more robust cache of R5 jar

r-package/DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: r5r
 Title: Rapid Realistic Routing with 'R5'
-Version: 1.1.0999
+Version: 1.1.0.9000
 Authors@R: c(
     person("Marcus", "Saraiva", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0001-6218-2338")),
@@ -34,7 +34,7 @@ Description: Rapid realistic routing on multimodal transport networks
     <https://docs.conveyal.com/changelog>) corresponds with the R5 version
     that r5r depends on.
 License: MIT + file LICENSE
-URL: https://github.com/ipeaGIT/r5r, https://ipeagit.github.io/r5r/
+URL: https://github.com/ipeaGIT/r5r
 BugReports: https://github.com/ipeaGIT/r5r/issues
 Depends:
     R (>= 3.6)

r-package/NAMESPACE

@@ -7,6 +7,7 @@ export(expanded_travel_time_matrix)
 export(find_snap)
 export(isochrone)
 export(pareto_frontier)
+export(r5r_cache)
 export(r5r_sitrep)
 export(read_fare_structure)
 export(setup_fare_structure)

r-package/NEWS.md

@@ -8,7 +8,7 @@
 
 **Major changes**
 
-- r5r now stores R5 Jar file at `tools::R_user_dir("r5r", which = "cache")`
+- r5r now stores R5 Jar file at user dir using `tools::R_user_dir()`
 - By using the JDK 21, this version of r5r also fixed an incompatibility with MAC ARM processors. Closed [#315](https://github.com/ipeaGIT/r5r/issues/315)
 
 **Minor changes**

r-package/R/download_r5.R

@@ -40,15 +40,17 @@ download_r5 <- function(version = "7.0.0",
   options(timeout = max(600, getOption("timeout")))
 
 
-  # download R5's jar -----------------------------------------------------
+  # download R5 jar -----------------------------------------------------
+
+  if (!dir.exists(r5r_env$cache_dir)) dir.create(r5r_env$cache_dir, recursive = TRUE)
 
   file_url <- fileurl_from_metadata(version)
   filename <- basename(file_url)
 
   jar_file <- data.table::fifelse(
     temp_dir,
     file.path(tempdir(), filename),
-    file.path(tools::R_user_dir("r5r", which = "cache"), filename)
+    file.path( r5r_env$cache_dir , filename)
   )
 
 

r-package/R/onLoad.R

@@ -0,0 +1,32 @@
+# initial message about ram memory
+.onAttach <- function(lib, pkg) {
+  packageStartupMessage(
+    "Please make sure you have already allocated ",
+    "some memory to Java by running:\n",
+    "  options(java.parameters = '-Xmx2G').\n",
+    "You should replace '2G' by the amount of memory you'll require. ",
+    "Currently, Java memory is set to ", getOption("java.parameters")
+    )
+  }
+
+# package global variables
+r5r_env <- new.env(parent = emptyenv()) # nocov start
+
+.onLoad <- function(lib, pkg) {
+
+  # JAR version
+  r5r_env$r5_jar_version <- "7.0.0"
+
+  # create dir to store R5 Jar
+  cache_d <- paste0('r5r/r5_jar_v', r5r_env$r5_jar_version)
+  r5r_env$cache_dir <- tools::R_user_dir(cache_d, which = 'cache')
+  if (!dir.exists(r5r_env$cache_dir)) dir.create(r5r_env$cache_dir, recursive = TRUE)
+  # gsub("\\\\", "/", r5r_env$cache_dir)
+
+  ## delete any JAR files from old releases
+  dir_above <- dirname(r5r_env$cache_dir)
+  all_cache <- list.files(dir_above, pattern = 'r5',full.names = TRUE)
+  old_cache <- all_cache[!grepl(r5r_env$r5_jar_version, all_cache)]
+  if(length(old_cache)>0){ unlink(old_cache, recursive = TRUE) }
+
+}

r-package/R/r5r.R

@@ -83,18 +83,3 @@ if (getRversion() >= "2.15.1") {
     )
   )
 }
-
-.onAttach <- function(lib, pkg) {
-  packageStartupMessage(
-    "Please make sure you have already allocated ",
-    "some memory to Java by running:\n",
-    "  options(java.parameters = '-Xmx2G').\n",
-    "You should replace '2G' by the amount of memory you'll require. ",
-    "Currently, Java memory is set to ", getOption("java.parameters")
-  )
-
-  # create dir to store R5 Jar
-  jar_dir <- tools::R_user_dir("r5r", which = "cache")
-  if (!dir.exists(jar_dir)) dir.create(jar_dir, recursive = TRUE)
-
-}

r-package/R/r5r_cache.R

@@ -0,0 +1,70 @@
+#' Manage cached files from the r5r package
+#'
+#' @param list_files Logical. Whether to print a message with the address of r5r
+#'        JAR files cached locally. Defaults to `TRUE`.
+#' @param delete_file String. The file name (basename) of a JAR file cached
+#'        locally that should be deleted. Defaults to `NULL`, so that no
+#'        file is deleted. If `delete_file = "all"`, then all cached files are
+#'        deleted.
+#'
+#' @return A message indicating which file exist and/or which ones have been
+#'         deleted from local cache directory.
+#' @export
+#' @family Cache data
+#' @examplesIf identical(tolower(Sys.getenv("NOT_CRAN")), "true")
+#' # list all files cached
+#' r5r_cache(list_files = TRUE)
+#'
+#' # delete particular file
+#' r5r_cache(delete_file = '2010_deaths')
+#'
+r5r_cache <- function(list_files = TRUE,
+                      delete_file = NULL){
+
+  # check inputs
+  checkmate::assert_logical(list_files)
+  checkmate::assert_character(delete_file, null.ok = TRUE)
+
+  # find / create local dir
+  if (!dir.exists(r5r_env$cache_dir)) { dir.create(r5r_env$cache_dir, recursive=TRUE) }
+
+  # list cached files
+  files <- list.files(dirname(r5r_env$cache_dir), full.names = TRUE)
+
+  # if wants to delete file
+  # delete_file = "2_families.parquet"
+  if (!is.null(delete_file)) {
+
+    # IF file does not exist, print message
+    if (!any(grepl(delete_file, files)) & delete_file != "all") {
+      message(paste0("The file '", delete_file, "' is not cached."))
+    }
+
+    # IF file exists, delete file
+    if (any(grepl(delete_file, files))) {
+      f <- files[grepl(delete_file, files)]
+      unlink(f, recursive = TRUE)
+      message(paste0("The file '", delete_file, "' has been removed."))
+    }
+
+    # Delete ALL file
+    if (delete_file=='all') {
+
+      # delete any files from censobr, current and old data releases
+      dir_above <- dirname(r5r_env$cache_dir)
+      unlink(dir_above, recursive = TRUE)
+      message(paste0("All files have been removed."))
+
+    }
+  }
+
+  # list cached files
+  files <- list.files(r5r_env$cache_dir, full.names = TRUE)
+
+  # print file names
+  if(isTRUE(list_files)){
+    message('Files currently chached:')
+    message(paste0(files, collapse = '\n'))
+  }
+}
+

r-package/R/r5r_sitrep.R

@@ -19,13 +19,13 @@
 r5r_sitrep <- function() {
   r5r_package_version <- utils::packageVersion("r5r")
 
-  jar_dir <- tools::R_user_dir("r5r", which = "cache")
+  jar_dir <- r5r_env$cache_dir
   jar_dir_files <- list.files(jar_dir)
   jar_dir_files_full_names <- list.files(jar_dir, full.names = TRUE)
 
   r5r_jar <- jar_dir_files[grepl("r5r_\\d_\\d_\\d.*\\.jar", jar_dir_files)]
-  r5r_jar_version <- sub("\\.jar", "", sub("r5r_", "", r5r_jar))
-  r5r_jar_version <- gsub("_", "\\.", r5r_jar_version)
+
+  r5r_jar_version <- r5r_env$r5_jar_version
   r5r_jar_path <- jar_dir_files_full_names[
     grepl("\\/r5r_\\d_\\d_\\d*\\.jar", jar_dir_files_full_names)
   ]

r-package/R/setup_r5.R

@@ -116,7 +116,7 @@ setup_r5 <- function(data_path,
   jar_file <- data.table::fifelse(
     temp_dir,
     file.path(tempdir(), filename),
-    file.path(tools::R_user_dir("r5r", which = "cache"), filename)
+    file.path( r5r_env$cache_dir, filename)
   )
 
   # If there isn't a JAR already, download it

r-package/tests/tests_rafa/test_rafa.R

@@ -762,6 +762,9 @@ lapply(X=docs, FUN = tools::showNonASCIIfile)
 library(tictoc)
 library(beepr)
 
+# run only the tests
+testthat::test_local()
+
 
 # LOCAL
 utils::remove.packages('r5r')
@@ -780,6 +783,7 @@ tictoc::tic()
 Sys.setenv(NOT_CRAN = "false")
 devtools::check(pkg = ".",  cran = TRUE, env_vars = c(NOT_CRAN = "false"))
 tictoc::toc()
+beepr::beep()
 
 
 devtools::check_win_release(pkg = ".")
@@ -797,6 +801,14 @@ devtools::check(pkg = ".",  cran = TRUE, env_vars = c(NOT_CRAN = "false"))
 tictoc::toc()
 
 
+# extrachecks -----------------
+#' https://github.com/JosiahParry/extrachecks
+#' remotes::install_github("JosiahParry/extrachecks")
+
+library(extrachecks)
+extrachecks::extrachecks()
+
+
 
 # submit to CRAN -----------------
 usethis::use_cran_comments('teste 2222, , asdadsad')

r-package/tests/testthat/test-write_fare_structure.R

@@ -31,6 +31,4 @@ test_that("written structure is identical to original", {
 })
 
 # clean cache
-jar_dir <- tools::R_user_dir("r5r", which = "cache")
-f <- list.files(jar_dir, full.names = TRUE)
-unlink(f, recursive = TRUE)
+r5r::r5r_cache(delete_file = 'all')

r-package/vignettes/r5r.Rmd

@@ -364,9 +364,8 @@ rJava::.jgc(R.gc = TRUE)
 
 ```{r, eval = TRUE, include = FALSE, message = FALSE}
 # clean cache (CRAN policy)
-jar_dir <- tools::R_user_dir("r5r", which = "cache")
-f <- list.files(jar_dir, full.names = TRUE)
-unlink(f, recursive = TRUE)
+r5r::r5r_cache(delete_file = 'all')
+
 ```
 
 If you have any suggestions or want to report an error, please visit [the package GitHub page](https://github.com/ipeaGIT/r5r).

r-package/vignettes/time_window.Rmd

@@ -194,8 +194,6 @@ The `detailed_itineraries()`, on the other hand, does not return travel times or
 
 
 
-
-
 ### Cleaning up after usage
 
 `r5r` objects are still allocated to any amount of memory previously set after they are done with their calculations. In order to remove an existing `r5r` object and reallocate the memory it had been using, we use the `stop_r5` function followed by a call to Java's garbage collector, as follows:

r-package/vignettes/travel_time_matrix.Rmd

@@ -166,9 +166,7 @@ rJava::.jgc(R.gc = TRUE)
 
 ```{r, eval = TRUE, include = FALSE, message = FALSE}
 # clean cache (CRAN policy)
-jar_dir <- tools::R_user_dir("r5r", which = "cache")
-f <- list.files(jar_dir, full.names = TRUE)
-unlink(f, recursive = TRUE)
+r5r::r5r_cache(delete_file = 'all')
 
 ```