GitHub - Bioconductor/BiocArchive: Match the CRAN archive repository with a previous Bioconductor release (original) (raw)

BiocArchive

BiocArchive is a package dedicated to preserving reproducibility with older Bioconductor versions. It works for older Bioconductor releases, for example version 3.14. Note that users must have the proper 3.14setup to be able to install packages from the archive. This means that users should be running R version 4.1.

It is highly recommended that users run docker containers with the appropriate R version installation and install the package via GitHub or via source.

Installation

Currently, it is available via GitHub.

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("Bioconductor/BiocArchive")

Load the package

Last release version

The lastBuilt helper function finds the last built date for the supplied Bioconductor version. Other functions rely on this date to install the appropriate packages.

lastBuilt(version = "3.14") #> 3.14 #> "2022-04-13"

Archived installations

To install Bioconductor packages from previous releases, we strongly recommend using Bioconductor Docker containers, where possible. Such containers will have BiocManager installed. BiocArchive allows versioned installations of CRAN packages from either the Posit Public Package Manager (P3M) or the CRANarchive.

Docker installation

To download the Docker container, one can run the docker command:

docker pull bioconductor/bioconductor_docker:RELEASE_3_14

For more information, see the Docker for Bioconductor page:https://www.bioconductor.org/help/docker/

Bioconductor installations

Installations of Bioconductor packages are handled by BiocManager and will work as normal within a legacy container or local installation.

install("DESeq2", version = "3.14", dry.run = TRUE) #> CRAN #> "https://packagemanager.posit.co/cran/2022-04-13"

install("MultiAssayExperiment", version = "3.14", dry.run = TRUE) #> CRAN #> "https://packagemanager.posit.co/cran/2022-04-13"

Note. The dry.run argument returns the CRAN repository location. The default is to install CRAN packages from the P3M snapshot repository.

P3M installations

The Posit Public Package Manager (P3M) allows installations of packages from their respective snapshot repositories. To enable installation from these repositories, users must either set their getOption("BiocArchive.snapshot") option or the snapshotargument to P3M. By default, the package uses P3M snapshots tied to the last build date of the Bioconductor version.

install("DESeq2", version = "3.14", dry.run = TRUE, snapshot = "P3M") #> CRAN #> "https://packagemanager.posit.co/cran/2022-04-13"

install( "MultiAssayExperiment", version = "3.14", dry.run = TRUE, snapshot = "P3M" ) #> CRAN #> "https://packagemanager.posit.co/cran/2022-04-13"

CRAN installations from the source archive

Packages on CRAN have a history of versions at a particular URL location:

https://cran.r-project.org/src/contrib/Archive

A CRAN package from the archive can be installed (from source) usingCRANinstall:

CRANinstall("dplyr", "3.14", dry.run = TRUE) #> https://cran.r-project.org/src/contrib/Archive/dplyr/dplyr_1.0.8.tar.gz #> #> The downloaded source packages are in #> '/tmp/RtmpUQWJ6y/downloaded_packages'

The function will attempt to satisfy all dependencies from the CRAN archive.

Repository URLs

To see the list of active repositories based on option configurations, use the repositories() function:

repositories(version = "3.14")

Note. The R version must coincide with the Bioconductor version sought.

Package validity

To check whether all packages are within the valid time interval of the Bioconductor release, the valid() function will compare package versions with those in the P3M repository.

Note. The R version must coincide with the Bioconductor version sought.

Session Information

sessionInfo() #> R version 4.4.0 Patched (2024-04-29 r86495) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #> #> Matrix products: default #> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 #> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 #> #> locale: #> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#> #> time zone: America/New_York #> tzcode source: system (glibc) #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base
#> #> other attached packages: #> [1] tinytest_1.4.1 BiocArchive_0.99.19 colorout_1.3-0.1
#> #> loaded via a namespace (and not attached): #> [1] vctrs_0.6.5 httr_1.4.7 cli_3.6.2 knitr_1.46 rlang_1.1.3
#> [6] xfun_0.44 pkgload_1.3.4 generics_0.1.3 glue_1.7.0 htmltools_0.5.8.1
#> [11] fansi_1.0.6 rmarkdown_2.27 tibble_3.2.1 evaluate_0.23 fastmap_1.2.0
#> [16] yaml_2.3.8 lifecycle_1.0.4 memoise_2.0.1 BiocManager_1.30.23 compiler_4.4.0
#> [21] rvest_1.0.4 codetools_0.2-20 pkgconfig_2.0.3 timechange_0.3.0 rstudioapi_0.16.0
#> [26] digest_0.6.35 R6_2.5.1 utf8_1.2.4 pillar_1.9.0 curl_5.2.1
#> [31] parallel_4.4.0 magrittr_2.0.3 tools_4.4.0 lubridate_1.9.3 xml2_1.3.6
#> [36] cachem_1.1.0