R session information

This book was last updated on 2022-04-08 18:50:30.

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] "2022-04-08 18:50:30 UTC"
proc.time()
##    user  system elapsed 
##  22.529   0.926  56.869
options(width = 120)
session_info()
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value
##  version  R Under development (unstable) (2022-03-14 r81896)
##  os       Ubuntu 20.04.4 LTS
##  system   x86_64, linux-gnu
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       UTC
##  date     2022-04-08
##  pandoc   2.17.1.1 @ /usr/local/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package              * version  date (UTC) lib source
##  assertthat             0.2.1    2019-03-21 [1] CRAN (R 4.2.0)
##  Biobase              * 2.55.2   2022-04-07 [1] Bioconductor
##  BiocFileCache          2.3.4    2022-01-20 [1] Bioconductor
##  BiocGenerics         * 0.41.2   2021-11-15 [1] Bioconductor
##  BiocIO                 1.5.0    2021-10-26 [1] Bioconductor
##  BiocManager            1.30.16  2021-06-15 [2] CRAN (R 4.2.0)
##  BiocParallel           1.29.20  2022-04-05 [1] Bioconductor
##  BiocStyle            * 2.23.1   2021-12-17 [1] Bioconductor
##  Biostrings             2.63.3   2022-03-29 [1] Bioconductor
##  bit                    4.0.4    2020-08-04 [1] CRAN (R 4.2.0)
##  bit64                  4.0.5    2020-08-30 [1] CRAN (R 4.2.0)
##  bitops                 1.0-7    2021-04-24 [1] CRAN (R 4.2.0)
##  blob                   1.2.2    2021-07-23 [1] CRAN (R 4.2.0)
##  bookdown               0.25     2022-03-16 [1] CRAN (R 4.2.0)
##  brio                   1.1.3    2021-11-30 [2] CRAN (R 4.2.0)
##  bslib                  0.3.1    2021-10-06 [1] CRAN (R 4.2.0)
##  cachem                 1.0.6    2021-08-19 [2] CRAN (R 4.2.0)
##  cli                    3.2.0    2022-02-14 [2] CRAN (R 4.2.0)
##  cmdfun                 1.0.2    2020-10-10 [1] CRAN (R 4.2.0)
##  crayon                 1.5.1    2022-03-26 [1] CRAN (R 4.2.0)
##  curl                   4.3.2    2021-06-23 [2] CRAN (R 4.2.0)
##  data.table             1.14.2   2021-09-27 [1] CRAN (R 4.2.0)
##  DBI                    1.1.2    2021-12-20 [1] CRAN (R 4.2.0)
##  dbplyr                 2.1.1    2021-04-06 [1] CRAN (R 4.2.0)
##  DelayedArray           0.21.2   2021-11-16 [1] Bioconductor
##  desc                   1.4.1    2022-03-06 [2] CRAN (R 4.2.0)
##  digest                 0.6.29   2021-12-01 [2] CRAN (R 4.2.0)
##  dplyr                  1.0.8    2022-02-08 [2] CRAN (R 4.2.0)
##  ellipsis               0.3.2    2021-04-29 [2] CRAN (R 4.2.0)
##  evaluate               0.15     2022-02-18 [2] CRAN (R 4.2.0)
##  fansi                  1.0.3    2022-03-24 [1] CRAN (R 4.2.0)
##  fastmap                1.1.0    2021-01-25 [2] CRAN (R 4.2.0)
##  filelock               1.0.2    2018-10-05 [1] CRAN (R 4.2.0)
##  fs                     1.5.2    2021-12-08 [2] CRAN (R 4.2.0)
##  generics               0.1.2    2022-01-31 [2] CRAN (R 4.2.0)
##  GenomeInfoDb         * 1.31.7   2022-04-01 [1] Bioconductor
##  GenomeInfoDbData       1.2.7    2022-04-08 [1] Bioconductor
##  GenomicAlignments      1.31.2   2021-11-05 [1] Bioconductor
##  GenomicRanges        * 1.47.6   2022-01-12 [1] Bioconductor
##  glue                   1.6.2    2022-02-24 [2] CRAN (R 4.2.0)
##  highr                  0.9      2021-04-16 [2] CRAN (R 4.2.0)
##  hms                    1.1.1    2021-09-26 [1] CRAN (R 4.2.0)
##  htmltools              0.5.2    2021-08-25 [1] CRAN (R 4.2.0)
##  httr                   1.4.2    2020-07-20 [2] CRAN (R 4.2.0)
##  IRanges              * 2.29.1   2021-11-16 [1] Bioconductor
##  jquerylib              0.1.4    2021-04-26 [1] CRAN (R 4.2.0)
##  jsonlite               1.8.0    2022-02-22 [2] CRAN (R 4.2.0)
##  knitr                  1.37     2021-12-16 [2] CRAN (R 4.2.0)
##  lattice                0.20-45  2021-09-22 [3] CRAN (R 4.2.0)
##  lifecycle              1.0.1    2021-09-24 [2] CRAN (R 4.2.0)
##  magrittr               2.0.3    2022-03-30 [1] CRAN (R 4.2.0)
##  Matrix                 1.4-0    2021-12-08 [3] CRAN (R 4.2.0)
##  MatrixGenerics       * 1.7.0    2021-10-26 [1] Bioconductor
##  matrixStats          * 0.61.0   2021-09-17 [1] CRAN (R 4.2.0)
##  megadepth            * 1.5.0    2022-04-08 [1] Github (LieberInstitute/megadepth@3609d89)
##  memoise                2.0.1    2021-11-26 [2] CRAN (R 4.2.0)
##  pillar                 1.7.0    2022-02-01 [2] CRAN (R 4.2.0)
##  pkgconfig              2.0.3    2019-09-22 [2] CRAN (R 4.2.0)
##  pkgload                1.2.4    2021-11-30 [2] CRAN (R 4.2.0)
##  postcards            * 0.2.3    2022-01-07 [1] CRAN (R 4.2.0)
##  purrr                * 0.3.4    2020-04-17 [2] CRAN (R 4.2.0)
##  R.methodsS3            1.8.1    2020-08-26 [1] CRAN (R 4.2.0)
##  R.oo                   1.24.0   2020-08-26 [1] CRAN (R 4.2.0)
##  R.utils                2.11.0   2021-09-26 [1] CRAN (R 4.2.0)
##  R6                     2.5.1    2021-08-19 [2] CRAN (R 4.2.0)
##  rappdirs               0.3.3    2021-01-31 [2] CRAN (R 4.2.0)
##  Rcpp                   1.0.8.3  2022-03-17 [1] CRAN (R 4.2.0)
##  RCurl                  1.98-1.6 2022-02-08 [1] CRAN (R 4.2.0)
##  readr                  2.1.2    2022-01-30 [1] CRAN (R 4.2.0)
##  recount3             * 1.5.1    2022-04-08 [1] Github (LieberInstitute/recount3@6eb14b8)
##  restfulr               0.0.13   2017-08-06 [1] CRAN (R 4.2.0)
##  rjson                  0.2.21   2022-01-09 [1] CRAN (R 4.2.0)
##  rlang                  1.0.2    2022-03-04 [2] CRAN (R 4.2.0)
##  rmarkdown              2.13     2022-03-10 [1] CRAN (R 4.2.0)
##  rprojroot              2.0.3    2022-04-02 [1] CRAN (R 4.2.0)
##  Rsamtools              2.11.0   2021-10-27 [1] Bioconductor
##  RSQLite                2.2.12   2022-04-02 [1] CRAN (R 4.2.0)
##  rstudioapi             0.13     2020-11-12 [2] CRAN (R 4.2.0)
##  rtracklayer            1.55.4   2022-03-23 [1] Bioconductor
##  S4Vectors            * 0.33.17  2022-04-06 [1] Bioconductor
##  sass                   0.4.1    2022-03-23 [1] CRAN (R 4.2.0)
##  sessioninfo          * 1.2.2    2021-12-06 [2] CRAN (R 4.2.0)
##  snapcount            * 1.3.1    2022-04-08 [1] Github (langmead-lab/snapcount@19cf747)
##  stringi                1.7.6    2021-11-29 [2] CRAN (R 4.2.0)
##  stringr                1.4.0    2019-02-10 [2] CRAN (R 4.2.0)
##  SummarizedExperiment * 1.25.3   2021-12-08 [1] Bioconductor
##  testthat               3.1.3    2022-03-29 [1] CRAN (R 4.2.0)
##  tibble                 3.1.6    2021-11-07 [2] CRAN (R 4.2.0)
##  tidyselect             1.1.2    2022-02-21 [2] CRAN (R 4.2.0)
##  tzdb                   0.3.0    2022-03-28 [1] CRAN (R 4.2.0)
##  utf8                   1.2.2    2021-07-24 [2] CRAN (R 4.2.0)
##  vctrs                  0.4.0    2022-03-30 [1] CRAN (R 4.2.0)
##  vroom                  1.5.7    2021-11-30 [1] CRAN (R 4.2.0)
##  withr                  2.5.0    2022-03-03 [2] CRAN (R 4.2.0)
##  xfun                   0.30     2022-03-02 [2] CRAN (R 4.2.0)
##  XML                    3.99-0.9 2022-02-24 [1] CRAN (R 4.2.0)
##  XVector                0.35.0   2021-10-26 [1] Bioconductor
##  yaml                   2.3.5    2022-02-21 [2] CRAN (R 4.2.0)
##  zlibbioc               1.41.0   2021-10-26 [1] Bioconductor
## 
##  [1] /usr/local/lib/R/host-site-library
##  [2] /usr/local/lib/R/site-library
##  [3] /usr/local/lib/R/library
## 
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────