On 06/05/2022 23:56, Max Nikulin wrote:
Mark Barton to emacs-orgmode, emacs-devel. master 4a1f69ebca 2/2: Use (TICKS . HZ) for current-time etc. Tue, 26 Apr 2022 23:37:50 -0700. https://list.orgmode.org/bf5b9308-3fef-4dc6-98c9-bff36f19d...@gmail.com

The change also breaks org-file-newer-than-p function that triggered the
debugger while loading my init that uses org babel.

I think, it should be fixed in the bugfix Org branch.  The attached patch is a compromise to some degree, but I do not see a robust solution.

Thinking more I realized that `org-file-newer-than-p' should not be reused for `org-babel-load-file'. I am attaching an updated patch for which I do not see any real drawback.

The only change in behavior is that if a file had modification time in future and it is overwritten by `org-compile-time' to current time than the function reports failure. I consider such case as a rare and peculiar one.
From e5f98dbc729904297bef529009ade96361dd4dd2 Mon Sep 17 00:00:00 2001
From: Max Nikulin <maniku...@gmail.com>
Date: Fri, 6 May 2022 23:34:52 +0700
Subject: [PATCH] org-macs.el: Do not compare wall time and file modification
 time

* lisp/org-macs.el (org-file-newer-than-p): Fix Emacs-29 problem with
changed representation of system clock timestamp.  Recommend passing
file modification time and do not truncate its precision.
(org-compile-file): Store file modification time instead of system clock
for later comparison by `org-file-newer-than-p'.
* lisp/org.el (org-babel-load-file): Do not use `org-file-newer-than-p'
to consider the .el file as up to date when its modification time is the
same as for the source .org file.

Unchanged timestamp of a file means failure of `org-compile-file' but in
`org-babel-load-file' the target may be considered up to date if its
timestamp is equal to the one for prerequisite.
So `org-file-newer-than-p' is not suitable for both cases.  The
difference matter for filesystems with coarse timestamp resolution, for
example HFS+.

Reported by Mark Barton <mbarto...@gmail.com>
https://list.orgmode.org/bf5b9308-3fef-4dc6-98c9-bff36f19d...@gmail.com

During discussion of the issue Paul Eggert <egg...@cs.ucla.edu>
suggested over variants of the changes in the same thread.
---
 lisp/org-macs.el | 32 +++++++++++++++++++++-----------
 lisp/org.el      | 18 ++++++++++++------
 2 files changed, 33 insertions(+), 17 deletions(-)

diff --git a/lisp/org-macs.el b/lisp/org-macs.el
index b10725bd5..556bf658d 100644
--- a/lisp/org-macs.el
+++ b/lisp/org-macs.el
@@ -256,16 +256,26 @@ ignored in this case."
 ;;; File
 
 (defun org-file-newer-than-p (file time)
-  "Non-nil if FILE is newer than TIME.
-FILE is a filename, as a string, TIME is a list of integers, as
-returned by, e.g., `current-time'."
-  (and (file-exists-p file)
-       ;; Only compare times up to whole seconds as some file-systems
-       ;; (e.g. HFS+) do not retain any finer granularity.  As
-       ;; a consequence, make sure we return non-nil when the two
-       ;; times are equal.
-       (not (time-less-p (cl-subseq (nth 5 (file-attributes file)) 0 2)
-			 (cl-subseq time 0 2)))))
+  "Non-nil if FILE modification time is greater than TIME.
+TIME should be obtained earlier for the same FILE name using
+
+  (file-attribute-modification-time (file-attributes file))
+
+If TIME is nil (file did not exist) then any existing FILE
+is considered as a newer one.  Some file systems have coarse
+timestamp resolution, for example 1 second on HFS+ or 2 seconds on FAT,
+so nil may be returned when file is updated twice within a short period
+of time.  File timestamp and system clock `current-time' may have
+different resolution, so attempts to compare them may give unexpected
+results.
+
+Attempt to check whether a derived file has been updated in
+response to modification of its source file may give unreliable
+result.  Equal timestamps in such case may mean that the derived
+file is up to date however this function returns nil assuming
+that the FILE is not modified."
+  (let ((mtime (file-attribute-modification-time (file-attributes file))))
+    (and mtime (or (not time) (time-less-p time mtime)))))
 
 (defun org-compile-file (source process ext &optional err-msg log-buf spec)
   "Compile a SOURCE file using PROCESS.
@@ -299,7 +309,7 @@ it for output."
 	 (full-name (file-truename source))
 	 (out-dir (or (file-name-directory source) "./"))
 	 (output (expand-file-name (concat base-name "." ext) out-dir))
-	 (time (current-time))
+	 (time (file-attribute-modification-time (file-attributes output)))
 	 (err-msg (if (stringp err-msg) (concat ".  " err-msg) "")))
     (save-window-excursion
       (pcase process
diff --git a/lisp/org.el b/lisp/org.el
index 54350faee..c1ce57c4d 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -232,12 +232,18 @@ and then loads the resulting file using `load-file'.  With
 optional prefix argument COMPILE, the tangled Emacs Lisp file is
 byte-compiled before it is loaded."
   (interactive "fFile to load: \nP")
-  (let ((tangled-file (concat (file-name-sans-extension file) ".el")))
-    ;; Tangle only if the Org file is newer than the Elisp file.
-    (unless (org-file-newer-than-p
-	     tangled-file
-	     (file-attribute-modification-time
-	      (file-attributes (file-truename file))))
+  (let* ((tangled-file (concat (file-name-sans-extension file) ".el"))
+         (file-mtime (file-attribute-modification-time
+                      (file-attributes (file-truename file))))
+         (tangled-mtime (file-attribute-modification-time
+                         (file-attributes (file-truename tangled-file)))))
+    ;; Tangle only if the Elisp file is older than the Org file.
+    ;; Filesystem may have coarse timestamp resolution (HFS+, FAT)
+    ;; so no need to update if timestamps are equal and thus
+    ;; `org-file-newer-than-p' can not be used here.
+    (unless (and file-mtime
+                 tangled-mtime
+                 (not (time-less-p tangled-mtime file-mtime)))
       (org-babel-tangle-file file
                              tangled-file
                              (rx string-start
-- 
2.25.1

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