.24.0 |
| devtools | 2.3.0 |
| DEXSeq | 1.36.0 |
| diffobj |
| 0.3.2 | digest | 0.6.25 | 0.6.27 | doParallel | 1.0.15 |
| dplyr | 0.8.3 | 1.0.2 | dqrng | 0.2.1 |
| DT | 0.13 | 0.16 | dygraphs | 1.1.1.6 | 1.1.1.6 | edgeR | 3.26.8 |
| ellipsis | 0.3.0 | 0.3.1 | evaluate | 0.14 | 0.14 | expm | 0.999-4 |
| fansi | 0.4.0 | 0.4.1 | farver |
| 2.0.3 | fastcluster | 1.1.25 |
| fastmap |
| 1.0.1 | fastmatch | 1.1-0 |
| findpython | 1.0.5 |
| fitdistrplus | 1.0-14 |
| flexdashboard |
| 0.5.2 | FNN | 1.1.3 |
| forcats | 0.4.0 | 0.5.0 | foreach | 1.4.7 | 1.5.1 | foreign | 0.8-72 | 0.8-80 | foreign | 0.8-81 | 0.8-80 | formatR | 1.7 | 1.7 | Formula | 1.2-3 |
| fs | 1.3.1 | 1.5.0 | futile.logger | 1.4.3 |
| futile.options | 1.0.1 |
| future | 1.14.0 |
| future.apply | 1.3.0 |
| gbRd | 0.4-11 |
| gdata | 2.18.0 |
| genefilter | 1.72.1 |
| geneLenDataBase | 1.20.0 |
| geneplotter | 1.62.0 |
| generics | 0.0.2 | 0.1.0 | GenomeInfoDb | 1.20.0 |
| GenomeInfoDbData | 1.2.1 |
| GenomicAlignments | 1.20.1 |
| GenomicFeatures | 1.36.4 |
| GenomicRanges | 1.36.1 |
| ggdendro | 0.1-20 |
| ggplot2 | 3.2.0 | 3.3.2 | ggrepel | 0.8.1 |
| ggridges | 0.5.1 |
| gh | 1.1.0 |
| gistr | 0.4.2 | 0.9.0 | git2r | 0.27.1 |
| Glimma | 1.12.0 |
| glmnet |
| 4.0-2 | globals | 0.12.4 |
| glue | 1.4.1 | 1.4.2 | gmodels | 2.18.1 |
| GO.db | 3.4.1 |
| GOplot | 1.0.2 |
|
goseq | 1.36.0 |
| gower | 0.2.1 | 0.2.2 | gplots | 3.0.1.1 |
| graphics | 4.0.3 | 4.0.3 | grDevices | 4.0.3 | 4.0.3 | grid | 4.0.3 | 4.0.3 | gridExtra | 2.3 |
| gsubfn | 0.7 |
| gtable | 0.3.0 | 0.3.0 | gtools | 3.8.1 |
| haven | 2.1.1 | 2.3.1 | hdf5r | 1.2.0 |
| hexbin | 1.27.3 | 1.28.1 | highr | 0.8 | 0.8 | Hmisc | 4.4-0 |
| hms | 0.5.0 | 0.5.3 | htmlTable | 1.13.1 |
| htmltools | 0.3.6 | 0.5.0 | htmlwidgets | 1.3 | 1.5.2 | httpcode |
| 0.3.0 | httpuv | 1.5.1 | 1.5.4 | httr | 1.4.1 | 1.4.2 | hwriter | 1.3.2 |
| ica | 1.0-2 |
| igraph | 1.2.4.1 |
| ini | 0.3.1 |
| inline | 0.3.15 |
| ipred | 0.9-9 | 0.9-9 | IRanges | 2.22.2 |
| IRdisplay |
| 0.7.0 | IRkernel |
| 1.1.1 | irlba | 2.3.3 |
| isoband |
| 0.2.2 | iterators | 1.0.12 | 1.0.13 | janitor | 1.2.0 |
| jsonlite | 1.6.1 | 1.7.1 | kableExtra |
| 1.3.1 | KernSmooth | 2.23-15 | 2.23-18 | KernSmooth | 2.23-18 | 2.23-18 | knitr | 1.28 | 1.30 | labeling | 0.3 | 0.4.2 | lambda.r | 1.2.3 |
| later | 0.8.0 | 1.1.0.1 | lattice | 0.20-38 | 0.20-41 | lattice | 0.20-41 | 0.20-41 | latticeExtra | 0.6-28 |
| lava | 1.6.6 | 1.6.8.1 | lazyeval | 0.2.2 | 0.2.2 | leiden | 0.3.1 |
| lifecycle |
| 0.2.0 | limma | 3.40.6 |
| listenv | 0.7.0 |
| lme4 | 1.1-21 |
| lmtest | 0.9-37 |
| locfit | 1.5-9.1 |
| loo | 2.1.0 |
| lsei | 1.2-0 |
| lubridate | 1.7.4 | 1.7.9.2 | magick | 2.1 |
| magrittr | 1.5 | 2.0.1 | maps | 3.3.0 | 3.3.0 | markdown | 1.1 | 1.1 | MASS | 7.3-51.5 | 7.3-53 | MASS | 7.3-53.1 | 7.3-53 | Matrix | 1.2-17 | 1.2-18 | Matrix | 1.3-2 | 1.2-18 | matrixStats | 0.55.0 |
| memoise | 1.1.0 |
| metap | 1.1 |
| methods | 4.0.3 | 4.0.3 | mgcv | 1.8-28 | 1.8-33 | mgcv | 1.8-34 | 1.8-33 | mime | 0.7 | 0.9 | minqa | 1.2.4 |
| mlr | 2.15.0 |
| mnormt | 1.5-5 |
| ModelMetrics | 1.2.2 | 1.2.2.2 | modelr | 0.1.5 | 0.1.8 | multtest | 2.40.0 |
| munsell | 0.5.0 | 0.5.0 | ncdf4 | 1.16.1 |
| nlme | 3.1-141 | 3.1-150 | nlme | 3.1-152 | 3.1-150 | nloptr | 1.2.1 |
| nnet | 7.3-12 | 7.3-14 | nnet | 7.3-15 | 7.3-14 | npsurv | 0.4-0 |
| numDeriv | 2016.8-1.1 | 2016.8-1.1 | openssl | 1.4.1 | 1.4.3 | openxlsx | 4.1.0.1 |
| pacman | 0.5.1 |
| parallel | 4.0.3 | 4.0.3 | parallelMap | 1.4 |
| ParamHelpers | 1.12 |
| pbapply | 1.4-1 |
| pbdZMQ |
| 0.3-3.1 | phangorn | 2.5.5 |
| phytools | 0.6-99 |
| pillar | 1.4.2 | 1.4.7 | pkgbuild | 1.0.8 | 1.1.0 | pkgconfig | 2.0.2 | 2.0.3 | pkgload | 1.0.2 | 1.1.0 | plogr | 0.2.0 |
| plotly | 4.9.0 | 4.9.2.1 | plotrix | 3.7-6 |
| plyr | 1.8.4 | 1.8.6 | png | 0.1-7 |
| praise | 1.0.0 | 1.0.0 | prettyunits | 1.0.2 | 1.1.1 | pROC |
| 1.16.2 | processx | 3.4.1 | 3.4.4 | prodlim | 2018.04.18 | 2019.11.13 | progress | 1.2.2 | 1.2.2 | promises | 1.0.1 | 1.1.1 | proto | 1.0.0 |
| pryr | 0.1.4 | 0.1.4 | ps | 1.3.0 | 1.4.0 | purrr | 0.3.4 | 0.3.4 | quadprog | 1.5-7 |
| quantmod | 0.4-15 | 0.4.17 | qvalue | 2.16.0 |
| R.methodsS3 | 1.7.1 |
| R.oo | 1.23.0 |
| R.utils | 2.9.0 |
| R6 | 2.4.0 | 2.5.0 | randomForest | 4.6-14 | 4.6-14 | RANN | 2.6.1 |
| rappdirs | 0.3.1 | 0.3.1 | rbokeh | 0.5.0 | 0.5.1 | rcmdcheck | 1.3.3 |
| RColorBrewer | 1.1-2 | 1.1-2 | Rcpp | 1.0.4.6 | 1.0.5 | RcppAnnoy | 0.0.12 |
| RcppArmadillo | 0.9.600.4.0 |
| RcppEigen | 0.3.3.5.0 |
| RcppParallel | 4.4.3 |
| RcppProgress | 0.4.1 |
| RCurl | 1.98-1.2 |
| Rdpack | 0.11-0 |
| readr | 1.3.1 | 1.4.0 | readxl | 1.3.1 | 1.3.1 | recipes | 0.1.6 | 0.1.15 | rematch | 1.0.1 | 1.0.1 | rematch2 | 2.1.2 | 2.1.2 | remotes | 2.1.1 |
| repr |
| 1.1.0 | reprex | 0.3.0 | 0.3.0 | reshape2 | 1.4.3 | 1.4.4 | reticulate | 1.15 | 1.18 | rex | 1.1.2 |
| rhdf5 | 2.28.1 |
| Rhdf5lib | 1.6.3 |
| Rhtslib | 1.18.1 |
| rlang | 0.4.6 | 0.4.8 | rmarkdown | 1.14 | 2.5 | ROCR | 1.0-7 |
| ROTS | 1.12.0 |
| roxygen2 | 7.1.0 |
| rpart | 4.1-15 | 4.1-15 | rpart | 4.1-15 | 4.1-15 | RPostgreSQL | 0.6-2 |
| rprojroot | 1.3-2 | 2.0.2 | Rsamtools | 2.2.1 |
| RSpectra | 0.15-0 |
| RSQLite | 2.1.2 |
| rstan | 2.19.2 |
| rstudioapi | 0.11 | 0.13 | rsvd | 1.0.2 |
| rtracklayer | 1.44.4 |
| Rtsne | 0.15 |
| rversions | 2.0.1 |
| rvest | 0.3.4 | 0.3.6 | S4Vectors | 0.26.1 |
| scales | 1.0.0 | 1.1.1 | scatterplot3d | 0.3-41 |
| sctransform | 0.2.0 |
| SDMTools | 1.1-221.1 |
| selectr | 0.4-1 | 0.4-2 | sessioninfo | 1.1.1 |
| Seurat | 3.1.0 |
| shape |
| 1.4.5 | shiny | 1.3.2 | 1.5.0 | sitmo | 2.0.1 |
| sm | 2.2-5.6 |
| snakecase | 0.11.0 |
| snow | 0.4-3 |
| sourcetools | 0.1.7 | 0.1.7 | spatial |
| 7.3-12 | splines | 4.0.3 | 4.0.3 | splitstackshape | 1.4.8 |
| sqldf | 0.4-11 |
| SQUAREM | 2017.10-1 | 2020.5 | StanHeaders | 2.18.1-10 |
| statmod | 1.4.32 |
| stats | 4.0.3 | 4.0.3 | stats4 | 4.0.3 | 4.0.3 | stringi | 1.4.3 | 1.5.3 | stringr | 1.4.0 | 1.4.0 | SummarizedExperiment | 1.18.2 |
| survival | 3.1-12 | 3.2-7 | survival | 3.2-7 | 3.2-7 | sys | 3.2 | 3.4 | tcltk | 4.0.3 | 4.0.3 | testthat | 2.3.2 | 3.0.0 | tibble | 2.1.3 | 3.0.4 | tidyr | 0.8.3 | 1.1.2 | tidyselect | 0.2.5 | 1.1.0 | tidyverse | 1.2.1 | 1.3.0 | timeDate | 3043.102 | 3043.102 | tinytex | 0.15 | 0.27 | tools | 4.0.3 | 4.0.3 | triebeard |
| 0.3.0 | tsne | 0.1-3 |
| TTR | 0.23-4 | 0.24.2 | tximport | 1.12.3 |
| tximportData | 1.18.0 |
| urltools |
| 1.7.3 | usethis | 1.6.1 |
| utf8 | 1.1.4 | 1.1.4 | utils | 4.0.3 | 4.0.3 | uuid |
| 0.1-4 | uwot | 0.1.3 |
| vctrs | 0.2.0 | 0.3.5 | viridis | 0.5.1 |
| viridisLite | 0.3.0 | 0.3.0 | waldo |
| 0.2.3 | webshot |
| 0.5.2 | whisker | 0.3-2 | 0.4 | withr | 2.2.0 | 2.3.0 | xfun | 0.8 | 0.19 | XML | 3.98-1.20 |
| xml2 | 1.3.2 | 1.3.2 | xopen | 1.0.0 |
| xtable | 1.8-4 | 1.8-4 | xts | 0.11-2 | 0.12.1 | XVector | 0.24.0 |
| yaml | 2.2.0 | 2.2.1 | zeallot | 0.1.0 | 0.1.0 | zip | 2.0.3 |
| zlibbioc | 1.30.0 |
| zoo | 1.8-6 | 1.8-8 |
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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.
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.
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