install.packages('BiocManager')
pkgs = c('VariantAnnotation',
'GenomicRanges',
'dplyr',
'remotes',
'ggplot2',
'tidyr')
ap.db <- available.packages(contrib.url(BiocManager::repositories()))
ap <- rownames(ap.db)
pkgs_to_install <- pkgs[pkgs %in% ap]
BiocManager::install(pkgs_to_install, update=FALSE, ask=FALSE)
# just in case there were warnings, we want to see them
# without having to scroll up:
warnings()
if (!is.null(warnings()))
{
w <- capture.output(warnings())
if (length(grep("is not available|had non-zero exit status", w)))
quit("no", 1L)
}
## suppressWarnings(BiocManager::install(update=TRUE, ask=FALSE))
remotes::install_local()
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