[BUG] org-element--cache: Unregistered buffer modifications detected saving org-agenda-files buffers [9.5.3 (9.5.3-g8e69ad @ /Users/enrikes/.emacs.d/straight/build/org/)]

["Enrique Kessler Martínez" <qkessler@gmail.com>]

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Hi there!

I'm running into the Unregistered buffer modifications bug in the past few
weeks. The current workflow that causes it is:
- Open org-agenda.
- Trigger org-save-all-buffers.

After that, the warnings appear. I build the org-agenda files automatically
with a query for PROJECT tags on my org-roam directory. I set that up using
this post, that might help debugging:
https://d12frosted.io/posts/2021-01-16-task-management-with-roam-vol5.html

Thank you for your work!
Best,
Quique.

Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

     https://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org mailing list.
------------------------------------------------------------------------



Emacs  : GNU Emacs 29.0.50 (build 1, x86_64-apple-darwin19.6.0, NS
appkit-1894.60 Version 10.15.7 (Build 19H1824))
 of 2022-05-05
Package: Org mode version 9.5.3 (9.5.3-g8e69ad @
/Users/enrikes/.emacs.d/straight/build/org/)

current state:
==============
(setq
 org-agenda-prefix-format "  %?-12t% s"
 org-archive-location "~/Documents/org_files/archive/%s_archive::"
 org-roam-db-location "/Users/enrikes/.emacs.d/var/org/org-roam.db"
 org-link-elisp-confirm-function 'yes-or-no-p
 org-shiftdown-final-hook '(evil-org-shift-fallback-command)
 org-directory "~/Documents/org_files"
 org-after-refile-insert-hook '(qk-org-clean-tags)
 org-hide-emphasis-markers t
 org-bibtex-headline-format-function #[257 "\300.\236A\207" [:title] 3
"\n\n(fn ENTRY)"]
 org-pdftools-get-desc-function 'org-pdftools-get-desc-default
 org-agenda-custom-commands '(("d" "Agenda"
                               ((agenda ""
                                 ((org-agenda-overriding-header "Today's
Schedule:") (org-agenda-span 'day) (org-agenda-ndays 1)
(org-agenda-start-on-weekday nil) (org-agenda-start-day "+0d")
                                  (org-agenda-skip-function '(cond ((equal
(file-name-nondirectory (buffer-file-name)) "refile.org")
(outline-next-heading) (1- (point))) (t (org-agenda-skip-entry-if 'todo
'done))))
                                  (org-agenda-todo-ignore-deadlines nil))
                                 )
                                (todo "PROJECT"
((org-agenda-overriding-header "Project list:")
(org-tags-match-list-sublevels nil))) (tags "REFILING"
((org-agenda-overriding-header "Tasks to Refile:")
(org-tags-match-list-sublevels nil)))
                                (todo "TODO" ((org-agenda-overriding-header
"Unscheduled Tasks:") (org-tags-match-list-sublevels nil)
(org-agenda-skip-function '(org-agenda-skip-entry-if 'deadline
'scheduled))))
                                (todo "WAITING|SOMEDAY"
((org-agenda-overriding-header "Waiting/Someday Tasks:")
(org-tags-match-list-sublevels nil))) (todo "NOTE"
((org-agenda-overriding-header "Notes:") (org-tags-match-list-sublevels
nil)))
                                (agenda ""
                                 ((org-agenda-overriding-header
"Upcoming:") (org-agenda-span 7) (org-agenda-start-day "+1d")
(org-agenda-start-on-weekday nil)
                                  (org-agenda-skip-function '(cond ((equal
(file-name-nondirectory (buffer-file-name)) "refile.org")
(outline-next-heading) (1- (point))) (t (org-agenda-skip-entry-if 'todo
'done))))
                                  (org-agenda-todo-ignore-deadlines nil))
                                 )
                                )
                               )
                              )
 org-agenda-files '("/Users/enrikes/Documents/slipbox/pages/
amazon_meetings.org" "/Users/enrikes/Documents/slipbox/pages/
nabyinotifications_push_notifications_channels_not_showing.org"
"/Users/enrikes/Documents/slipbox/pages/nabyi_cgp.org"
                    "/Users/enrikes/Documents/slipbox/pages/book_list.org"
"/Users/enrikes/Documents/slipbox/pages/ramping_up_to_the_team.org"
"/Users/enrikes/Documents/slipbox/pages/
deep_dive_on_the_google_billing_project.org"
                    "/Users/enrikes/Documents/slipbox/pages/
notifications_spike_add_tests_for_the_android_12_migration.org"
"/Users/enrikes/Documents/slipbox/pages/
nabyinotifications_monitor_the_notifications_post_merge_on_the_r9_release.org
"
                    "/Users/enrikes/Documents/slipbox/pages/
nabyinotifications.org" "/Users/enrikes/Documents/slipbox/pages/
life_items.org" "/Users/enrikes/Documents/slipbox/pages/inbox_review.org"
"/Users/enrikes/Documents/slipbox/pages/anki.org"
                    "/Users/enrikes/Documents/slipbox/pages/
follow_up_review.org" "/Users/enrikes/Documents/slipbox/pages/meetings.org"
"/Users/enrikes/Documents/slipbox/pages/
nabyinotifications_oncall_shadowing.org"
                    "/Users/enrikes/Documents/slipbox/pages/
nabyinotifications_uncertified_orange_app_in_production_needs_to_be_certified_or_deprecated.org
")
 org-capture-templates '(("#" "used by gnus-icalendar-org" entry (file+olp
"~/Documents/slipbox//pages/meetings.org" "Meetings") "%i"
:immediate-finish t)
                         ("a" "Anki basic" entry (file
org-default-notes-file) (concat "* %<%H:%M>   %^g\n:PROPERTIES:\n"
":ANKI_NOTE_TYPE: Basic\n" ":ANKI_DECK: %?\n" ":VISIBILITY: folded\n"
":END:\n" "** Front\n\n" "** Back\n\n"))
                         ("t" "Todo" entry (file+headline
org-default-notes-file "Refile items") "* TODO %? :REFILING:\n%a\n"
:clock-in t :clock-resume t)
                         ("m" "Meeting/Interruption" entry (file+headline
org-default-notes-file "Refile items") "* MEETING %? :REFILING:MEETING:\n"
:clock-in t :clock-resume t)
                         ("i" "Idea" entry (file+headline
org-default-notes-file "Refile items") "* %? :REFILING:IDEA:\n" :clock-in t
:clock-resume t)
                         ("s" "Someday" entry (file+headline
org-default-notes-file "Refile items") "* SOMEDAY %? :REFILING:SOMEDAY:\n"
:clock-in t :clock-resume t) ("p" "Project creation: @work or @home")
                         ("pw" "@work Project entry" entry (file+headline
org-default-notes-file "Refile items") "* PROJECT %?
:@work:REFILING:PROJECT:\n" :clock-in t :clock-resume t)
                         ("ph" "@home Project entry" entry (file+headline
org-default-notes-file "Refile items") "* PROJECT %?
:@home:REFILING:PROJECT:\n" :clock-in t :clock-resume t)
                         ("b" "Book" entry (file org-book-list-file) "*
%^{TITLE}\n:PROPERTIES:\n:ADDED:
%<[%Y-%02m-%02d]>\n:END:%^{AUTHOR}p\n%^{URL}p\n"))
 org-roam-node-display-template "${title}
       ${tags}"
 org-persist-after-read-hook '(org-element--cache-persist-after-read)
 org-refile-targets '((nil :maxlevel . 5) (org-agenda-files :maxlevel . 5)
(org-book-list-file :maxlevel . 2))
 org-export-before-parsing-hook '(org-attach-expand-links)
 org-cycle-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand
                            (closure (t) nil (if (org-in-src-block-p t)
(progn (let* ((elt (org-element-at-point)) (lang (intern
(org-element-property :language elt))) (langs org-babel-load-languages))
(if (alist-get lang langs) nil (indent-to 4)))))))
 org-default-notes-file "~/Documents/slipbox//pages/refile.org"
 org-roam-find-file-hook '(org-roam-buffer--setup-redisplay-h
org-roam--register-completion-functions-h
org-roam--replace-roam-links-on-save-h
org-roam-db-autosync--setup-update-on-save-h sc-org-hide-properties)
 org-refile-use-outline-path 'file
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-columns-default-format "%50ITEM(Task) %10Effort{:} %10CLOCKSUM"
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines
org-cycle-optimize-window-after-visibility-change)
 org-persist-before-read-hook '(org-element--cache-persist-before-read)
 org-link-from-user-regexp
"\\<enrikes@5c52309ccb1e\\.ant\\.amazon\\.com\\>\\|\\<Kessler
Martinez\\>"
 org-mode-hook '(#[0 "\301\211.\207" [imenu-create-index-function
org-imenu-get-tree] 2] evil-collection-mu4e-org-set-header-to-normal-mode
#[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook
org-fold-show-all append local] 5]
                 #[0 "\300\301\302\303\304$\207" [add-hook
change-major-mode-hook org-babel-show-result-all append local] 5]
org-babel-result-hide-spec org-babel-hide-all-hashes
org-pdftools-setup-link bg-org-fill-paragraph-config visual-line-mode
                 evil-org-mode)
 org-id-locations-file "/Users/enrikes/.emacs.d/var/org/id-locations.el"
 org-clock-in-hook-hook '(org-save-all-org-buffers)
 org-shiftup-final-hook '(evil-org-shift-fallback-command)
 org-roam-ref-annotation-function 'org-roam-ref-read--annotation
 org-roam-directory "~/Documents/slipbox/"
 org-roam-db-node-include-function #[0 "\300\207" [t] 1]
 org-confirm-shell-link-function 'yes-or-no-p
 org-agenda-skip-scheduled-if-deadline-is-shown t
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-agenda-hide-tags-regexp ".*"
 org-roam-capture-preface-hook '(org-roam-capture--try-capture-to-ref-h)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-capture-prepare-finalize-hook '(org-roam-capture--install-finalize-h)
 org-roam-preview-function 'org-roam-preview-default-function
 org-src-mode-hook '(doom-modeline-set-org-src-modeline
org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-roam-db-autosync-mode t
 org-confirm-elisp-link-function 'yes-or-no-p
 org-todo-state-tags-triggers '(("CANCELLED" ("CANCELLED" . t)) ("WAITING"
("WAITING" . t)) (done ("WAITING") ("CANCELLED")) ("DONE" ("WAITING")
("CANCELLED")) ("TODO" ("WAITING") ("CANCELLED")))
 org-clock-out-remove-zero-time-clocks t
 org-log-buffer-setup-hook '(org-roam-log--setup)
 org-hide-leading-stars t
 org-todo-keywords '((sequence "TODO(t)" "|" "DONE(d)") (sequence
"PROJECT(p)" "|" "DONE(d)" "CANCELLED(c)") (sequence "WAITING(w)" "|")
(sequence "REVIEW (r)" "|") (sequence "|" "CANCELLED(c)") (sequence "|"
"OPTIONAL(o)")
                     (sequence "SOMEDAY(s)" "|" "CANCELLED(c)") (sequence
"MEETING(m)" "|" "DONE(d)") (sequence "NOTE(n)" "|" "DONE(d)"))
 org-deadline-warning-days 3
 org-roam-capture-new-node-hook '(org-roam-capture--insert-captured-ref-h)
 org-blocker-hook '(org-block-todo-from-children-or-siblings-or-parent)
 org-shiftright-final-hook '(evil-org-shift-fallback-command)
 org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
 org-clock-persist-file "/Users/enrikes/.emacs.d/var/org/clock-persist.el"
 org-persist-directory "/Users/enrikes/.emacs.d/var/org/persist/"
 org-export-backends '(md ascii html icalendar latex odt)
 org-enforce-todo-dependencies t
 org-confirm-babel-evaluate nil
 org-fold-core-isearch-open-function 'org-fold-core--isearch-reveal
 org-clock-in-resume t
 org-clock-out-hook-hook '(org-save-all-org-buffers)
 org-clock-persist t
 org-pdftools-markup-pointer-function
'pdf-annot-add-underline-markup-annotation
 org-persist-before-write-hook '(org-element--cache-persist-before-write)
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand
                      (closure (t) nil (if (org-in-src-block-p t) (progn
(let* ((elt (org-element-at-point)) (lang (intern (org-element-property
:language elt))) (langs org-babel-load-languages)) (if (alist-get lang
langs) nil (indent-to 4)))))))
 org-link-shell-confirm-function 'yes-or-no-p
 org-shiftleft-final-hook '(evil-org-shift-fallback-command)
 org-babel-pre-tangle-hook '(save-buffer)
 org-agenda-loop-over-headlines-in-active-region nil
 org-todo-keyword-faces '(("PROJECT" :foreground "#a87600" :weight bold)
("OPTIONAL" :foreground "#08a838" :weight bold) ("WAITING" :foreground
"#fe2f92" :weight bold) ("CANCELLED" :foreground "#999999" :weight bold)
                          ("SOMEDAY" :foreground "#ab82ff" :weight bold)
("MEETING" :foreground "#81A1C1" :weight bold) ("NOTE" :foreground
"#fcba03" :weight bold))
 org-capture-mode-hook '((closure (t) nil (let* ((headline '(:inherit
default :weight bold))) (face-remap-add-relative 'org-level-1 '((\,@
headline))))))
 org-occur-hook '(org-first-headline-recenter)
 org-capture-after-finalize-hook '(org-save-all-org-buffers)
 org-roam-log-setup-hook '(org-roam--register-completion-functions-h)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-roam-node-annotation-function 'org-roam-node-read--annotation
 org-link-parameters '(("pdf" :follow org-pdftools-open :complete
org-pdftools-complete-link :store org-pdftools-store-link :export
org-pdftools-export) ("eww" :follow org-eww-open :store org-eww-store-link)
                       ("rmail" :follow org-rmail-open :store
org-rmail-store-link) ("mhe" :follow org-mhe-open :store
org-mhe-store-link) ("irc" :follow org-irc-visit :store org-irc-store-link
:export org-irc-export)
                       ("info" :follow org-info-open :export
org-info-export :store org-info-store-link) ("gnus" :follow org-gnus-open
:store org-gnus-store-link)
                       ("docview" :follow org-docview-open :export
org-docview-export :store org-docview-store-link) ("bibtex" :follow
org-bibtex-open :store org-bibtex-store-link)
                       ("bbdb" :follow org-bbdb-open :export
org-bbdb-export :complete org-bbdb-complete-link :store
org-bbdb-store-link) ("w3m" :store org-w3m-store-link) ("doi" :follow
org-link-doi-open :export org-link-doi-export)
                       ("roam" :follow org-roam-link-follow-link)
("attachment" :follow org-attach-follow :complete org-attach-complete-link)
("id" :follow org-roam-id-open) ("mu4e" :follow mu4e-org-open :store
mu4e-org-store-link) ("file+sys")
                       ("file+emacs") ("shell" :follow
org-link--open-shell) ("news" :follow #[514 "\301\300\302.Q.\"\207" ["news"
browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("mailto" :follow #[514 "\301\300\302.Q.\"\207"
["mailto" browse-url ":"] 6 "\n\n(fn URL ARG)"]) ("https" :follow #[514
"\301\300\302.Q.\"\207" ["https" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("http" :follow #[514 "\301\300\302.Q.\"\207"
["http" browse-url ":"] 6 "\n\n(fn URL ARG)"]) ("ftp" :follow #[514
"\301\300\302.Q.\"\207" ["ftp" browse-url ":"] 6 "\n\n(fn URL ARG)"])
                       ("help" :follow org-link--open-help :store
org-link--store-help) ("file" :complete org-link-complete-file) ("elisp"
:follow org-link--open-elisp))
 org-roam-capture-templates '(("d" "default" plain "%?" :if-new (file+head
"pages/${slug}.org" ":PROPERTIES:\n:ID: %(org-id-uuid)\n:END:\n#+title:
${title}\n#+filetags: \n\n") :unnarrowed t))
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-refile-allow-creating-parent-nodes 'confirm
 org-agenda-restore-windows-after-quit t
 org-agenda-skip-comment-trees nil
 org-return-follows-link t
 org-outline-path-complete-in-steps nil
 org-agenda-block-separator 8212
 org-roam-indirect-buffer-hook '(org-roam--register-completion-functions-h)
 org-refile-target-verify-function 'qk-org-refile-target-verify-function
 )

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