From caed34fa8625724b78567b2341f7e9b3316a7697 Mon Sep 17 00:00:00 2001
From: Florian Angerer <florian.angerer@oracle.com>
Date: Wed, 10 Jan 2018 18:44:40 +0100
Subject: [PATCH] Make package cache aware of package versions.
---
.../r/install.cache.R | 89 ++++++++++++-------
.../r/install.packages.R | 23 -----
2 files changed, 56 insertions(+), 56 deletions(-)
diff --git a/com.oracle.truffle.r.test.packages/r/install.cache.R b/com.oracle.truffle.r.test.packages/r/install.cache.R
index ff0183f2c2..c9a4047965 100644
--- a/com.oracle.truffle.r.test.packages/r/install.cache.R
+++ b/com.oracle.truffle.r.test.packages/r/install.cache.R
@@ -30,26 +30,34 @@ log.message <- function(..., level=0) {
cat(..., "\n")
}
-pkg.cache.install <- function(pkg.cache.env, pkgname, lib.install, install.cmd) {
- is.cached <- pkg.cache.get(pkg.cache.env, pkgname, lib.install)
+pkg.cache.install <- function(pkg.cache.env, pkgname, pkg.version, lib.install, install.cmd) {
+ pkg <- list(Package=pkgname, Version=pkg.version)
+ is.cached <- pkg.cache.get(pkg.cache.env, pkg, lib.install)
if (!is.cached) {
res <- install.cmd()
# 0L stands for success
if (res == 0L) {
- pkg.cache.insert(pkg.cache.env, pkgname, lib.install)
+ pkg.cache.insert(pkg.cache.env, pkg, lib.install)
}
}
}
-pkg.cache.get <- function(pkg.cache.env, pkgname, lib) {
+pkg.cache.entry.filename <- function(pkg) {
+ paste0(as.character(pkg["Package"]), "_", as.character(pkg["Version"]), ".gz")
+}
+
+pkg.cache.get <- function(pkg.cache.env, pkg, lib) {
version.dir <- pkg.cache.check(pkg.cache.env)
if(is.null(version.dir)) {
return (FALSE)
}
+ pkgname <- as.character(pkg["Package"])
+ pkg.version <- as.character(pkg["Version"])
+
log.message("using package cache directory ", version.dir, level=1)
- cache.entry.name <- paste0(pkgname, ".gz")
+ cache.entry.name <- pkg.cache.entry.filename(pkg)
# lookup package dir
pkg.dirs <- list.files(version.dir, full.names=FALSE, recursive=FALSE)
@@ -73,7 +81,7 @@ pkg.cache.get <- function(pkg.cache.env, pkgname, lib) {
FALSE
}
-pkg.cache.insert <- function(pkg.cache.env, pkgname, lib) {
+pkg.cache.insert <- function(pkg.cache.env, pkg, lib) {
version.dir <- pkg.cache.check(pkg.cache.env)
if(is.null(version.dir)) {
return (FALSE)
@@ -86,10 +94,12 @@ pkg.cache.insert <- function(pkg.cache.env, pkgname, lib) {
dir.create(version.dir)
}
+ pkgname <- as.character(pkg["Package"])
+ pkg.version <- as.character(pkg["Version"])
fromPath <- file.path(lib, pkgname)
- toPath <- file.path(version.dir, paste0(pkgname, ".gz"))
+ toPath <- file.path(version.dir, pkg.cache.entry.filename(pkg))
- # to produce a TAR with relative paths, we need to change the working dir
+ # to produce a ZIP with relative paths, we need to change the working dir
prev.wd <- getwd()
setwd(lib)
if(zip(toPath, pkgname, flags="-r9Xq") != 0L) {
@@ -261,9 +271,11 @@ base.packages <- c("base", "compiler", "datasets", "grDevices", "graphics", "gri
# the list of packages that will be excluded in the transitive dependecies
ignored.packages <- if (is.fastr()) recommended.base.packages else base.packages
-package.dependencies <- function(pkg, lib, dependencies = c("Depends", "Imports", "LinkingTo"), pl = available.packages()) {
+# Computes the direct dependencies of a package.
+# Returns a data frame containing the with rows c("Package", "Version")
+package.dependencies <- function(pkg, lib, dependencies = c("Depends", "Imports", "LinkingTo"), pl = as.data.frame(available.packages(), stringAsFactors=FALSE)) {
if (!(pkg %in% rownames(pl))) {
- log.message("Package", pkg, "not on CRAN\n", level=1)
+ log.message("Package", as.character(pkg), "not on CRAN\n", level=1)
return (NULL)
}
fields <- pl[pkg, dependencies]
@@ -272,32 +284,39 @@ package.dependencies <- function(pkg, lib, dependencies = c("Depends", "Imports"
# remove newline artefacts '\n' and split by ','
deps <- unlist(strsplit(gsub("\\n", " ", fields), ","))
- # remove version
+ # remove version constraints like '(>= 3.4.0)'
deps <- trimws(sub("\\(.*\\)", "", deps))
# ignore dependency to "R" and ignore already installed packages
- installed.pkgs.list <- tryCatch({
- # query base and recommended packages
- ip <- available.packages(lib.loc=lib)
- ip[as.logical(match(ip[,"Priority"], c("base", "recommended"), nomatch=0L)),"Package"]
- installed.packages(lib.loc=lib)
+ installed.pkgs.table <- tryCatch({
+ as.data.frame(installed.packages(lib.loc=lib)[,c("Package", "Version")], stringAsFactors=FALSE)
}, error = function(e) {
- character(0)
+ data.frame(Package=character(0), Version=character(0))
}, warning = function(e) {
- character(0)
+ data.frame(Package=character(0), Version=character(0))
})
- setdiff(deps, c("R", installed.pkgs.list, ignored.packages))
+ # Remove ignored packages from dependencies vector
+ non.ignored.names <- setdiff(deps, c("R", ignored.packages))
+
+ # Convert vector to data frame (query from package list data frame)
+ non.ignored.deps <- pl[pl$Package %in% non.ignored.names,]
+
+ # Remove any installed packages
+ non.ignored.deps[!(non.ignored.deps$Package %in% installed.pkgs.table$Package & non.ignored.deps$Version %in% installed.pkgs.table$Version),c("Package", "Version")]
}
-transitive.dependencies <- function(pkg, lib, pl = available.packages(), deptype=c("Depends", "Imports", "LinkingTo"), suggests=FALSE) {
- deps <- c()
+# Computes the transitive dependencies of a package by ignoring installed packages and 'ignored.packages'.
+# The result is a data frame with columns named "Package" and "Version".
+# Every row represents a package by the name and its version.
+transitive.dependencies <- function(pkg, lib, pl = as.data.frame(available.packages(), stringAsFactors=FALSE), deptype=c("Depends", "Imports", "LinkingTo"), suggests=FALSE) {
+ deps <- data.frame(Package=character(0), Version=character(0))
more <- pkg
# Also add "Suggests" to dependencies but do not recurse
if (suggests) {
this.suggests <- package.dependencies(pkg, dependencies = "Suggests", pl = pl)
if (!is.null(this.suggests)) {
- more <- c(more, this.suggests)
+ more <- c(more, as.character(this.suggests$Package))
}
}
@@ -318,8 +337,8 @@ transitive.dependencies <- function(pkg, lib, pl = available.packages(), deptype
processed <- unique(c(processed, this))
this.deps <- package.dependencies(this, lib, dependencies = deptype, pl = pl)
if (!is.null(this.deps)) {
- deps <- c(deps, this.deps)
- more <- c(more, this.deps[!(this.deps %in% processed)])
+ deps <- rbind(deps, this.deps)
+ more <- c(more, as.character(this.deps[!(this.deps$Package %in% processed), "Package"]))
}
}
@@ -333,25 +352,29 @@ pkg.cache.internal.install <- function(pkg.cache.env, pkgname, contriburl, lib.i
tryCatch({
if (pkg.cache.env$enabled) {
# determine available packages
- pkg.list <- available.packages(contriburl=contriburl)
+ pkg.list <- as.data.frame(available.packages(contriburl=contriburl), stringAsFactors=FALSE)
+
+ # query version of the package
+ #pkg.version <- as.character(pkg.list[pkg.list$Package == pkgname, "Version"])
+ pkg <- pkg.list[pkgname, c("Package", "Version")]
# compute transitive dependencies of the package to install
- log.message("Computing transitive package dependencies for ", pkgname, level=1)
- transitive.pkg.list <- c(transitive.dependencies(pkgname, lib=lib.install, pl=pkg.list), pkgname)
- log.message("transitive deps: ", transitive.pkg.list, level=1)
+ log.message("Computing transitive package dependencies for ", paste0(pkgname, "_", as.character(pkg$Version)), level=1)
+ transitive.pkg.list <- rbind(transitive.dependencies(pkgname, lib=lib.install, pl=pkg.list), pkg)
+ log.message("transitive deps: ", as.character(transitive.pkg.list$Package), level=1)
# apply pkg cache to fetch cached packages first
- cached.pkgs <- sapply(transitive.pkg.list, function(pkgname) pkg.cache.get(pkg.cache.env, pkgname, lib.install))
- log.message("Number of uncached packages:", length(transitive.pkg.list[!cached.pkgs]), level=1)
+ cached.pkgs <- apply(transitive.pkg.list, 1, function(pkg) pkg.cache.get(pkg.cache.env, pkg, lib.install))
+ log.message("Number of uncached packages:", nrow(transitive.pkg.list[!cached.pkgs, ]), level=1)
# if there was at least one non-cached package
if (any(!cached.pkgs) || length(cached.pkgs) == 0L) {
# install the package (and the transitive dependencies implicitly)
- install.packages(pkgname, contriburl=contriburl, type="source", lib=lib.install, INSTALL_opts="--install-tests")
+ install.packages(as.character(transitive.pkg.list[!cached.pkgs, "Package"]), contriburl=contriburl, type="source", lib=lib.install, INSTALL_opts="--install-tests")
# cache packages that were not in the cache before
- log.message("Caching uncached dependencies:", transitive.pkg.list[!cached.pkgs], level=1)
- lapply(transitive.pkg.list[!cached.pkgs], function(pkgname) pkg.cache.insert(pkg.cache.env, pkgname, lib.install))
+ log.message("Caching uncached dependencies:", as.character(transitive.pkg.list[!cached.pkgs, "Package"]), level=1)
+ apply(transitive.pkg.list[!cached.pkgs, ], 1, function(pkg) pkg.cache.insert(pkg.cache.env, pkg, lib.install))
}
} else {
install.packages(pkgname, contriburl=contriburl, type="source", lib=lib.install, INSTALL_opts="--install-tests")
diff --git a/com.oracle.truffle.r.test.packages/r/install.packages.R b/com.oracle.truffle.r.test.packages/r/install.packages.R
index 1aeeb63ee9..b34e598cb4 100644
--- a/com.oracle.truffle.r.test.packages/r/install.packages.R
+++ b/com.oracle.truffle.r.test.packages/r/install.packages.R
@@ -742,20 +742,6 @@ fastr_error_log_size <- function() {
install.pkg <- function(pkgname) {
error_log_size <- fastr_error_log_size()
if (run.mode == "system") {
- #system.install.wrapper <- function() {
- #tryCatch(
- #system.install(pkgname)
- #, error = function(e) {
- #log.message(e$message)
- #return (1L)
- #}, warning = function(e) {
- #log.message(e$message)
- ## According to the documentation of 'system2', a warning will provide a status field.
- #return (e$status)
- #})
- #}
- #pkg.cache.install(pkg.cache, pkgname, lib.install, system.install.wrapper)
-
tryCatch(
system.install(pkgname)
, error = function(e) {
@@ -767,15 +753,6 @@ install.pkg <- function(pkgname) {
e$status
})
} else if (run.mode == "internal") {
- #internal.install.wrapper <- function() {
- #tryCatch(
- #install.packages(pkgname, type="source", lib=lib.install, INSTALL_opts="--install-tests")
- #, error = function(e) {
- #log.message(e$message)
- #return (1)
- #})
- #}
- #pkg.cache.install(pkg.cache, pkgname, lib.install, internal.install.wrapper)
pkg.cache.internal.install(pkg.cache.env=pkg.cache, pkgname=pkgname, lib.install=lib.install)
} else if (run.mode == "context") {
stop("context run-mode not implemented\n")
--
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