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 patterninstall()
installs and/or updates packages either CRAN or Bioconductorrepositories()
shows all package repository URL endpointsvalid()
checks and returns packages that are out-of-date or too newversion()
returns the current Bioconductor version number
install.packages("BiocManager")
library(BiocManager)
version()
#> [1] '3.8'
install(c("GenomicRanges", "SummarizedExperiment"))
valid()
#> Warning: 0 packages out-of-date; 1 packages too new
#>
#> * sessionInfo()
#>
#> R version 3.5.2 Patched (2019-02-12 r76095)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.10
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0
#>
#> 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
#>
#> other attached packages:
#> [1] BiocManager_1.30.5
#>
#> loaded via a namespace (and not attached):
#> [1] compiler_3.5.1 magrittr_1.5 tools_3.5.1 htmltools_0.3.6
#> [5] yaml_2.2.0 Rcpp_1.0.1 stringi_1.4.3 rmarkdown_1.12
#> [9] knitr_1.22 stringr_1.4.0 xfun_0.6 digest_0.6.18
#> [13] evaluate_0.13
#>
#> Bioconductor version '3.8'
#>
#> * 0 packages out-of-date
#> * 1 packages too new
#>
#> create a valid installation with
#>
#> BiocManager::install("BiocManager", update = TRUE, ask = FALSE)
#>
#> more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
Please see the package vignette for more detailed information such as changing Bioconductor version, offline use, and other advanced usage.
To report apparent bugs, create a minimal and reproducible example on github