* org-ref / Edit notes problem
@ 2021-03-19 13:58 Christian Barthel
2021-03-19 21:11 ` Christian Barthel
0 siblings, 1 reply; 3+ messages in thread
From: Christian Barthel @ 2021-03-19 13:58 UTC (permalink / raw)
To: emacs-orgmode
Hi,
I am using Emacs 27.1 on OpenBSD 6.8 and org-ref
(20210315.1730). When I am trying to Edit notes on an existing
org-ref entry ([f9] Edit Notes), emacs stops working and hangs.
By some observation, I saw that emacs is consuming a lot of
memory and the garbage collector seems to run quite frequently
(see the trace above). This happens after pressing [f9].
Output top(1)
--8<---------------cut here---------------start------------->8---
$ top
PID USERNAME PRI NICE SIZE RES STATE WAIT TIME CPU COMMAND
45199 bch 43 -5 273M 307M onproc/1 - 0:13 36.33% emacs-27.1
...
PID USERNAME PRI NICE SIZE RES STATE WAIT TIME CPU COMMAND
45199 bch 47 -5 409M 444M onproc/1 - 0:25 49.27% emacs-27.1
--8<---------------cut here---------------end--------------->8---
The profile-report was generated by pressing [f9] and pressing
C-g a few seconds afterwards. (emacs will become unresponsive
when waiting longer)
Profile:
--8<---------------cut here---------------start------------->8---
- command-execute 52 51%
- call-interactively 52 51%
- funcall-interactively 52 51%
- org-ref-helm-insert-cite-link 51 50%
- helm-bibtex 48 47%
- bibtex-completion-candidates 30 29%
- bibtex-completion-parse-bibliography 18 17%
- parsebib-read-entry 11 10%
- parsebib--find-bibtex-field 9 8%
- parsebib--parse-value 9 8%
- parsebib--expand-strings 7 6%
- mapcar 7 6%
- #<compiled 0xe4803b2339> 7 6%
replace-regexp-in-string 6 5%
parsebib--looking-at-goto-end 1 0%
- parsebib--match-paren-forward 1 0%
- parsebib--match-brace-forward 1 0%
forward-sexp 1 0%
- bibtex-completion-prepare-entry 7 6%
- mapcar 3 2%
- #<compiled 0xe48c386fc9> 3 2%
- bibtex-completion-find-note-multiple-files 2 1%
f-directory? 2 1%
- bibtex-completion-find-note-one-file 1 0%
f-file? 1 0%
- bibtex-completion-find-pdf 2 1%
- bibtex-completion-find-pdf-in-library 2 1%
- -first 1 0%
f-file? 1 0%
- f-join 1 0%
- -map 1 0%
- mapcar 1 0%
- #<compiled 0xe49feddbc5> 1 0%
f-expand 1 0%
member-ignore-case 1 0%
- bibtex-completion-remove-duplicated-fields 1 0%
- cl-remove-duplicates 1 0%
- cl--delete-duplicates 1 0%
cl--position 1 0%
- secure-hash 8 7%
- select-safe-coding-system 8 7%
find-coding-systems-region 8 7%
- message 1 0%
- redisplay_internal (C function) 1 0%
- funcall 1 0%
- #<compiled 0xe4acccdd6f> 1 0%
- gui-backend-selection-exists-p 1 0%
- apply 1 0%
#<compiled 0xe4acc95353> 1 0%
- bibtex-completion-resolve-crossrefs 1 0%
- bibtex-completion-make-entry-hash 1 0%
- bibtex-completion-get-value 1 0%
replace-regexp-in-string 1 0%
- helm 18 17%
- apply 18 17%
- helm 18 17%
- apply 18 17%
- helm-internal 18 17%
- helm-read-from-minibuffer 17 16%
- helm-update 12 11%
- helm--collect-matches 12 11%
- helm-compute-matches 8 7%
- helm-process-filtered-candidate-transformer 8 7%
- helm-apply-functions-from-source 8 7%
- apply 8 7%
- helm-bibtex-candidates-formatter 8 7%
- bibtex-completion-format-entry 8 7%
- s-format 8 7%
- replace-regexp-in-string 7 6%
- #<compiled 0xe4976d474d> 5 4%
- #<compiled 0xe48c3873e9> 5 4%
- bibtex-completion-shorten-authors 2 1%
- s-split 2 1%
split-string 2 1%
- bibtex-completion-clean-string 1 0%
replace-regexp-in-string 1 0%
- require 2 1%
- byte-code 2 1%
- require 1 0%
- byte-code 1 0%
- require 1 0%
byte-code 1 0%
read-from-minibuffer 3 2%
- helm-execute-selection-action 1 0%
- helm-execute-selection-action-1 1 0%
- helm-bibtex-edit-notes 1 0%
- bibtex-completion-edit-notes 1 0%
- bibtex-completion-edit-notes-default 1 0%
- bibtex-completion-get-entry 1 0%
bibtex-completion-get-entry1 1 0%
- org-ref-find-bibliography 3 2%
- reftex-locate-bibliography-files 3 2%
reftex-using-biblatex-p 1 0%
- execute-extended-command 1 0%
- sit-for 1 0%
redisplay 1 0%
- ... 49 48%
Automatic GC 44 43%
- after-find-file 4 3%
- run-hooks 4 3%
- vc-refresh-state 4 3%
- vc-backend 4 3%
- vc-registered 4 3%
- mapc 4 3%
- #<compiled 0xe48ec19ff1> 4 3%
- vc-call-backend 4 3%
- apply 4 3%
- vc-git-registered 4 3%
- vc-git--out-ok 4 3%
- apply 4 3%
- vc-git--call 4 3%
- apply 4 3%
- process-file 4 3%
apply 4 3%
- minibuffer-complete 1 0%
- completion-in-region 1 0%
- completion--in-region 1 0%
- #<compiled 0xe49fad1be5> 1 0%
- apply 1 0%
- #<compiled 0xe4acc98035> 1 0%
- completion--in-region-1 1 0%
- completion--do-completion 1 0%
- completion-try-completion 1 0%
- completion--nth-completion 1 0%
- completion--some 1 0%
- #<compiled 0xe4a8d497dd> 1 0%
- completion-basic-try-completion 1 0%
- try-completion 1 0%
- #<compiled 0xe4accb70af> 1 0%
complete-with-action 1 0%
--8<---------------cut here---------------end--------------->8---
I tried to reduce my init.el as much as possible: I started with
-Q and executed this and were able to reproduce it with this:
--8<---------------cut here---------------start------------->8---
(require 'package)
(package-initialize)
(add-to-list 'package-archives
'("melpa" . "http://melpa.org/packages/") t)
(when (not (package-installed-p 'use-package))
(package-refresh-contents)
(package-install 'use-package))
(require 'org)
(setq org-agenda-files
orgfile list... )
(require 'org-ref)
(setq reftex-default-bibliography
'("bib"))
(setq
bibtex-completion-bibliography
"bib"
bibtex-completion-library-path
"literature"
bibtex-completion-notes-path
"notes"
)
(setq
org-ref-bibliography-notes "notes.org"
org-ref-default-bibliography
'("bib")
org-ref-pdf-directory
"bib")
--8<---------------cut here---------------end--------------->8---
Other observation: when I am starting emacs with "-nw" (no GUI),
"Edit Notes" seems to work as expected and opens a new file as
expected.
I have re-installed all packages with MELPA.
Has anyone seen a similar problem?
How can I further debug and analyze this to present a better
error report?
Thanks a lot,
Christian
^ permalink raw reply [flat|nested] 3+ messages in thread* Re: org-ref / Edit notes problem
2021-03-19 13:58 org-ref / Edit notes problem Christian Barthel
@ 2021-03-19 21:11 ` Christian Barthel
2021-03-20 12:51 ` yank freeze (org-ref / Edit notes problem) Maxim Nikulin
0 siblings, 1 reply; 3+ messages in thread
From: Christian Barthel @ 2021-03-19 21:11 UTC (permalink / raw)
To: emacs-orgmode
Christian Barthel writes:
> I am using Emacs 27.1 on OpenBSD 6.8 and org-ref
> (20210315.1730). When I am trying to Edit notes on an existing
> org-ref entry ([f9] Edit Notes), emacs stops working and hangs.
>
> By some observation, I saw that emacs is consuming a lot of
[..]
> Other observation: when I am starting emacs with "-nw" (no GUI),
> "Edit Notes" seems to work as expected and opens a new file as
> expected.
OK, I guess I found a solution: I have had a similar issue with
org-capture were emacs freezed as well. However, org-capture did
work in xterm and I thought about some weird usage of the X11
clipboard manager. After doing some more research, I found [1].
According to Daimrod's Blog, the workaround is:
(setq x-selection-timeout 10)
This seems to work for org-ref as well as org-capture.
[1] https://www.omecha.info/blog/org-capture-freezes-emacs.html
--
Christian Barthel <bch@online.de>
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: yank freeze (org-ref / Edit notes problem)
2021-03-19 21:11 ` Christian Barthel
@ 2021-03-20 12:51 ` Maxim Nikulin
0 siblings, 0 replies; 3+ messages in thread
From: Maxim Nikulin @ 2021-03-20 12:51 UTC (permalink / raw)
To: emacs-orgmode
On 20/03/2021 04:11, Christian Barthel wrote:
>
> OK, I guess I found a solution: I have had a similar issue with
> org-capture were emacs freezed as well. However, org-capture did
> work in xterm and I thought about some weird usage of the X11
> clipboard manager. After doing some more research, I found [1].
> According to Daimrod's Blog, the workaround is:
>
> (setq x-selection-timeout 10)
Accordingly to emacs bug tracker your problem was fixed 5 years ago:
https://debbugs.gnu.org/cgi/bugreport.cgi?bug=16737
Yank causes hang
I saw hangs trying to paste from X clipboard but I decided that
conditions were quite exotic. I experimented with running browser as
untrusted X client. Firefox was unhappy, emacs (running as usual)
started to eat CPU on attempt to yank text copied from browser. Since I
was unsure what selection operations are not allowed to untrusted X
clients, I decided to just give up. However I believe that emacs could
behave better in such cases.
If you have steps to reproduce, you could file a new bug.
^ permalink raw reply [flat|nested] 3+ messages in thread
end of thread, other threads:[~2021-03-20 12:54 UTC | newest]
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2021-03-19 13:58 org-ref / Edit notes problem Christian Barthel
2021-03-19 21:11 ` Christian Barthel
2021-03-20 12:51 ` yank freeze (org-ref / Edit notes problem) Maxim Nikulin
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