From 7e153c547a024e293c88465b642c7847d6b3a555 Mon Sep 17 00:00:00 2001
From: Henrik Bengtsson <henrik.bengtsson@gmail.com>
Date: Sat, 16 Aug 2025 17:32:13 -0700
Subject: [PATCH 1/2] Write RDS files atomically (write to *.rds.tmp, then
 rename to *.rds)

---
 R/files.R         | 27 +++++++++++++++++++++++----
 R/updateRegisty.R |  4 ++--
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/R/files.R b/R/files.R
index e64690d6..ab5ddac4 100644
--- a/R/files.R
+++ b/R/files.R
@@ -42,9 +42,28 @@ file_mtime = function(x) {
   fs::file_info(x)$modification_time
 }
 
-writeRDS = function(object, file, compress = "gzip") {
-  file_remove(file)
-  saveRDS(object, file = file, version = 2L, compress = compress)
-  waitForFile(file, 300)
+writeRDS = function(object, file, compress = "gzip", wait = 300) {
+  # (a) Write to *.rds.tmp
+  tmp_file <- sprintf("%s.tmp", file)
+  saveRDS(object, file = tmp_file, version = 2L, compress = compress)
+
+  # (b) Wait for it to be found
+  if (wait > 0) waitForFile(tmp_file, timeout = wait)
+
+  # (c) Assert file exists
+  if (!file_test("-f", tmp_file)) {
+    stop(sprintf("Failed to save to temporary RDS file: %s", sQuote(tmp_file)))
+  }
+
+  # (d) Remove old file, if it exists
+  if (file_test("-f", file)) file_remove(file)
+
+  # (e) Rename *.rds.tmp to *.rds
+  file.rename(tmp_file, file)
+  if (!file_test("-f", file)) {
+    stop(sprintf("Failed to rename temporarily saved RDS file: %s -> %s",
+      sQuote(tmp_file), sQuote(file)))
+  }
+  
   invisible(TRUE)
 }
diff --git a/R/updateRegisty.R b/R/updateRegisty.R
index 47680e54..1430daea 100644
--- a/R/updateRegisty.R
+++ b/R/updateRegisty.R
@@ -78,7 +78,7 @@ updateRegistry = function(reg = getDefaultRegistry()) { # nocov start
         uri = getProblemURI(reg, id)
         p = readRDS(uri)
         p$cache = FALSE
-        saveRDS(p, file = uri, version = 2L)
+        writeRDS(p, file = uri, compress = TRUE, wait = 0)
       }
     }
   }
@@ -99,7 +99,7 @@ updateRegistry = function(reg = getDefaultRegistry()) { # nocov start
         } else {
           if (hasName(x, "memory")) {
             setnames(x, "memory", "mem.used")
-            saveRDS(x, file = fn, version = 2L)
+            writeRDS(x, file = fn, compress = TRUE, wait = 0)
           }
         }
       })

From c18e6f92e7d8b1e6c7d44a2ac1709c63aa9262d8 Mon Sep 17 00:00:00 2001
From: Henrik Bengtsson <henrik.bengtsson@gmail.com>
Date: Sat, 16 Aug 2025 19:16:54 -0700
Subject: [PATCH 2/2] ROBUSTNESS: Now sweepRegistry(), syncRegistry(),
 updateRegistry() searches for '\\.rds$' files in jobs/, results/, and
 updates/ folders [#317]

---
 R/sweepRegistry.R | 4 ++--
 R/syncRegistry.R  | 2 +-
 R/updateRegisty.R | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/sweepRegistry.R b/R/sweepRegistry.R
index 2467c58a..1e6efbad 100644
--- a/R/sweepRegistry.R
+++ b/R/sweepRegistry.R
@@ -14,7 +14,7 @@ sweepRegistry = function(reg = getDefaultRegistry()) {
 
   submitted = reg$status[.findSubmitted(reg = reg), c("job.id", "job.hash")]
   obsolete = chsetdiff(
-    list.files(dir(reg, "results"), full.names = TRUE),
+    list.files(dir(reg, "results"), pattern = "\\.rds$", full.names = TRUE),
     getResultFiles(reg, submitted)
   )
   if (length(obsolete)) {
@@ -31,7 +31,7 @@ sweepRegistry = function(reg = getDefaultRegistry()) {
     fs::file_delete(obsolete)
   }
 
-  obsolete = list.files(dir(reg, "jobs"), pattern = "\\.rds", full.names = TRUE)
+  obsolete = list.files(dir(reg, "jobs"), pattern = "\\.rds$", full.names = TRUE)
   if (length(obsolete)) {
     info("Removing %i obsolete job collection files ...", length(obsolete))
     fs::file_delete(obsolete)
diff --git a/R/syncRegistry.R b/R/syncRegistry.R
index cee150ed..d28a0180 100644
--- a/R/syncRegistry.R
+++ b/R/syncRegistry.R
@@ -21,7 +21,7 @@ syncRegistry = function(reg = getDefaultRegistry()) {
 
 sync = function(reg) {
   "!DEBUG [syncRegistry]: Triggered syncRegistry"
-  fns = list.files(dir(reg, "updates"), full.names = TRUE)
+  fns = list.files(dir(reg, "updates"), pattern = "\\.rds$", full.names = TRUE)
   if (length(fns) == 0L)
     return(character())
 
diff --git a/R/updateRegisty.R b/R/updateRegisty.R
index 1430daea..402ae845 100644
--- a/R/updateRegisty.R
+++ b/R/updateRegisty.R
@@ -89,7 +89,7 @@ updateRegistry = function(reg = getDefaultRegistry()) { # nocov start
       setnames(reg$status, "memory", "mem.used")
     }
 
-    fns = list.files(dir(reg, "updates"), full.names = TRUE)
+    fns = list.files(dir(reg, "updates"), pattern = "\\.rds$", full.names = TRUE)
     if (length(fns) > 0L) {
       info("Renaming memory column in update files")
       updates = lapply(fns, function(fn) {