R session information
This book was last updated on 2023-01-11 17:24:49.090631.
Details on the R version used for making this book. The source code is available at LieberInstitute/recount3-docs.
## Load the package at the top of your script
library("sessioninfo")
## Reproducibility information
print('Reproducibility information:')## [1] "Reproducibility information:"Sys.time()## [1] "2023-01-11 17:24:49 UTC"proc.time()## user system elapsed
## 28.450 1.320 67.585options(width = 120)
session_info()## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R Under development (unstable) (2023-01-05 r83566)
## os Ubuntu 22.04.1 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2023-01-11
## pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.3.0)
## Biobase * 2.59.0 2022-11-01 [1] Bioconductor
## BiocFileCache 2.7.1 2022-12-09 [1] Bioconductor
## BiocGenerics * 0.45.0 2022-11-01 [1] Bioconductor
## BiocIO 1.9.1 2022-11-24 [1] Bioconductor
## BiocManager 1.30.19 2022-10-25 [2] CRAN (R 4.3.0)
## BiocParallel 1.33.9 2022-12-23 [1] Bioconductor
## BiocStyle * 2.27.0 2022-11-01 [1] Bioconductor
## Biostrings 2.67.0 2022-11-01 [1] Bioconductor
## bit 4.0.5 2022-11-15 [1] CRAN (R 4.3.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.3.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
## blob 1.2.3 2022-04-10 [1] CRAN (R 4.3.0)
## bookdown 0.31 2022-12-13 [1] CRAN (R 4.3.0)
## brio 1.1.3 2021-11-30 [2] CRAN (R 4.3.0)
## bslib 0.4.2 2022-12-16 [2] CRAN (R 4.3.0)
## cachem 1.0.6 2021-08-19 [2] CRAN (R 4.3.0)
## cli 3.6.0 2023-01-09 [1] CRAN (R 4.3.0)
## cmdfun 1.0.2 2020-10-10 [1] CRAN (R 4.3.0)
## codetools 0.2-18 2020-11-04 [3] CRAN (R 4.3.0)
## crayon 1.5.2 2022-09-29 [2] CRAN (R 4.3.0)
## curl 4.3.3 2022-10-06 [2] CRAN (R 4.3.0)
## data.table 1.14.6 2022-11-16 [1] CRAN (R 4.3.0)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.3.0)
## dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.3.0)
## DelayedArray 0.25.0 2022-11-01 [1] Bioconductor
## desc 1.4.2 2022-09-08 [2] CRAN (R 4.3.0)
## digest 0.6.31 2022-12-11 [2] CRAN (R 4.3.0)
## dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.3.0)
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.3.0)
## evaluate 0.19 2022-12-13 [2] CRAN (R 4.3.0)
## fansi 1.0.3 2022-03-24 [2] CRAN (R 4.3.0)
## fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.3.0)
## filelock 1.0.2 2018-10-05 [1] CRAN (R 4.3.0)
## fs 1.5.2 2021-12-08 [2] CRAN (R 4.3.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
## GenomeInfoDb * 1.35.10 2023-01-03 [1] Bioconductor
## GenomeInfoDbData 1.2.9 2022-12-06 [1] Bioconductor
## GenomicAlignments 1.35.0 2022-11-01 [1] Bioconductor
## GenomicRanges * 1.51.4 2022-12-15 [1] Bioconductor
## glue 1.6.2 2022-02-24 [2] CRAN (R 4.3.0)
## highr 0.10 2022-12-22 [2] CRAN (R 4.3.0)
## hms 1.1.2 2022-08-19 [1] CRAN (R 4.3.0)
## htmltools 0.5.4 2022-12-07 [2] CRAN (R 4.3.0)
## httr 1.4.4 2022-08-17 [2] CRAN (R 4.3.0)
## IRanges * 2.33.0 2022-11-01 [1] Bioconductor
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.3.0)
## jsonlite 1.8.4 2022-12-06 [2] CRAN (R 4.3.0)
## knitr 1.41 2022-11-18 [2] CRAN (R 4.3.0)
## lattice 0.20-45 2021-09-22 [3] CRAN (R 4.3.0)
## lifecycle 1.0.3 2022-10-07 [2] CRAN (R 4.3.0)
## magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.3.0)
## Matrix 1.5-3 2022-11-11 [3] CRAN (R 4.3.0)
## MatrixGenerics * 1.11.0 2022-11-01 [1] Bioconductor
## matrixStats * 0.63.0 2022-11-18 [1] CRAN (R 4.3.0)
## megadepth * 1.5.0 2023-01-10 [1] Github (LieberInstitute/megadepth@3609d89)
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.3.0)
## pillar 1.8.1 2022-08-19 [2] CRAN (R 4.3.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.3.0)
## pkgload 1.3.2 2022-11-16 [2] CRAN (R 4.3.0)
## postcards * 0.2.3 2022-01-07 [1] CRAN (R 4.3.0)
## purrr * 1.0.1 2023-01-10 [1] CRAN (R 4.3.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
## R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.3.0)
## R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.3.0)
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.3.0)
## Rcpp 1.0.9 2022-07-08 [2] CRAN (R 4.3.0)
## RCurl 1.98-1.9 2022-10-03 [1] CRAN (R 4.3.0)
## readr 2.1.3 2022-10-01 [1] CRAN (R 4.3.0)
## recount3 * 1.9.1 2023-01-11 [1] Github (LieberInstitute/recount3@7c4e68e)
## restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.3.0)
## rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
## rlang 1.0.6 2022-09-24 [2] CRAN (R 4.3.0)
## rmarkdown 2.19 2022-12-15 [2] CRAN (R 4.3.0)
## rprojroot 2.0.3 2022-04-02 [2] CRAN (R 4.3.0)
## Rsamtools 2.15.1 2022-12-30 [1] Bioconductor
## RSQLite 2.2.20 2022-12-22 [1] CRAN (R 4.3.0)
## rstudioapi 0.14 2022-08-22 [2] CRAN (R 4.3.0)
## rtracklayer 1.59.1 2022-12-27 [1] Bioconductor
## S4Vectors * 0.37.3 2022-12-07 [1] Bioconductor
## sass 0.4.4 2022-11-24 [2] CRAN (R 4.3.0)
## sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.3.0)
## snapcount * 1.7.2 2023-01-10 [1] Github (langmead-lab/snapcount@257a66e)
## stringi 1.7.8 2022-07-11 [2] CRAN (R 4.3.0)
## stringr 1.5.0 2022-12-02 [2] CRAN (R 4.3.0)
## SummarizedExperiment * 1.29.1 2022-11-04 [1] Bioconductor
## testthat 3.1.6 2022-12-09 [2] CRAN (R 4.3.0)
## tibble 3.1.8 2022-07-22 [2] CRAN (R 4.3.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
## tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.3.0)
## utf8 1.2.2 2021-07-24 [2] CRAN (R 4.3.0)
## vctrs 0.5.1 2022-11-16 [2] CRAN (R 4.3.0)
## vroom 1.6.0 2022-09-30 [1] CRAN (R 4.3.0)
## withr 2.5.0 2022-03-03 [2] CRAN (R 4.3.0)
## xfun 0.36 2022-12-21 [2] CRAN (R 4.3.0)
## XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.3.0)
## XVector 0.39.0 2022-11-01 [1] Bioconductor
## yaml 2.3.6 2022-10-18 [2] CRAN (R 4.3.0)
## zlibbioc 1.45.0 2022-11-01 [1] Bioconductor
##
## [1] /usr/local/lib/R/host-site-library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────