R session information
This book was last updated on 2025-09-22 14:34:37.43544.
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:"## [1] "2025-09-22 14:34:37 UTC"## user system elapsed
## 17.036 1.272 52.224## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.5.1 (2025-06-13)
## os Ubuntu 24.04.3 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2025-09-22
## pandoc 3.8 @ /usr/bin/ (via rmarkdown)
## quarto 1.7.32 @ /usr/local/bin/quarto
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-8 2024-09-12 [1] RSPM (R 4.5.0)
## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.5.0)
## Biobase * 2.69.1 2025-09-14 [1] Bioconductor 3.22 (R 4.5.1)
## BiocFileCache 2.99.6 2025-08-25 [1] Bioconductor 3.22 (R 4.5.1)
## BiocGenerics * 0.55.1 2025-07-28 [1] Bioconductor 3.22 (R 4.5.1)
## BiocIO 1.19.0 2025-04-15 [1] Bioconductor 3.22 (R 4.5.0)
## BiocManager 1.30.26 2025-06-05 [2] CRAN (R 4.5.1)
## BiocParallel 1.43.4 2025-06-16 [1] Bioconductor 3.22 (R 4.5.1)
## BiocStyle * 2.37.1 2025-08-03 [1] Bioconductor 3.22 (R 4.5.1)
## Biostrings 2.77.2 2025-06-22 [1] Bioconductor 3.22 (R 4.5.1)
## bit 4.6.0 2025-03-06 [1] RSPM (R 4.5.0)
## bit64 4.6.0-1 2025-01-16 [1] RSPM (R 4.5.0)
## bitops 1.0-9 2024-10-03 [1] RSPM (R 4.5.0)
## blob 1.2.4 2023-03-17 [1] RSPM (R 4.5.0)
## bookdown 0.44 2025-08-21 [1] RSPM (R 4.5.0)
## brio 1.1.5 2024-04-24 [2] RSPM (R 4.5.0)
## bslib 0.9.0 2025-01-30 [2] RSPM (R 4.5.0)
## cachem 1.1.0 2024-05-16 [2] RSPM (R 4.5.0)
## cli 3.6.5 2025-04-23 [2] RSPM (R 4.5.0)
## cmdfun 1.0.2 2020-10-10 [1] RSPM (R 4.5.0)
## codetools 0.2-20 2024-03-31 [3] CRAN (R 4.5.1)
## crayon 1.5.3 2024-06-20 [2] RSPM (R 4.5.0)
## curl 7.0.0 2025-08-19 [2] RSPM (R 4.5.0)
## data.table 1.17.8 2025-07-10 [1] RSPM (R 4.5.0)
## DBI 1.2.3 2024-06-02 [1] RSPM (R 4.5.0)
## dbplyr 2.5.1 2025-09-10 [1] RSPM (R 4.5.0)
## DelayedArray 0.35.3 2025-09-14 [1] Bioconductor 3.22 (R 4.5.1)
## desc 1.4.3 2023-12-10 [2] RSPM (R 4.5.0)
## digest 0.6.37 2024-08-19 [2] RSPM (R 4.5.0)
## dplyr 1.1.4 2023-11-17 [1] RSPM (R 4.5.0)
## evaluate 1.0.5 2025-08-27 [2] RSPM (R 4.5.0)
## fastmap 1.2.0 2024-05-15 [2] RSPM (R 4.5.0)
## filelock 1.0.3 2023-12-11 [1] RSPM (R 4.5.0)
## fs 1.6.6 2025-04-12 [2] RSPM (R 4.5.0)
## generics * 0.1.4 2025-05-09 [1] RSPM (R 4.5.0)
## GenomicAlignments 1.45.4 2025-09-14 [1] Bioconductor 3.22 (R 4.5.1)
## GenomicRanges * 1.61.4 2025-09-15 [1] Bioconductor 3.22 (R 4.5.1)
## glue 1.8.0 2024-09-30 [2] RSPM (R 4.5.0)
## hms 1.1.3 2023-03-21 [1] RSPM (R 4.5.0)
## htmltools 0.5.8.1 2024-04-04 [2] RSPM (R 4.5.0)
## httr 1.4.7 2023-08-15 [1] RSPM (R 4.5.0)
## httr2 1.2.1 2025-07-22 [2] RSPM (R 4.5.0)
## IRanges * 2.43.2 2025-09-16 [1] Bioconductor 3.22 (R 4.5.1)
## jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.5.0)
## jsonlite 2.0.0 2025-03-27 [2] RSPM (R 4.5.0)
## knitr 1.50 2025-03-16 [2] RSPM (R 4.5.0)
## lattice 0.22-7 2025-04-02 [3] CRAN (R 4.5.1)
## lifecycle 1.0.4 2023-11-07 [2] RSPM (R 4.5.0)
## magrittr 2.0.4 2025-09-12 [2] RSPM (R 4.5.0)
## Matrix 1.7-4 2025-08-28 [2] RSPM (R 4.5.0)
## MatrixGenerics * 1.21.0 2025-04-15 [1] Bioconductor 3.22 (R 4.5.0)
## matrixStats * 1.5.0 2025-01-07 [1] RSPM (R 4.5.0)
## megadepth * 1.17.0 2025-09-22 [1] Github (LieberInstitute/megadepth@d53868d)
## memoise 2.0.1 2021-11-26 [2] RSPM (R 4.5.0)
## pillar 1.11.1 2025-09-17 [2] RSPM (R 4.5.0)
## pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.5.0)
## pkgload 1.4.0 2024-06-28 [2] RSPM (R 4.5.0)
## postcards * 0.2.3 2022-01-07 [1] RSPM (R 4.5.0)
## purrr * 1.1.0 2025-07-10 [2] RSPM (R 4.5.0)
## R.methodsS3 1.8.2 2022-06-13 [1] RSPM (R 4.5.0)
## R.oo 1.27.1 2025-05-02 [1] RSPM (R 4.5.0)
## R.utils 2.13.0 2025-02-24 [1] RSPM (R 4.5.0)
## R6 2.6.1 2025-02-15 [2] RSPM (R 4.5.0)
## rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.5.0)
## RCurl 1.98-1.17 2025-03-22 [1] RSPM (R 4.5.0)
## readr 2.1.5 2024-01-10 [1] RSPM (R 4.5.0)
## recount3 * 1.19.2 2025-09-22 [1] Github (LieberInstitute/recount3@05c6261)
## restfulr 0.0.16 2025-06-27 [1] RSPM (R 4.5.1)
## rjson 0.2.23 2024-09-16 [1] RSPM (R 4.5.0)
## rlang 1.1.6 2025-04-11 [2] RSPM (R 4.5.0)
## rmarkdown 2.29 2024-11-04 [2] RSPM (R 4.5.0)
## rprojroot 2.1.1 2025-08-26 [2] RSPM (R 4.5.0)
## Rsamtools 2.25.3 2025-09-03 [1] Bioconductor 3.22 (R 4.5.1)
## RSQLite 2.4.3 2025-08-20 [1] RSPM (R 4.5.0)
## rstudioapi 0.17.1 2024-10-22 [2] RSPM (R 4.5.0)
## rtracklayer 1.69.1 2025-06-22 [1] Bioconductor 3.22 (R 4.5.1)
## S4Arrays 1.9.1 2025-05-29 [1] Bioconductor 3.22 (R 4.5.1)
## S4Vectors * 0.47.2 2025-09-19 [1] Bioconductor 3.22 (R 4.5.1)
## sass 0.4.10 2025-04-11 [2] RSPM (R 4.5.0)
## Seqinfo * 0.99.2 2025-07-22 [1] Bioconductor 3.22 (R 4.5.1)
## sessioninfo * 1.2.3 2025-02-05 [2] RSPM (R 4.5.0)
## snapcount * 1.7.2 2025-09-22 [1] Github (langmead-lab/snapcount@257a66e)
## SparseArray 1.9.1 2025-07-18 [1] Bioconductor 3.22 (R 4.5.1)
## stringi 1.8.7 2025-03-27 [2] RSPM (R 4.5.0)
## stringr 1.5.2 2025-09-08 [2] RSPM (R 4.5.0)
## SummarizedExperiment * 1.39.2 2025-09-15 [1] Bioconductor 3.22 (R 4.5.1)
## testthat 3.2.3 2025-01-13 [2] RSPM (R 4.5.0)
## tibble 3.3.0 2025-06-08 [2] RSPM (R 4.5.0)
## tidyselect 1.2.1 2024-03-11 [1] RSPM (R 4.5.0)
## tzdb 0.5.0 2025-03-15 [1] RSPM (R 4.5.0)
## vctrs 0.6.5 2023-12-01 [2] RSPM (R 4.5.0)
## vroom 1.6.6 2025-09-19 [1] RSPM (R 4.5.0)
## withr 3.0.2 2024-10-28 [2] RSPM (R 4.5.0)
## xfun 0.53 2025-08-19 [2] RSPM (R 4.5.0)
## XML 3.99-0.19 2025-08-22 [1] RSPM (R 4.5.0)
## XVector 0.49.1 2025-09-14 [1] Bioconductor 3.22 (R 4.5.1)
## yaml 2.3.10 2024-07-26 [2] RSPM (R 4.5.0)
##
## [1] /usr/local/lib/R/host-site-library
## [2] /usr/local/lib/R/site-library
## [3] /usr/local/lib/R/library
## * ── Packages attached to the search path.
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────