R session information
This book was last updated on 2024-12-13 16:45:04.090991.
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] "2024-12-13 16:45:04 UTC"## user system elapsed
## 17.102 1.332 51.625## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R Under development (unstable) (2024-12-04 r87420)
## os Ubuntu 24.04.1 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz UTC
## date 2024-12-13
## pandoc 3.5 @ /usr/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## abind 1.4-8 2024-09-12 [1] CRAN (R 4.5.0)
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.5.0)
## Biobase * 2.67.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## BiocFileCache 2.15.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## BiocGenerics * 0.53.3 2024-11-14 [1] Bioconductor 3.21 (R 4.5.0)
## BiocIO 1.17.1 2024-11-21 [1] Bioconductor 3.21 (R 4.5.0)
## BiocManager 1.30.25 2024-08-28 [2] CRAN (R 4.5.0)
## BiocParallel 1.41.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## BiocStyle * 2.35.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## Biostrings 2.75.2 2024-12-08 [1] Bioconductor 3.21 (R 4.5.0)
## bit 4.5.0.1 2024-12-03 [1] CRAN (R 4.5.0)
## bit64 4.5.2 2024-09-22 [1] CRAN (R 4.5.0)
## bitops 1.0-9 2024-10-03 [1] CRAN (R 4.5.0)
## blob 1.2.4 2023-03-17 [1] CRAN (R 4.5.0)
## bookdown 0.41 2024-10-16 [1] CRAN (R 4.5.0)
## brio 1.1.5 2024-04-24 [2] CRAN (R 4.5.0)
## bslib 0.8.0 2024-07-29 [2] CRAN (R 4.5.0)
## cachem 1.1.0 2024-05-16 [2] CRAN (R 4.5.0)
## cli 3.6.3 2024-06-21 [2] CRAN (R 4.5.0)
## cmdfun 1.0.2 2020-10-10 [1] CRAN (R 4.5.0)
## codetools 0.2-20 2024-03-31 [3] CRAN (R 4.5.0)
## crayon 1.5.3 2024-06-20 [2] CRAN (R 4.5.0)
## curl 6.0.1 2024-11-14 [2] CRAN (R 4.5.0)
## data.table 1.16.4 2024-12-06 [1] CRAN (R 4.5.0)
## DBI 1.2.3 2024-06-02 [1] CRAN (R 4.5.0)
## dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.5.0)
## DelayedArray 0.33.3 2024-12-02 [1] Bioconductor 3.21 (R 4.5.0)
## desc 1.4.3 2023-12-10 [2] CRAN (R 4.5.0)
## digest 0.6.37 2024-08-19 [2] CRAN (R 4.5.0)
## dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.5.0)
## evaluate 1.0.1 2024-10-10 [2] CRAN (R 4.5.0)
## fansi 1.0.6 2023-12-08 [2] CRAN (R 4.5.0)
## fastmap 1.2.0 2024-05-15 [2] CRAN (R 4.5.0)
## filelock 1.0.3 2023-12-11 [1] CRAN (R 4.5.0)
## fs 1.6.5 2024-10-30 [2] CRAN (R 4.5.0)
## generics * 0.1.3 2022-07-05 [1] CRAN (R 4.5.0)
## GenomeInfoDb * 1.43.2 2024-11-27 [1] Bioconductor 3.21 (R 4.5.0)
## GenomeInfoDbData 1.2.13 2024-12-13 [1] Bioconductor
## GenomicAlignments 1.43.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## GenomicRanges * 1.59.1 2024-11-15 [1] Bioconductor 3.21 (R 4.5.0)
## glue 1.8.0 2024-09-30 [2] CRAN (R 4.5.0)
## hms 1.1.3 2023-03-21 [1] CRAN (R 4.5.0)
## htmltools 0.5.8.1 2024-04-04 [2] CRAN (R 4.5.0)
## httr 1.4.7 2023-08-15 [1] CRAN (R 4.5.0)
## IRanges * 2.41.2 2024-12-03 [1] Bioconductor 3.21 (R 4.5.0)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.5.0)
## jsonlite 1.8.9 2024-09-20 [2] CRAN (R 4.5.0)
## knitr 1.49 2024-11-08 [2] CRAN (R 4.5.0)
## lattice 0.22-6 2024-03-20 [3] CRAN (R 4.5.0)
## lifecycle 1.0.4 2023-11-07 [2] CRAN (R 4.5.0)
## magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.5.0)
## Matrix 1.7-1 2024-10-18 [3] CRAN (R 4.5.0)
## MatrixGenerics * 1.19.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## matrixStats * 1.4.1 2024-09-08 [1] CRAN (R 4.5.0)
## megadepth * 1.17.0 2024-12-13 [1] Github (LieberInstitute/megadepth@d53868d)
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.5.0)
## pillar 1.9.0 2023-03-22 [2] CRAN (R 4.5.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.5.0)
## pkgload 1.4.0 2024-06-28 [2] CRAN (R 4.5.0)
## postcards * 0.2.3 2022-01-07 [1] CRAN (R 4.5.0)
## purrr * 1.0.2 2023-08-10 [2] CRAN (R 4.5.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.5.0)
## R.oo 1.27.0 2024-11-01 [1] CRAN (R 4.5.0)
## R.utils 2.12.3 2023-11-18 [1] CRAN (R 4.5.0)
## R6 2.5.1 2021-08-19 [2] CRAN (R 4.5.0)
## RCurl 1.98-1.16 2024-07-11 [1] CRAN (R 4.5.0)
## readr 2.1.5 2024-01-10 [1] CRAN (R 4.5.0)
## recount3 * 1.17.0 2024-12-13 [1] Github (LieberInstitute/recount3@1edc399)
## restfulr 0.0.15 2022-06-16 [1] CRAN (R 4.5.0)
## rjson 0.2.23 2024-09-16 [1] CRAN (R 4.5.0)
## rlang 1.1.4 2024-06-04 [2] CRAN (R 4.5.0)
## rmarkdown 2.29 2024-11-04 [2] CRAN (R 4.5.0)
## rprojroot 2.0.4 2023-11-05 [2] CRAN (R 4.5.0)
## Rsamtools 2.23.1 2024-11-27 [1] Bioconductor 3.21 (R 4.5.0)
## RSQLite 2.3.9 2024-12-03 [1] CRAN (R 4.5.0)
## rstudioapi 0.17.1 2024-10-22 [2] CRAN (R 4.5.0)
## rtracklayer 1.67.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## S4Arrays 1.7.1 2024-10-30 [1] Bioconductor 3.21 (R 4.5.0)
## S4Vectors * 0.45.2 2024-11-15 [1] Bioconductor 3.21 (R 4.5.0)
## sass 0.4.9 2024-03-15 [2] CRAN (R 4.5.0)
## sessioninfo * 1.2.2 2021-12-06 [2] CRAN (R 4.5.0)
## snapcount * 1.7.2 2024-12-13 [1] Github (langmead-lab/snapcount@257a66e)
## SparseArray 1.7.2 2024-11-14 [1] Bioconductor 3.21 (R 4.5.0)
## stringi 1.8.4 2024-05-06 [2] CRAN (R 4.5.0)
## stringr 1.5.1 2023-11-14 [2] CRAN (R 4.5.0)
## SummarizedExperiment * 1.37.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## testthat 3.2.2 2024-12-10 [1] CRAN (R 4.5.0)
## tibble 3.2.1 2023-03-20 [2] CRAN (R 4.5.0)
## tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.5.0)
## tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.5.0)
## UCSC.utils 1.3.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## utf8 1.2.4 2023-10-22 [2] CRAN (R 4.5.0)
## vctrs 0.6.5 2023-12-01 [2] CRAN (R 4.5.0)
## vroom 1.6.5 2023-12-05 [1] CRAN (R 4.5.0)
## withr 3.0.2 2024-10-28 [2] CRAN (R 4.5.0)
## xfun 0.49 2024-10-31 [2] CRAN (R 4.5.0)
## XML 3.99-0.17 2024-06-25 [1] CRAN (R 4.5.0)
## XVector 0.47.0 2024-10-29 [1] Bioconductor 3.21 (R 4.5.0)
## yaml 2.3.10 2024-07-26 [2] CRAN (R 4.5.0)
## zlibbioc 1.53.0 2024-10-29 [1] Bioconductor 3.21 (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
##
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