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Get/install an R package's dependencies.
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getDependencies <- function(p, | |
rep = c("BioCsoft", "BioCann", "BioCexp", "BioCextra", "CRAN"), | |
biocVersion = "2.12", | |
depLevels = c("Depends", "Imports", "Suggests"), | |
filter = TRUE) { | |
rep <- match.arg(rep) | |
if (rep == "CRAN") { | |
rep <- getOption("repos")["CRAN"] | |
} else { | |
biocMirror <- getOption("BioC_mirror", "http://bioconductor.org") | |
biocPaths <- switch(rep, | |
BioCsoft = "bioc", | |
BioCann = "data/annotation", | |
BioCexp = "data/experiment", | |
BioCextra = "extra") | |
rep <- paste(biocMirror, | |
"packages", | |
biocVersion, | |
biocPaths, | |
sep = "/") | |
} | |
pDetails <- available.packages(contrib.url(rep))[p, ] | |
depLevels <- match.arg(depLevels, several.ok = TRUE) | |
deps <- sapply(depLevels, | |
function(.depLevel) | |
tools:::package.dependencies(pDetails, depLevel = .depLevel)[[1]][, 1]) | |
deps <- unlist(deps) | |
i <- match("R", deps) | |
if (length(i) > 0) | |
deps <- deps[-i] | |
if (filter) { | |
installedP <- installed.packages()[,"Package"] | |
deps <- deps[!deps %in% installedP] | |
} | |
return(deps) | |
} | |
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getPackagesInBiocView <- function(view, | |
rep = c("BioCsoft", "BioCann", | |
"BioCexp", "BioCextra"), | |
biocVersion = "2.12") { | |
suppressPackageStartupMessages(require("biocViews")) | |
data(biocViewsVocab) | |
rep <- match.arg(rep) | |
biocMirror <- getOption("BioC_mirror", "http://bioconductor.org") | |
biocPaths <- switch(rep, | |
BioCsoft = "bioc", | |
BioCann = "data/annotation", | |
BioCexp = "data/experiment", | |
BioCextra = "extra") | |
rep <- paste(biocMirror, | |
"packages", | |
biocVersion, | |
biocPaths, | |
sep = "/") | |
bv <- getBiocViews(rep, biocViewsVocab, "NoViewProvided") | |
if (!view %in% names(bv)) { | |
message("BiocView ", view, " not found.") | |
return(NULL) | |
} | |
return(bv[[view]]) | |
} |
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installDependencies <- function(p, ...) { | |
message("Installing ",p, " dependencies and updating available packages...") | |
deps <- getDependencies(p, ...) | |
if (!require(BiocInstaller)) | |
source("http://bioconductor.org/biocLite.R") | |
biocLite(deps, ask = FALSE) | |
invisible(NULL) | |
} | |
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installPackages <- function(ps) { | |
installed <- installed.packages()[,"Package"] | |
ps <- ps[!ps %in% installed] | |
message("Installing dependencies and updating available packages...") | |
if (!require(BiocInstaller)) | |
source("http://bioconductor.org/biocLite.R") | |
biocLite(ps, ask = FALSE) | |
invisible(NULL) | |
} |
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