Merge pull request #43 from databio/dev

Release 0.4.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: simpleCache
 Version: 0.4.1
-Date: 2018-03-01
+Date: 2019-02-26
 Title: Simply Caching R Objects
 Description: Provides intuitive functions for caching R objects, encouraging
     reproducible, restartable, and distributed R analysis. The user selects a
@@ -22,4 +22,4 @@ License: BSD_2_clause + file LICENSE
 Encoding: UTF-8
 URL: https://www.github.com/databio/simpleCache
 BugReports: https://www.github.com/databio/simpleCache
-RoxygenNote: 6.0.1.9000
+RoxygenNote: 6.1.0

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(addCacheSearchEnvironment)
 export(deleteCaches)
+export(getCacheDir)
 export(listCaches)
 export(loadCaches)
 export(resetCacheSearchEnvironment)

NEWS → NEWS.md

@@ -1,37 +1,43 @@
 # Change log
 All notable changes to this project will be documented in this file.
 
-## [0.4.0] -- 2017-12-20
+## simpleCache [0.4.1] -- 2019-02-26
+
+	- fixes unit tests on windows
+	- fixes lifespan bug that used creation time instead of modification time
+	- allow arg-less directory setting to default to current working dir
+
+## simpleCache [0.4.0] -- 2017-12-20
 
 	- adds a lifespan arg to simpleCache() to create auto-expiring caches
 	- remove unnecessary parse argument to simpleCache()
 	- viewCacheDirs() renamed to simpleCacheOptions()
 
-## [0.3.1] -- 2017-08-21
+## simpleCache [0.3.1] -- 2017-08-21
 
 	- fixed a bug in unit tests that left behind a test cache in user home dir.
 	- changes cache building to happen in parent.frame()
 	- repaired vignette so R code is displayed properly
 	- added deleteCaches() function and docs
 	- reduced size of unit test cache for speed increase
 
-## [0.3.0] -- 2017-08-21
+## simpleCache [0.3.0] -- 2017-08-21
 
 	- switched default cache dir to tempdir()
 	- changed availCaches() to listCaches()
 	- changes cache building to happen in globalenv(), so that any loaded
 	  packages are available for cache building
 
 
-## [0.2.1] -- 2017-07-30
+## simpleCache [0.2.1] -- 2017-07-30
 
 	- added examples
 
-## [0.2.0] -- 2017-07-30
+## simpleCache [0.2.0] -- 2017-07-30
 
 	- support for batchjobs parallel processing
 	- docs, prep for submission to CRAN
 
-## [0.0.1]
+## simpleCache [0.0.1]
 
 	- long-term stable version

R/cacheDirectories.R

@@ -12,9 +12,16 @@
 #' @export
 #' @example
 #' R/examples/example.R
-setCacheDir = function(cacheDir) {
-	options(RCACHE.DIR=cacheDir)
-}
+setCacheDir = function(cacheDir=NULL) { .setDir("RCACHE.DIR", cacheDir) }
+
+#' Fetcher of the currently set cache directory.
+#'
+#' \code{getCacheDir} retrieves the value of the option that stores the currently 
+#' set cache directory path.
+#'
+#' @return If the option is set, the path to the currently set cache directory; otherwise, \code{NULL}.
+#' @export
+getCacheDir = function() { getOption("RCACHE.DIR") }
 
 #' Set shared cache directory
 #'
@@ -24,25 +31,21 @@ setCacheDir = function(cacheDir) {
 #'
 #' @param sharedCacheDir Directory where shared caches should be stored
 #' @export
-setSharedCacheDir = function(sharedCacheDir) {
-	options(RESOURCES.RCACHE=sharedCacheDir)
-}
+setSharedCacheDir = function(sharedCacheDir=NULL) { .setDir("RESOURCES.RCACHE", sharedCacheDir) }
 
 #' Sets local cache build directory with scripts for building files.
 #'
 #' @param cacheBuildDir Directory where build scripts are stored.
 #' @export
-setCacheBuildDir = function(cacheBuildDir) {
-	options(RBUILD.DIR=cacheBuildDir)
-}
+setCacheBuildDir = function(cacheBuildDir=NULL) { .setDir("RBUILD.DIR", cacheBuildDir) }
 
 #' View simpleCache options
 #'
 #' Views simpleCache global variables
 #' @export
 simpleCacheOptions = function() {
 	message("RESOURCES.RCACHE:\t", getOption("RESOURCES.RCACHE"))
-	message("RCACHE.DIR:\t", getOption("RCACHE.DIR"))
+	message("RCACHE.DIR:\t", getCacheDir())
 	message("RBUILD.DIR:\t", getOption("RBUILD.DIR"))
 	message("SIMPLECACHE.ENV:\t", getOption("SIMPLECACHE.ENV"))
 }
@@ -66,3 +69,9 @@ resetCacheSearchEnvironment = function() {
 	options(SIMPLECACHE.ENV=NULL)
 }
 
+
+.setDir = function(optname, dirpath=NULL) {
+  diropts = list(ifelse(is.null(dirpath), getwd(), dirpath))
+  names(diropts) = optname
+  do.call(options, diropts)
+}

R/deleteCache.R

@@ -8,7 +8,7 @@
 #' @export
 #' @example
 #' R/examples/example.R
-deleteCaches = function(cacheNames, cacheDir=getOption("RCACHE.DIR"),
+deleteCaches = function(cacheNames, cacheDir=getCacheDir(),
 	force=FALSE) {
 
 	if (force) {

R/listCaches.R

@@ -9,6 +9,7 @@
 #' @example
 #' R/examples/example.R
 listCaches = function(cacheSubDir="") {
-	list.files(paste0(getOption("RCACHE.DIR"), cacheSubDir))
+	cacheDirFiles = list.files(paste0(getCacheDir(), cacheSubDir))
+	cacheDirFiles[which(sapply(cacheDirFiles, function(f) endsWith(f, ".RData")))]
 }
 

R/simpleCache.R

@@ -88,7 +88,7 @@
 #' R/examples/example.R
 simpleCache = function(cacheName, instruction=NULL, buildEnvir=NULL,
 	reload=FALSE, recreate=FALSE, noload=FALSE,
-	cacheDir=getOption("RCACHE.DIR"), cacheSubDir=NULL, timer=FALSE,
+	cacheDir=getCacheDir(), cacheSubDir=NULL, timer=FALSE,
 	buildDir=getOption("RBUILD.DIR"), assignToVariable=NULL,
 	loadEnvir=parent.frame(), searchEnvir=getOption("SIMPLECACHE.ENV"),
 	nofail=FALSE, batchRegistry=NULL, batchResources=NULL, pepSettings=NULL, 
@@ -134,7 +134,9 @@ simpleCache = function(cacheName, instruction=NULL, buildEnvir=NULL,
 	cacheWhere = NULL
 
 	for ( curEnv in searchEnvir ) {
-		if(exists(cacheName, where=get(curEnv))) {
+		if(! ( exists(curEnv) && is.environment(get(curEnv))) ) {
+			warning(curEnv, " is not an environment.")
+		} else if( exists(cacheName, where=get(curEnv))) {
 			cacheExists = TRUE
 			cacheWhere = curEnv
 			break

R/storeCache.R

@@ -19,7 +19,7 @@
 #' @export
 #' @example
 #' R/examples/example.R
-storeCache = function(cacheName, cacheDir = getOption("RCACHE.DIR"),
+storeCache = function(cacheName, cacheDir = getCacheDir(),
 	cacheSubDir = NULL, recreate=FALSE) {
 
 	if(!is.null(cacheSubDir)) {

R/utility.R

@@ -29,7 +29,7 @@
 	if (!utils::file_test("-f", pathCacheFile)) { return(FALSE) }
 	if (is.null(lifespan)) { lifespan = getOption("MAX.CACHE.AGE") }
 	if (is.null(lifespan)) { return(FALSE) }
-	cacheTime = file.info(pathCacheFile)$ctime
+	cacheTime = file.info(pathCacheFile)$mtime
 	cacheAge = difftime(Sys.time(), cacheTime, units="days")
 	as.numeric(cacheAge) > as.numeric(lifespan)
 }

tests/testthat/test_all.R

@@ -2,6 +2,22 @@ library(simpleCache)
 
 context("error checking")
 
+
+# Map option name to its setter.
+kSetters = list(RCACHE.DIR=setCacheDir, RESOURCES.RCACHE=setSharedCacheDir, RBUILD.DIR=setCacheBuildDir)
+
+
+# Test a cache dir setting in managed context fashion, resetting before and after test.
+test_dir_default = function(cacheDirOptname) {
+  resetCacheSearchEnvironment()
+  test_that(sprintf("%s setter uses current folder for argument-less call", cacheDirOptname), {
+    do.call(kSetters[[cacheDirOptname]], args=list())
+    expect_equal(getwd(), getOption(cacheDirOptname))
+  })
+  resetCacheSearchEnvironment()
+}
+
+
 test_that("notifications and messages as expected", {
 
   # message if cache exists
@@ -106,12 +122,16 @@ test_that("option setting works", {
   setCacheBuildDir(tempdir())
   addCacheSearchEnvironment("cacheEnv")
 
+  # Windows uses double slashes, which get consumed weirdly by grep;
+  # This command will replace double slashes with quadruple slashes,
+  # which behave correctly in grep.
+  grep_tempdir = gsub("\\\\", "\\\\\\\\", tempdir())
   # capture output and check
   options_out <- capture_messages(simpleCacheOptions())
 
-  expect_true(grepl(tempdir(), options_out[1]))
-  expect_true(grepl(tempdir(), options_out[2]))
-  expect_true(grepl(tempdir(), options_out[3]))
+  expect_true(grepl(grep_tempdir, options_out[1]))
+  expect_true(grepl(grep_tempdir, options_out[2]))
+  expect_true(grepl(grep_tempdir, options_out[3]))
   expect_true(grepl("cacheEnv", options_out[4]))
 
   # reset the cache search option
@@ -123,6 +143,18 @@ test_that("option setting works", {
 
 })
 
+test_that("Cache dir fetch works", {
+  options(RCACHE.DIR = NULL)
+  expect_true(is.null(getCacheDir()))
+  setCacheDir(tempdir())
+  expect_false(is.null(getCacheDir()))
+  expect_equal(getCacheDir(), tempdir())
+})
+
+# Test each cache directory option setter.
+for (optname in names(kSetters)) { test_dir_default(optname) }
+
+
 test_that("objects pass through in buildEnvir", {
 
   setCacheDir(tempdir())