inst/doc/BiocManager.R

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, eval = interactive())

## ---- eval = FALSE------------------------------------------------------------
#  chooseCRANmirror()
#  install.packages("BiocManager")

## ---- eval = FALSE------------------------------------------------------------
#  BiocManager::install(c("GenomicRanges", "Organism.dplyr"))

## ---- eval = FALSE------------------------------------------------------------
#  BiocManager::install()

## -----------------------------------------------------------------------------
#  BiocManager::version()

## -----------------------------------------------------------------------------
#  BiocManager::valid()

## -----------------------------------------------------------------------------
#  avail <- BiocManager::available()
#  length(avail)                               # all CRAN & Bioconductor packages
#  BiocManager::available("BSgenome.Hsapiens") # BSgenome.Hsapiens.* packages

## ---- eval = FALSE------------------------------------------------------------
#  BiocManager::install()

## ---- eval = FALSE------------------------------------------------------------
#  BiocManager::valid()

## ---- eval = FALSE------------------------------------------------------------
#  BiocManager::install(version="3.7")

## ---- eval = FALSE------------------------------------------------------------
#  .libPaths()

## ---- eval = FALSE------------------------------------------------------------
#  options(
#      repos = c(CRAN_mirror = "file:///path/to/CRAN-mirror"),
#      BioC_mirror = "file:///path/to/Bioc-mirror"
#  )

## ---- eval = FALSE------------------------------------------------------------
#  options(
#      BIOCONDUCTOR_ONLINE_VERSION_DIAGNOSIS = FALSE
#  )

## ---- eval = FALSE------------------------------------------------------------
#  install.package(c("BiocManager", "BiocVersion"))

## ---- eval = FALSE------------------------------------------------------------
#  options(
#      BIOCONDUCTOR_CONFIG_FILE = "file:///path/to/config.yaml"
#  )

## ---- eval = TRUE-------------------------------------------------------------
sessionInfo()

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BiocManager documentation built on June 16, 2021, 1:06 a.m.