BiocManager

Overview

The BiocManager package, as the modern successor package to BiocInstaller, allows users to install and manage packages from the Bioconductor project. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data.

Current Bioconductor packages are available on a ‘release’ version intended for every-day use, and a ‘devel’ version where new features are continually introduced. A new release version is created every six months. Using the BiocManager package helps users accurately install packages from the appropriate release.

available() shows all packages associated with a search pattern
install() installs and/or updates packages either CRAN or Bioconductor
repositories() shows all package repository URL endpoints
valid() checks and returns packages that are out-of-date or too new
version() returns the current Bioconductor version number

Installation

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

Usage

Checking Bioconductor version currently installed

BiocManager::version()
#> [1] '3.11'

Installing Bioconductor packages

BiocManager::install(c("GenomicRanges", "SummarizedExperiment"))

Verifying a valid Bioconductor installation

BiocManager::valid()
#> Warning: 0 packages out-of-date; 1 packages too new
#> 
#> * sessionInfo()
#> 
#> R Under development (unstable) (2019-10-07 r77258)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.04.3 LTS
#> 
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] BiocManager_1.30.9 compiler_4.0.0     magrittr_1.5      
#>  [4] tools_4.0.0        htmltools_0.4.0    yaml_2.2.0        
#>  [7] Rcpp_1.0.2         stringi_1.4.3      rmarkdown_1.16    
#> [10] knitr_1.25         stringr_1.4.0      xfun_0.10         
#> [13] digest_0.6.22      rlang_0.4.1        evaluate_0.14     
#> 
#> Bioconductor version '3.11'
#> 
#>   * 0 packages out-of-date
#>   * 1 packages too new
#> 
#> create a valid installation with
#> 
#>   BiocManager::install("rapiclient", update = TRUE, ask = FALSE)
#> 
#> more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

More information

Please see the package vignette for more detailed information such as changing Bioconductor version, offline use, and other advanced usage.

Getting help

To report apparent bugs, create a minimal and reproducible example on github.

MitsuhaMiyamizu / BiocManager