Replace qs backend with qs2

frenkiboy · claude · frenkiboy · commit 77da5fa88c2d · 2026-03-06T18:53:12.000+01:00
The qs package was removed from CRAN; its successor qs2 is actively
maintained and available on CRAN with improved performance.

- DESCRIPTION: qs -&gt; qs2 in Imports
- R/cacheFile.R: backend "qs" -&gt; "qs2", qs::qsave/qread -&gt; qs2::qs_save/qs_read
- R/zzz.R: .onLoad defaults to qs2 backend when available
- R/utils.R: file patterns .qs -&gt; .qs2, cacheInfo uses qs2::qs_read
- Tests: updated backend names, patterns, and manual load calls
- Vignette: updated documentation and examples

Note: qs2 format is NOT backward-compatible with old .qs files.

Co-Authored-By: Claude Opus 4.6 &lt;noreply@anthropic.com&gt;
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     digest,
     tools,
     codetools,
-    qs,
+    qs2,
     compiler,
     filelock
 Suggests:
diff --git a/R/cacheFile.R b/R/cacheFile.R
@@ -833,7 +833,7 @@ cacheFile <- function(cache_dir       = NULL,
       warning("cacheR: cache directory is not writable: ", cache_dir, call. = FALSE)
     }
     cache_dir <- normalizePath(cache_dir, mustWork = FALSE)
-    backend   <- match.arg(backend, c("rds", "qs"))
+    backend   <- match.arg(backend, c("rds", "qs2"))
     if (is.null(env_vars)) env_vars <- getOption("cacheR.env_vars", NULL)
 
     # Sync Graph from disk on init
@@ -1146,7 +1146,7 @@ cachePrune <- function(cache_dir, days_old = 30) {
   if (!dir.exists(cache_dir)) return(invisible(NULL))
 
   # Prune old cache files
-  cache_files <- list.files(cache_dir, pattern = "\\.(rds|qs)$", full.names = TRUE)
+  cache_files <- list.files(cache_dir, pattern = "\\.(rds|qs2)$", full.names = TRUE)
   if (length(cache_files) > 0) {
     infos <- file.info(cache_files)
     cutoff <- Sys.time() - (days_old * 24 * 60 * 60)
@@ -1236,7 +1236,7 @@ export_targets_file <- function(path = "_targets.R") {
 .atomic_save <- function(object, path, backend) {
   tmp_path <- paste0(path, ".tmp.", paste(sample(c(letters, 0:9), 8, replace=TRUE), collapse=""))
   tryCatch({
-    if (backend == "qs") { if (!requireNamespace("qs", quietly=TRUE)) stop("qs required"); qs::qsave(object, tmp_path) } 
+    if (backend == "qs2") { if (!requireNamespace("qs2", quietly=TRUE)) stop("qs2 required"); qs2::qs_save(object, tmp_path) }
     else { saveRDS(object, tmp_path) }
     file.rename(tmp_path, path)
   }, error = function(e) {
@@ -1245,7 +1245,7 @@ export_targets_file <- function(path = "_targets.R") {
   })
 }
 .safe_load <- function(path, backend) {
-  if (backend == "qs") { if (!requireNamespace("qs", quietly=TRUE)) stop("qs required"); qs::qread(path) } 
+  if (backend == "qs2") { if (!requireNamespace("qs2", quietly=TRUE)) stop("qs2 required"); qs2::qs_read(path) }
   else { readRDS(path) }
 }
 .get_recursive_closure_hash <- function(obj, visited=NULL, algo="xxhash64", version_checker=utils::packageVersion) {
diff --git a/R/utils.R b/R/utils.R
@@ -6,7 +6,7 @@
 #' file was cached, checking the arguments used to generate it, or auditing 
 #' creation times.
 #'
-#' @param file_path A character string specifying the path to the `.rds` or `.qs` 
+#' @param file_path A character string specifying the path to the `.rds` or `.qs2`
 #'   cache file.
 #'
 #' @return A list containing two elements:
@@ -29,10 +29,10 @@ cacheInfo <- function(file_path) {
   if (!file.exists(file_path)) stop("Cache file not found: ", file_path)
   
   # Determine backend based on extension (simple heuristic)
-  is_qs <- grepl("\\.qs$", file_path, ignore.case = TRUE)
-  
-  obj <- if (is_qs && requireNamespace("qs", quietly = TRUE)) {
-    qs::qread(file_path)
+  is_qs2 <- grepl("\\.qs2$", file_path, ignore.case = TRUE)
+
+  obj <- if (is_qs2 && requireNamespace("qs2", quietly = TRUE)) {
+    qs2::qs_read(file_path)
   } else {
     readRDS(file_path)
   }
@@ -87,7 +87,7 @@ cacheList <- function(cache_dir) {
     return(data.frame())
   }
 
-  files <- list.files(cache_dir, pattern = "\\.(rds|qs)$", full.names = TRUE)
+  files <- list.files(cache_dir, pattern = "\\.(rds|qs2)$", full.names = TRUE)
   
   if (length(files) == 0) return(data.frame())
   
@@ -139,7 +139,7 @@ cacheList <- function(cache_dir) {
 cache_stats <- function(cache_dir) {
   if (!dir.exists(cache_dir)) stop("Cache directory not found: ", cache_dir)
 
-  files <- list.files(cache_dir, pattern = "\\.(rds|qs)$", full.names = TRUE)
+  files <- list.files(cache_dir, pattern = "\\.(rds|qs2)$", full.names = TRUE)
   # Exclude graph.rds
   files <- files[!grepl("^graph\\.rds$", basename(files))]
 
diff --git a/R/zzz.R b/R/zzz.R
@@ -42,12 +42,12 @@
 
   # 2. Set defaults for anything still unset
   if (is.null(getOption("cacheR.backend"))) {
-    if (requireNamespace("qs", quietly = TRUE)) {
-      options(cacheR.backend = "qs")
+    if (requireNamespace("qs2", quietly = TRUE)) {
+      options(cacheR.backend = "qs2")
     } else {
       packageStartupMessage(
-        "Package 'qs' not installed; using RDS backend.\n",
-        "Install qs for faster caching: install.packages('qs')"
+        "Package 'qs2' not installed; using RDS backend.\n",
+        "Install qs2 for faster caching: install.packages('qs2')"
       )
       options(cacheR.backend = "rds")
     }
diff --git a/tests/testthat/test-cacheFile.R b/tests/testthat/test-cacheFile.R
@@ -1,7 +1,7 @@
 # --------------------------------------------------------#
 # Helper: Count cache entry files, excluding graph.rds
 # --------------------------------------------------------#
-count_cache_entries <- function(cache_dir, backend_pattern = "\\.(rds|qs)$") {
+count_cache_entries <- function(cache_dir, backend_pattern = "\\.(rds|qs2)$") {
   files <- list.files(cache_dir, pattern = backend_pattern)
   length(files[!grepl("^graph\\.rds", files)])
 }
@@ -112,28 +112,28 @@ test_that("cacheFile tracks multiple dir arguments and vector paths", {
 })
 
 # --------------------------------------------------------#
-test_that("cacheFile works with 'qs' backend", {
-  skip_if_not_installed("qs")
+test_that("cacheFile works with 'qs2' backend", {
+  skip_if_not_installed("qs2")
   if (exists("cacheTree_reset", mode = "function")) cacheTree_reset()
 
-  cache_dir <- file.path(tempdir(), "cache_qs_backend")
+  cache_dir <- file.path(tempdir(), "cache_qs2_backend")
   unlink(cache_dir, recursive = TRUE)
   dir.create(cache_dir, showWarnings = FALSE)
 
-  f <- cacheFile(cache_dir, backend = "qs") %@% function(x) {
+  f <- cacheFile(cache_dir, backend = "qs2") %@% function(x) {
     x * 2
   }
 
   res <- f(10)
   expect_equal(res, 20)
 
-  # Verify the file extension is actually .qs
+  # Verify the file extension is actually .qs2
   files <- list.files(cache_dir)
-  expect_true(any(grepl("\\.qs$", files)))
-  
+  expect_true(any(grepl("\\.qs2$", files)))
+
   # Verify we can load it back manually
   cache_path <- file.path(cache_dir, files[1])
-  loaded <- qs::qread(cache_path)
+  loaded <- qs2::qs_read(cache_path)
   expect_equal(loaded$value, 20)
 })
 
@@ -297,11 +297,11 @@ test_that("backend selection works", {
   cached_rds(1)
   expect_true(any(grepl("\\.rds$", list.files(cache_dir))))
   
-  # QS
-  if (requireNamespace("qs", quietly = TRUE)) {
-    cached_qs <- cacheFile(cache_dir, backend = "qs") %@% function(x) x
-    cached_qs(2)
-    expect_true(any(grepl("\\.qs$", list.files(cache_dir))))
+  # QS2
+  if (requireNamespace("qs2", quietly = TRUE)) {
+    cached_qs2 <- cacheFile(cache_dir, backend = "qs2") %@% function(x) x
+    cached_qs2(2)
+    expect_true(any(grepl("\\.qs2$", list.files(cache_dir))))
   }
 })
 
@@ -1507,7 +1507,7 @@ test_that("cache_stats returns correct aggregate statistics", {
   st2 <- cache_stats(tmp)
   expect_equal(st2$n_entries, 3L)
   # Files are small, so total_size_mb may round to 0 — check raw file sizes instead
-  files <- list.files(tmp, pattern = "\\.(rds|qs)$", full.names = TRUE)
+  files <- list.files(tmp, pattern = "\\.(rds|qs2)$", full.names = TRUE)
   files <- files[!grepl("graph\\.rds$", files)]
   expect_true(sum(file.size(files)) > 0)
   expect_true(!is.na(st2$oldest))
@@ -1616,7 +1616,7 @@ test_that(".load_cacheR_config does not override existing options", {
   on.exit(unlink(tmp, recursive = TRUE))
 
   yml_path <- file.path(tmp, ".cacheR.yml")
-  writeLines("backend: qs", yml_path)
+  writeLines("backend: qs2", yml_path)
 
   withr::with_options(list(cacheR.backend = "rds"), {
     cacheR:::.load_cacheR_config(yml_path)
diff --git a/tests/testthat/test-files.R b/tests/testthat/test-files.R
@@ -12,7 +12,7 @@ reset_if_needed <- function() {
 # --------------------------------------------------------#
 # Helper: Count cache entry files, excluding graph.rds
 # --------------------------------------------------------#
-count_cache_entries <- function(cache_dir, backend_pattern = "\\.(rds|qs)$") {
+count_cache_entries <- function(cache_dir, backend_pattern = "\\.(rds|qs2)$") {
   files <- list.files(cache_dir, pattern = backend_pattern)
   length(files[!grepl("^graph\\.rds", files)])
 }
@@ -923,7 +923,7 @@ test_that("Vector of file paths invalidates cache when any file changes", {
   on.exit(unlink(c(file1, file2)), add = TRUE)
 
   # Exclude graph.rds from count
-  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs)$"), invert = TRUE, value = TRUE))
+  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs2)$"), invert = TRUE, value = TRUE))
 
   f <- cacheFile(cache_dir = cache_dir) %@% function(paths) {
     paste(vapply(paths, function(p) readLines(p, warn = FALSE), character(1)), collapse = "|")
@@ -954,7 +954,7 @@ test_that("Vector of mixed file paths and regular strings invalidates on file ch
   on.exit(unlink(file1), add = TRUE)
 
   # Exclude graph.rds from count
-  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs)$"), invert = TRUE, value = TRUE))
+  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs2)$"), invert = TRUE, value = TRUE))
 
   f <- cacheFile(cache_dir = cache_dir) %@% function(items) {
     paste(items, collapse = ",")
@@ -987,7 +987,7 @@ test_that("Vector of file paths works with hash_file_paths = FALSE (portable mod
   file_B <- file.path(dir_B, "data.txt"); writeLines("SAME", file_B)
 
   # Exclude graph.rds from count
-  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs)$"), invert = TRUE, value = TRUE))
+  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs2)$"), invert = TRUE, value = TRUE))
 
   cache_dir <- file.path(base_dir, "cache")
 
@@ -1023,7 +1023,7 @@ test_that("Vector of directory paths invalidates when dir content changes", {
   file.create(file.path(dir2, "b.txt"))
 
   # Exclude graph.rds from count
-  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs)$"), invert = TRUE, value = TRUE))
+  count_cache <- function(d) length(grep("^graph\\.", list.files(d, pattern = "\\.(rds|qs2)$"), invert = TRUE, value = TRUE))
 
   f <- cacheFile(cache_dir = cache_dir) %@% function(dirs) {
     sum(vapply(dirs, function(d) length(list.files(d)), integer(1)))
diff --git a/tests/testthat/test-graph.R b/tests/testthat/test-graph.R
@@ -1,7 +1,7 @@
 test_that("helpers: count cache artifacts", {
   count_cache_files <- function(cache_dir) {
     # Only count final cache objects, not locks/tmp
-    length(list.files(cache_dir, pattern = "\\.(rds|qs)$", full.names = TRUE))
+    length(list.files(cache_dir, pattern = "\\.(rds|qs2)$", full.names = TRUE))
   }
   expect_true(is.function(count_cache_files))
 })
@@ -152,7 +152,7 @@ test_that("complex graph export: two Y-shapes merging into a final step", {
 test_that("helpers: count cache artifacts", {
   count_cache_files <- function(cache_dir) {
     # Only count final cache objects, not locks/tmp
-    length(list.files(cache_dir, pattern = "\\.(rds|qs)$", full.names = TRUE))
+    length(list.files(cache_dir, pattern = "\\.(rds|qs2)$", full.names = TRUE))
   }
   expect_true(is.function(count_cache_files))
 })
diff --git a/tests/testthat/test-metadata.R b/tests/testthat/test-metadata.R
@@ -15,8 +15,8 @@ test_that("cacheFile stores value and metadata in cache file", {
   # First call – should compute and write cache
   expect_equal(cached(10), 11)
   
-  # Filter for .rds or .qs files only, ignoring .lock files
-  files <- list.files(cache_dir, pattern = "\\.(rds|qs)$", full.names = TRUE)
+  # Filter for .rds or .qs2 files only, ignoring .lock files
+  files <- list.files(cache_dir, pattern = "\\.(rds|qs2)$", full.names = TRUE)
   expect_length(files, 1L)
 
   obj <- readRDS(files[1])
@@ -84,7 +84,7 @@ test_that("cacheInfo returns value and metadata", {
   # Generate cache
   cached(3)
 
-  files <- list.files(cache_dir, full.names = TRUE, pattern="\\.(rds|qs)$")
+  files <- list.files(cache_dir, full.names = TRUE, pattern="\\.(rds|qs2)$")
   expect_length(files, 1L)
 
   # Test cacheInfo
diff --git a/tests/testthat/test-recursive-deps.R b/tests/testthat/test-recursive-deps.R
@@ -79,7 +79,7 @@ test_that("cacheFile respects package boundaries (does not recurse into base/pac
 
   expect_equal(f(c(1, 2, 3)), 2)
 
-  # Count only cache files (rds/qs), ignore .lock
+  # Count only cache files (rds/qs2), ignore .lock
   backend <- getOption("cacheR.backend", "rds")
   files <- list.files(cache_dir, pattern = paste0("\\.", backend, "$"))
   expect_length(files, 1)
diff --git a/vignettes/cacheR-introduction.Rmd b/vignettes/cacheR-introduction.Rmd
@@ -262,22 +262,22 @@ plot_cache_graph(output = "cache_graph.png")
 
 ---
 
-# 5. Using the `qs` backend for faster serialization
+# 5. Using the `qs2` backend for faster serialization
 
-For large matrices, the [`qs`](https://github.com/qsbase/qs) backend can be faster than base RDS.
+For large matrices, the [`qs2`](https://github.com/qsbase/qs2) backend can be faster than base RDS.
 
 Install it once:
 
 ```{r, eval=FALSE}
-install.packages("qs")
+install.packages("qs2")
 ```
 
-Then create a cached function with `backend = "qs"`:
+Then create a cached function with `backend = "qs2"`:
 
 ```{r}
-cached_cor_qs <- cacheFile(
+cached_cor_qs2 <- cacheFile(
   cache_dir = cache_dir,
-  backend   = "qs"
+  backend   = "qs2"
 ) %@% function(mat) {
   cor_with_moments(mat)
 }
@@ -289,14 +289,14 @@ Compare timings:
 set.seed(999)
 mat_big <- matrix(rnorm(500 * 50), ncol = 50)
 
-system.time(r1 <- cached_cor_qs(mat_big))
-system.time(r2 <- cached_cor_qs(mat_big))
+system.time(r1 <- cached_cor_qs2(mat_big))
+system.time(r2 <- cached_cor_qs2(mat_big))
 
 identical(r1$cor, r2$cor)
 list.files(cache_dir, recursive = TRUE)
 ```
 
-You should see some `.qs` files in the cache directory.
+You should see some `.qs2` files in the cache directory.
 
 ---
 
