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check-cran.r
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check-cran.r
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#' Check a package from CRAN.
#'
#' This is useful for automatically checking that dependencies of your
#' packages work.
#'
#' The downloaded package and check directory are only removed if the check is
#' successful - this allows you to inspect the results to figure out what
#' went wrong.
#'
#' This function does not clean up after itself, but does work in a
#' session-specific temporary directory, so all files will be removed
#' when your current R session ends.
#'
#' @param pkgs Vector of package names - note that unlike other \pkg{devtools}
#' functions this is the name of a CRAN package, not a path.
#' @param libpath path to library to store dependencies packages - if you
#' you're doing this a lot it's a good idea to pick a directory and stick
#' with it so you don't have to download all the packages every time.
#' @param srcpath path to directory to store source versions of dependent
#' packages - again, this saves a lot of time because you don't need to
#' redownload the packages every time you run the package.
#' @param bioconductor include bioconductor packages in checking?
#' @param type binary package type of test
#' @param threads number of concurrent threads to use for checking.
#' @return invisible \code{TRUE} if successful and no ERRORs or WARNINGS,
#' @param ... other parameters passed onto \code{\link{download.packages}}
#' @importFrom tools package_dependencies
#' @importFrom parallel mclapply
#' @export
#' @examples
#' \dontrun{
#' dep <- revdep("ggplot2")
#' check_cran(dep, "~/documents/ggplot/ggplot-check")
#' # Or, equivalently:
#' revdep_check("ggplot2")
#' }
check_cran <- function(pkgs, libpath = file.path(tempdir(), "R-lib"),
srcpath = libpath, bioconductor = FALSE, type = getOption("pkgType"),
threads = 1, ...) {
stopifnot(is.character(pkgs))
if (length(pkgs) == 0) return()
message("Checking ", length(pkgs), " CRAN packages")
old <- options(warn = 1)
on.exit(options(old))
message("Determining available packages") # --------------------------------
repos <- c(
CRAN = "http://cran.rstudio.com/",
omegahat = "http://www.omegahat.org/R"
)
if (bioconductor) {
require("BiocInstaller")
repos <- c(repos, biocinstallRepos())
}
available_src <- available_packages(repos, "source")
available_bin <- available_packages(repos, type)
# Create and use temporary library
if (!file.exists(libpath)) dir.create(libpath)
libpath <- normalizePath(libpath)
.libPaths(c(libpath, .libPaths()))
on.exit(.libPaths(setdiff(.libPaths(), libpath)))
# Make sure existing dependencies are up to date ---------------------------
old <- old.packages(libpath, repos = repos, type = type,
available = available_bin)
if (!is.null(old)) {
message("Updating ", nrow(old), " existing dependencies")
install.packages(old[, "Package"], libpath, repos = repos, type = type,
Ncpus = threads)
}
# Install missing dependencies
deps <- unique(unlist(package_dependencies(pkgs, packages(),
which = "all")))
to_install <- setdiff(deps, installed.packages()[, 1])
known <- intersect(to_install, rownames(available_bin))
unknown <- setdiff(to_install, rownames(available_bin))
if (length(known) > 0) {
message("Installing ", length(known), " missing binary dependencies")
install.packages(known, lib = libpath, quiet = FALSE, repos = repos,
Ncpus = threads)
}
if (length(unknown) > 0) {
message("No binary packages available for dependenices: ",
paste(unknown, collapse = ", "))
}
# Download and check each package, parsing output as we go.
tmp <- tempdir()
check <- function(i) {
url <- package_url(pkgs[i], repos, available = available_src)
if (length(url$url) == 0) {
message("Can't find package source. Skipping...")
return(NULL)
}
local <- file.path(srcpath, url$name)
if (!file.exists(local)) {
message("Downloading ", pkgs[i])
download.file(url$url, local, quiet = TRUE)
}
message("Checking ", i , ": ", pkgs[i])
cmd <- paste("CMD check --as-cran --no-multiarch --no-manual --no-codoc ",
local, sep = "")
try(R(cmd, tmp, stdout = NULL), silent = TRUE)
check_path <- file.path(tmp, gsub("_.*?$", ".Rcheck", url$name))
results <- parse_check_results(check_path)
if (length(results) > 0) cat(results, "\n")
results
}
results <- mclapply(seq_along(pkgs), check, mc.preschedule = FALSE,
mc.cores = threads)
names(results) <- pkgs
n_problems <- sum(vapply(results, length, integer(1)))
if (n_problems > 0) {
warning("Found ", n_problems, call. = FALSE)
}
# Collect the output
collect_check_results(tmp)
invisible(results)
}
available_packages <- memoise(function(repos, type) {
suppressWarnings(available.packages(contrib.url(repos, type)))
})
package_url <- function(package, repos, available = available.packages(contrib.url(repos, "source"))) {
ok <- (available[, "Package"] == package)
ok <- ok & !is.na(ok)
vers <- package_version(available[ok, "Version"])
keep <- vers == max(vers)
keep[duplicated(keep)] <- FALSE
ok[ok][!keep] <- FALSE
name <- paste(package, "_", available[ok, "Version"], ".tar.gz", sep = "")
url <- file.path(available[ok, "Repository"], name)
list(name = name, url = url)
}
parse_check_results <- function(path) {
check_path <- file.path(path, "00check.log")
check_log <- paste(readLines(check_path), collapse = "\n")
pieces <- strsplit(check_log, "\n\\* ")[[1]]
problems <- grepl("... (WARN|ERROR)", pieces)
cran_version <- grepl("CRAN incoming feasibility", pieces)
messages <- pieces[problems & !cran_version]
if (length(messages)) {
paste("* ", messages, collapse = "\n")
}
}
# Collects all the results from running check_cran and puts in a
# directory results/ under the top level tempdir.
collect_check_results <- function(topdir = tempdir()) {
# Directory for storing results
rdir <- file.path(topdir, "results")
if (!dir.exists(rdir))
dir.create(rdir)
checkdirs <- list.dirs(topdir, recursive=FALSE)
checkdirs <- checkdirs[grepl("\\.Rcheck$", checkdirs)]
# Make it a named vector so that the output of lapply below contains names
names(checkdirs) <- sub("\\.Rcheck$", "", basename(checkdirs))
# Copy over all the 00check.log and 00install.out files
message("Copying check logs to ", rdir)
checklogs <- file.path(checkdirs, "00check.log")
checklogs_dest <- file.path(rdir, paste(names(checkdirs), "-check", sep=""))
names(checklogs_dest) <- names(checkdirs)
file.copy(checklogs, checklogs_dest, overwrite = TRUE)
message("Copying install logs to ", rdir)
installlogs <- file.path(checkdirs, "00install.out")
installlogs_dest <- file.path(rdir, paste(names(checkdirs), "-install", sep=""))
file.copy(installlogs, installlogs_dest, overwrite = TRUE)
checkresults <- lapply(checkdirs, parse_check_results)
message("Writing warnings and error summary for each package to ", rdir)
for (i in seq_along(checkresults)) {
pkgname <- names(checkresults[i])
result <- checkresults[[i]]
if (!is.null(result) && nzchar(result)) {
err_filename <- file.path(rdir, paste(pkgname, "-error", sep=""))
err_out <- file(err_filename, "w")
cat(pkgname, result, file = err_out)
close(err_out)
}
}
summary_filename <- file.path(rdir, "00check-summary.txt")
message("Creating summary of check warnings and errors in ", summary_filename)
summary_out <- file(summary_filename, "w")
on.exit(close(summary_out))
for (i in seq_along(checkresults)) {
pkgname <- names(checkresults[i])
linetext <- paste(rep("=", 72 - nchar(pkgname)), collapse = "")
cat(pkgname, linetext, "\n", checkresults[[i]], "\n\n\n", file = summary_out)
}
}