ivy-done and "Unregistered buffer modifications detected"

[William Denton]

I was fiddling with my init file and something with pdf-tools blew up and 
initialization went wrong and I lost my desktop history list of buffers I always 
have open.  When I fixed the problem (by dropping pdf-tools, which I realized I 
never used), I had to load all the files I like to have open.  I opened four, 
and for each one I got the same warning, as you can see below.  Further below 
that is the full Org debug dump.

I don't know if the ivy-done clue is enough to be helpful (maybe it just means 
there's something funny involving ivy), but if there's more I can do I'm glad to 
help.

Bill


Warning (org-element-cache): org-element--cache: Unregistered buffer 
modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode 
mailing list (M-x org-submit-bug-report).
The buffer is: reading-diary.org
 Current command: (ivy-done 7688 7689)
 Chars modified: 7688
 Buffer modified: 7689
 Backtrace:
nil Disable showing Disable logging
Warning (org-element-cache): org-element--cache: Unregistered buffer 
modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode 
mailing list (M-x org-submit-bug-report).
The buffer is: pepys-exchange-list.org
 Current command: (ivy-done 5351 5352)
 Chars modified: 5351
 Buffer modified: 5352
 Backtrace:
nil Disable showing Disable logging
Warning (org-element-cache): org-element--cache: Unregistered buffer 
modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode 
mailing list (M-x org-submit-bug-report).
The buffer is: l2a.org
 Current command: (ivy-done 26 27)
 Chars modified: 26
 Buffer modified: 27
 Backtrace:
nil Disable showing Disable logging
Warning (org-element-cache): org-element--cache: Unregistered buffer 
modifications detected. Resetting.
If this warning appears regularly, please report the warning text to Org mode 
mailing list (M-x org-submit-bug-report).
The buffer is: library.org
 Current command: (ivy-done 779 780)
 Chars modified: 779
 Buffer modified: 780
 Backtrace:
nil Disable showing Disable logging







Emacs  : GNU Emacs 29.0.50 (build 5, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, 
cairo version 1.16.0)
 of 2022-05-07
Package: Org mode version 9.5.3 (release_9.5.3-473-g15d256 @ 
/usr/local/src/org-mode/lisp/)

current state:
==============
(setq
 org-link-elisp-confirm-function 'yes-or-no-p
 org-ditaa-jar-path "/usr/share/ditaa/ditaa.jar"
 org-hide-emphasis-markers t
 org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn 
ENTRY)"]
 org-babel-after-execute-hook '(org-redisplay-inline-images)
 org-persist-after-read-hook '(org-element--cache-persist-after-read)
 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)
 org-archive-hook '(org-attach-archive-delete-maybe)
 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-image-actual-width nil
 org-mode-hook '((lambda nil
                  (org-superstar-mode 1))
                 wtd/org-ispell
                 add-org-toggle-src-key
                 org-appear-mode
                 turn-on-flyspell
                 (lambda nil
                  (setq
                   prettify-symbols-alist
                   (cons '("<=" . 8804)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons '(">=" . 8805)
                    prettify-symbols-alist)
                   )
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                   prettify-symbols-alist
                   (cons '("|>" . 9655)
                    prettify-symbols-alist)
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                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+BEGIN_SRC" . 9121)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+END_SRC" . 9123)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+begin_src" . 9121)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+end_src" . 9123)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+BEGIN_QUOTE" .
                      10077)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+END_QUOTE" . 10078)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+begin_quote" .
                      10077)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons
                    '("#+end_quote" . 10078)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons '("[ ]" . 9744)
                    prettify-symbols-alist)
                   )
                  (setq
                   prettify-symbols-alist
                   (cons '("[X]" . 9746)
                    prettify-symbols-alist)
                   )
                  )
                 add-org-close-all-drawers-key
                 (lambda

                                                nil

                                                (setq ispell-parser 'tex)

                                                )
                 (lambda nil
                  (org-toggle-inline-images))
                 org-clock-load
                 #[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
                 #[0 "\301\211\207"
                   [imenu-create-index-function org-imenu-get-tree]
                   2]
                 wrap-region-mode)
 org-babel-load-languages '((ditaa . t)
                            (dot . t)
                            (latex . t)
                            (lilypond . t)
                            (python . t)
                            (R . t)
                            (ruby . t)
                            (shell . t)
                            (sql . t)
                            (sqlite . t))
 org-src-window-setup 'current-window
 org-fold-core-first-unfold-functions '(org-fold--hide-drawers 
org-fold-hide-archived-subtrees)
 org-ellipsis " ⬎"
 org-confirm-shell-link-function 'yes-or-no-p
 outline-isearch-open-invisible-function 'outline-isearch-open-invisible
 org-startup-indented t
 org-highlight-latex-and-related '(latex)
 org-use-speed-commands t
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-src-preserve-indentation t
 org-babel-tangle-lang-exts '(("ruby" . "rb")
                              ("python" .
                               "py")
                              ("LilyPond" .
                               "ly")
                              ("latex" .
                               "tex")
                              ("emacs-lisp"
                               . "el")
                              ("elisp" .
                               "el")
                              )
 org-src-mode-hook '(org-src-babel-configure-edit-buffer 
org-src-mode-configure-edit-buffer)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-cycle-separator-lines 0
 org-superstar-headline-bullets-list '("⊢"
                                       "ǁ"
                                       "ǀ"
                                       "⋱"
                                       "◉"
                                       "○")
 org-support-shift-select t
 org-pretty-entities t
 org-fontify-whole-heading-line t
 org-speed-command-hook '(org-speed-command-activate 
org-babel-speed-command-activate)
 org-export-backends '(html latex md odt
                       beamer)
 org-confirm-babel-evaluate nil
 org-fold-core-isearch-open-function 'org-fold-core--isearch-reveal
 org-clock-persist 'history
 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)
 org-link-shell-confirm-function 'yes-or-no-p
 org-babel-pre-tangle-hook '(save-buffer)
 org-agenda-loop-over-headlines-in-active-region nil
 org-occur-hook '(org-first-headline-recenter)
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-link-parameters '(("attachment" :follow
                        org-attach-follow
                        :complete
                        org-attach-complete-link)
                       ("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)
                       ("id" :follow
                        org-id-open)
                       ("file+sys")
                       ("file+emacs")
                       ("shell" :follow
                        org-link--open-shell)
                       ("news" :follow
                        #[514
                          "\301\300\302Q\"\207"
                          ["news" browse-url
                           ":"]
                          6
                          "\n\n(fn URL ARG)"]
                        )
                       ("mailto" :follow
                        #[514
                          "\301\300\302Q\"\207"
                          ["mailto"
                           browse-url ":"]
                          6
                          "\n\n(fn URL ARG)"]
                        )
                       ("https" :follow
                        #[514
                          "\301\300\302Q\"\207"
                          ["https"
                           browse-url ":"]
                          6
                          "\n\n(fn URL ARG)"]
                        )
                       ("http" :follow
                        #[514
                          "\301\300\302Q\"\207"
                          ["http" browse-url
                           ":"]
                          6
                          "\n\n(fn URL ARG)"]
                        )
                       ("ftp" :follow
                        #[514
                          "\301\300\302Q\"\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-metaup-hook '(org-babel-load-in-session-maybe)
 org-startup-with-inline-images t
 org-return-follows-link t
 org-special-ctrl-a/e t
 org-tags-column 120
 org-hide-macro-markers t
 org-footnote-section nil
 org-list-allow-alphabetical t
 )
--



--
William Denton
https://www.miskatonic.org/
Librarian, artist and licensed private investigator.
Toronto, Canada