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installFromBiocViews.R
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installFromBiocViews.R
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# DO NOT EDIT 'installFromBiocViews.R'; instead, edit 'installFromBiocViews.R.in' and
# use 'rake' to generate 'installFromBiocViews.R'.
library(BiocInstaller) # shouldn't be necessary
# update installed pkgs
biocLite(ask=FALSE)
wantedBiocViews <- c("Metabolomics")
url <- "http://www.bioconductor.org/packages/3.2/bioc/VIEWS"
t <- tempfile()
download.file(url, t)
dcf <- as.data.frame(read.dcf(t), stringsAsFactors=FALSE)
pkgs_matching_views <- c()
for (i in 1:nrow(dcf))
{
row <- dcf[i,]
if ((!is.na(row$biocViews)) && (!is.null(row$biocViews)))
{
views <- strsplit(gsub("\\s", "", row$biocViews), ",")[[1]]
if(any(wantedBiocViews %in% views))
pkgs_matching_views <- append(pkgs_matching_views, row$Package)
}
}
ap.db <- available.packages(contrib.url(biocinstallRepos()))
ap <- rownames(ap.db)
pkgs_to_install <- pkgs_matching_views[pkgs_matching_views %in% ap]
# don't install casper until it is compatible with newest VGAM
pkgs_to_install <- pkgs_to_install[grep("casper", pkgs_to_install, invert=TRUE)]
# don't install COPDSexualDimorphism (probably to be removed from bioc, depends on defunct cran pkg)
pkgs_to_install <- pkgs_to_install[grep("COPDSexualDimorphism", pkgs_to_install, invert=TRUE)]
# don't install NGScopy because it is busted
pkgs_to_install <- pkgs_to_install[grep("NGScopy", pkgs_to_install, invert=TRUE)]
# don't install seqplots because Cairo won't build
pkgs_to_install <- pkgs_to_install[grep("seqplots", pkgs_to_install, invert=TRUE)]
if (length(wantedBiocViews) == 1 && wantedBiocViews == "Microarray")
pkgs_to_install <- pkgs_to_install[!pkgs_to_install == "flowVS"]
# don't reinstall anything that's installed already
pkgs_to_install <- setdiff(pkgs_to_install, rownames(installed.packages()))
#oldwarn <- getOption(warn)
#on.exit(options(warn=oldwarn))
#options(warn=1)
builtins <- c("Matrix", "KernSmooth", "mgcv")
for (builtin in builtins)
if(!do.call(require, list(builtin)))
biocLite(builtin)
cores <- max(2, parallel::detectCores()-2)
if (parallel::detectCores() == 1)
cores <- 1
tryCatch(biocLite(pkgs_to_install, Ncpus=cores),
warning=function(w){
if(length(grep("is not available|had non-zero exit status|installation of one or more packages failed", w$message)))
stop(sprintf("got a fatal warning: %s", w$message))
})
# 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|installation of one or more packages failed", w)))
quit("no", 1L)
}