BiocManager v1.30.10

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Access the Bioconductor Project Package Repository

A convenient tool to install and update Bioconductor packages.

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BiocManager

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status CRAN
release CRAN
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Travis build
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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  • valid() checks and returns packages that are out-of-date or too new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 Warning: 0 packages out-of-date; 1 packages too new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.

Functions in BiocManager

Name Description
install Install or update Bioconductor, CRAN, and GitHub packages
available Discover packages available for installation.
repositories Display current Bioconductor and CRAN repositories.
BiocManager-pkg Install or update Bioconductor, CRAN, or GitHub packages
valid Validate installed package versions against correct versions.
version Version of Bioconductor currently in use.
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Vignettes of BiocManager

Name
BiocManager.Rmd
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Last month downloads

Details

BugReports https://github.com/Bioconductor/BiocManager/issues
VignetteBuilder knitr
License Artistic-2.0
Encoding UTF-8
RoxygenNote 6.1.1
NeedsCompilation no
Packaged 2019-11-16 00:28:15 UTC; mramos
Repository CRAN
Date/Publication 2019-11-16 05:40:09 UTC

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