R session information

This book was last updated on 2021-09-15 14:27:28.

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] "2021-09-15 14:27:28 UTC"
proc.time()
##    user  system elapsed 
##  26.408   1.319  73.225
options(width = 120)
session_info()
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 4.1.1 (2021-08-10)
##  os       Ubuntu 20.04.3 LTS          
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       UTC                         
##  date     2021-09-15                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package              * version  date       lib source                                    
##  assertthat             0.2.1    2019-03-21 [1] RSPM (R 4.1.0)                            
##  Biobase              * 2.53.0   2021-05-19 [1] Bioconductor                              
##  BiocFileCache          2.1.1    2021-06-23 [1] Bioconductor                              
##  BiocGenerics         * 0.39.2   2021-08-18 [1] Bioconductor                              
##  BiocIO                 1.3.0    2021-05-19 [1] Bioconductor                              
##  BiocManager            1.30.16  2021-06-15 [2] CRAN (R 4.1.1)                            
##  BiocParallel           1.27.7   2021-09-09 [1] Bioconductor                              
##  BiocStyle            * 2.21.3   2021-06-16 [1] Bioconductor                              
##  Biostrings             2.61.2   2021-08-04 [1] Bioconductor                              
##  bit                    4.0.4    2020-08-04 [1] RSPM (R 4.1.0)                            
##  bit64                  4.0.5    2020-08-30 [1] RSPM (R 4.1.0)                            
##  bitops                 1.0-7    2021-04-24 [1] RSPM (R 4.1.0)                            
##  blob                   1.2.2    2021-07-23 [1] RSPM (R 4.1.0)                            
##  bookdown               0.24     2021-09-02 [1] RSPM (R 4.1.0)                            
##  bslib                  0.3.0    2021-09-02 [1] RSPM (R 4.1.0)                            
##  cachem                 1.0.6    2021-08-19 [2] RSPM (R 4.1.0)                            
##  cli                    3.0.1    2021-07-17 [2] RSPM (R 4.1.0)                            
##  cmdfun                 1.0.2    2020-10-10 [1] RSPM (R 4.1.0)                            
##  crayon                 1.4.1    2021-02-08 [2] RSPM (R 4.1.0)                            
##  curl                   4.3.2    2021-06-23 [2] RSPM (R 4.1.0)                            
##  data.table             1.14.0   2021-02-21 [1] RSPM (R 4.1.0)                            
##  DBI                    1.1.1    2021-01-15 [1] RSPM (R 4.1.0)                            
##  dbplyr                 2.1.1    2021-04-06 [1] RSPM (R 4.1.0)                            
##  DelayedArray           0.19.3   2021-09-12 [1] Bioconductor                              
##  desc                   1.3.0    2021-03-05 [2] RSPM (R 4.1.0)                            
##  digest                 0.6.27   2020-10-24 [2] RSPM (R 4.1.0)                            
##  dplyr                  1.0.7    2021-06-18 [2] RSPM (R 4.1.0)                            
##  ellipsis               0.3.2    2021-04-29 [2] RSPM (R 4.1.0)                            
##  evaluate               0.14     2019-05-28 [2] RSPM (R 4.1.0)                            
##  fansi                  0.5.0    2021-05-25 [2] RSPM (R 4.1.0)                            
##  fastmap                1.1.0    2021-01-25 [2] RSPM (R 4.1.0)                            
##  filelock               1.0.2    2018-10-05 [1] RSPM (R 4.1.0)                            
##  fs                     1.5.0    2020-07-31 [2] RSPM (R 4.1.0)                            
##  generics               0.1.0    2020-10-31 [2] RSPM (R 4.1.0)                            
##  GenomeInfoDb         * 1.29.8   2021-09-05 [1] Bioconductor                              
##  GenomeInfoDbData       1.2.6    2021-09-13 [1] Bioconductor                              
##  GenomicAlignments      1.29.0   2021-05-19 [1] Bioconductor                              
##  GenomicRanges        * 1.45.0   2021-05-19 [1] Bioconductor                              
##  glue                   1.4.2    2020-08-27 [2] RSPM (R 4.1.0)                            
##  highr                  0.9      2021-04-16 [2] RSPM (R 4.1.0)                            
##  hms                    1.1.0    2021-05-17 [1] RSPM (R 4.1.0)                            
##  htmltools              0.5.2    2021-08-25 [1] RSPM (R 4.1.0)                            
##  httr                   1.4.2    2020-07-20 [2] RSPM (R 4.1.0)                            
##  IRanges              * 2.27.2   2021-08-18 [1] Bioconductor                              
##  jquerylib              0.1.4    2021-04-26 [1] RSPM (R 4.1.0)                            
##  jsonlite               1.7.2    2020-12-09 [2] RSPM (R 4.1.0)                            
##  knitr                  1.34     2021-09-09 [2] RSPM (R 4.1.0)                            
##  lattice                0.20-44  2021-05-02 [3] CRAN (R 4.1.1)                            
##  lifecycle              1.0.0    2021-02-15 [2] RSPM (R 4.1.0)                            
##  magrittr               2.0.1    2020-11-17 [2] RSPM (R 4.1.0)                            
##  Matrix                 1.3-4    2021-06-01 [3] CRAN (R 4.1.1)                            
##  MatrixGenerics       * 1.5.4    2021-08-26 [1] Bioconductor                              
##  matrixStats          * 0.60.1   2021-08-23 [1] RSPM (R 4.1.0)                            
##  megadepth            * 1.3.3    2021-09-13 [1] Github (LieberInstitute/megadepth@6ea0179)
##  memoise                2.0.0    2021-01-26 [2] RSPM (R 4.1.0)                            
##  pillar                 1.6.2    2021-07-29 [2] RSPM (R 4.1.0)                            
##  pkgconfig              2.0.3    2019-09-22 [2] RSPM (R 4.1.0)                            
##  pkgload                1.2.2    2021-09-11 [1] RSPM (R 4.1.0)                            
##  postcards            * 0.2.2    2021-07-31 [1] RSPM (R 4.1.0)                            
##  purrr                * 0.3.4    2020-04-17 [2] RSPM (R 4.1.0)                            
##  R.methodsS3            1.8.1    2020-08-26 [1] RSPM (R 4.1.0)                            
##  R.oo                   1.24.0   2020-08-26 [1] RSPM (R 4.1.0)                            
##  R.utils                2.10.1   2020-08-26 [1] RSPM (R 4.1.0)                            
##  R6                     2.5.1    2021-08-19 [2] RSPM (R 4.1.0)                            
##  rappdirs               0.3.3    2021-01-31 [2] RSPM (R 4.1.0)                            
##  Rcpp                   1.0.7    2021-07-07 [1] RSPM (R 4.1.0)                            
##  RCurl                  1.98-1.4 2021-08-17 [1] RSPM (R 4.1.0)                            
##  readr                  2.0.1    2021-08-10 [1] RSPM (R 4.1.0)                            
##  recount3             * 1.3.8    2021-09-15 [1] Github (LieberInstitute/recount3@9cbdf7f) 
##  restfulr               0.0.13   2017-08-06 [1] RSPM (R 4.1.1)                            
##  rjson                  0.2.20   2018-06-08 [1] RSPM (R 4.1.0)                            
##  rlang                  0.4.11   2021-04-30 [2] RSPM (R 4.1.0)                            
##  rmarkdown              2.10     2021-08-06 [1] RSPM (R 4.1.0)                            
##  rprojroot              2.0.2    2020-11-15 [2] RSPM (R 4.1.0)                            
##  Rsamtools              2.9.1    2021-06-17 [1] Bioconductor                              
##  RSQLite                2.2.8    2021-08-21 [1] RSPM (R 4.1.0)                            
##  rstudioapi             0.13     2020-11-12 [2] RSPM (R 4.1.0)                            
##  rtracklayer            1.53.1   2021-08-13 [1] Bioconductor                              
##  S4Vectors            * 0.31.3   2021-08-26 [1] Bioconductor                              
##  sass                   0.4.0    2021-05-12 [1] RSPM (R 4.1.0)                            
##  sessioninfo          * 1.1.1    2018-11-05 [2] RSPM (R 4.1.0)                            
##  snapcount            * 1.3.1    2021-09-13 [1] Github (langmead-lab/snapcount@19cf747)   
##  stringi                1.7.4    2021-08-25 [2] RSPM (R 4.1.0)                            
##  stringr                1.4.0    2019-02-10 [2] RSPM (R 4.1.0)                            
##  SummarizedExperiment * 1.23.4   2021-08-25 [1] Bioconductor                              
##  testthat               3.0.4    2021-07-01 [2] RSPM (R 4.1.0)                            
##  tibble                 3.1.4    2021-08-25 [2] RSPM (R 4.1.0)                            
##  tidyselect             1.1.1    2021-04-30 [2] RSPM (R 4.1.0)                            
##  tzdb                   0.1.2    2021-07-20 [1] RSPM (R 4.1.0)                            
##  utf8                   1.2.2    2021-07-24 [2] RSPM (R 4.1.0)                            
##  vctrs                  0.3.8    2021-04-29 [2] RSPM (R 4.1.0)                            
##  vroom                  1.5.4    2021-08-05 [1] RSPM (R 4.1.0)                            
##  withr                  2.4.2    2021-04-18 [2] RSPM (R 4.1.0)                            
##  xfun                   0.25     2021-08-06 [2] RSPM (R 4.1.0)                            
##  XML                    3.99-0.7 2021-08-17 [1] RSPM (R 4.1.0)                            
##  XVector                0.33.0   2021-05-19 [1] Bioconductor                              
##  yaml                   2.2.1    2020-02-01 [2] RSPM (R 4.1.0)                            
##  zlibbioc               1.39.0   2021-05-19 [1] Bioconductor                              
## 
## [1] /usr/local/lib/R/host-site-library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library