From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id qMvVH0GuVGBAAwAA0tVLHw (envelope-from ) for ; Fri, 19 Mar 2021 13:59:29 +0000 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id DgaWG0GuVGDiGAAAB5/wlQ (envelope-from ) for ; Fri, 19 Mar 2021 13:59:29 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id BCB792DA31 for ; Fri, 19 Mar 2021 14:59:28 +0100 (CET) Received: from localhost ([::1]:40772 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1lNFex-0007ZT-S8 for larch@yhetil.org; Fri, 19 Mar 2021 09:59:27 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40978) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lNFeQ-0007WT-RK for emacs-orgmode@gnu.org; Fri, 19 Mar 2021 09:58:54 -0400 Received: from mout.kundenserver.de ([212.227.17.24]:34075) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lNFeN-00056T-7N for emacs-orgmode@gnu.org; Fri, 19 Mar 2021 09:58:54 -0400 Received: from t480.onfire.org ([84.189.147.49]) by mrelayeu.kundenserver.de (mreue108 [212.227.15.183]) with ESMTPSA (Nemesis) id 1M5fQq-1lLbkj0f1u-007Hm9 for ; Fri, 19 Mar 2021 14:58:47 +0100 From: Christian Barthel To: emacs-orgmode@gnu.org Subject: org-ref / Edit notes problem Date: Fri, 19 Mar 2021 14:58:45 +0100 Message-ID: <87o8fftfca.fsf@t480.onfire.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (berkeley-unix) MIME-Version: 1.0 Content-Type: text/plain X-Provags-ID: V03:K1:IN8ErHRixPDyXjnzCryLWgHEjsDHYCtY4f/8IN029VFfkpJxRQM FsOfcAuLuVKyA7ERg6394zxER7AI9BUoqqEDtSqt/bKyAdkCQSipxKoe9k8MXqGkVUkwHTO ffbGZMWE3gEBwGxcKHAvntZZ5lnCeUdDbyhLMNztEGWrKJJZIvBDe0syi3IQZAtFAeaM/Xa nyGTvouaF6lJwkZYvu8CA== X-UI-Out-Filterresults: notjunk:1;V03:K0:tHTDB4EvQs8=:LFmDrVI3Bs4N8b4C+pdSg6 yWZxqsCFq3J+Ku7iUyDPujdFi8sqSUUqA3dX+TDhwJT5H344EVtSgAw3DfY3EiEDOJ9aE8bXM PyEg6zwYqaDkv+KPQnAbFcbmV8wkf4Y45T8pzgrW8F04fXkS8Wr8fclFy2yD/O4pV5cmXWAna 2EEwmMUmZEGmzXgptjx6O4auzivvogDQaKuxnqZy/Fu9Emli502Gf1aAeA3o0Q325/lLbNBCJ X7a8mzSuK4ypRp9asyGk/WoJyD1RhQLuONf7OUH1dQOBGYm2lELBBxLNvbMA9njSavuZK+5PB rQTySg142+GJs8Ou9AbAlkaHq7tAOB+mExm78QH5h6yGXl1I6z9R0ZQ8IHF6c09OhOE/0czSk 4KlaNzm8+G+MnOK2oEkH1XpeRUotHdy4ecjSG75ufrdx006GjHwZixGkGiWSw Received-SPF: pass client-ip=212.227.17.24; envelope-from=bch@online.de; helo=mout.kundenserver.de X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: emacs-orgmode@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+larch=yhetil.org@gnu.org Sender: "Emacs-orgmode" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1616162368; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:mime-version:mime-version: content-type:content-type:list-id:list-help:list-unsubscribe: list-subscribe:list-post; bh=mvAGGRbYNOeOX/tocH81f1SRtlgj9y7MMeP9ID+Bu6Q=; b=HcJARebxPLVCJCCVbXlQa+L1qygfFazd9brw/6bvrvYtthwJLDGlyPiYuV6NaE3gHWV2GI sP19pSufPDqisufYbx+wg5KTxQNUIzYzrgW1JTy0soGKle0sigPZ4gI0HkLaxSBPURbnV6 93ScrBH66QP3lcUNn+HCZsnu0f51hcMmr41mCzE6duGITgYr4bgxbSS86pQxGGLxqE8Bwt YOTC1GrPR6Ex9uQ6KnwmWWtjiuTOE0vtZk1/5XYYV8CAmCqUQwh4pelyDMvzxq2IMMLfqB yMMzoiyJtNk6/vdcbyEqulbSuzeLHBEBcwGzlyTnPhNovEOQUMqbyUHdSIJCWQ== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1616162368; a=rsa-sha256; cv=none; b=giVVlQtTECkKqAODH0UBR2xsU2ZpO3qUGtQOAuj042ya/6nJTozlVx0UA0ogoLjCtRmOof lbA1yttoqP4RVt/Bn6DhBQ6iZfFtq3P2C16PrkSCjwW4FYFoeS0/6dVslQFIsg2kINAhCI I5XnJwQGzP+9hQ35x56Dv+e4Bd6zJO+Beslh6QRaraoa0rucyPVc8jhEGxBnuBe9UMjfaF Vupjmb02dkhm2TgE13L3csYC1ZJKOB2eLkQvffmeEG8G3/fyOaA7qRVv5PYUWntxmbG4Cj M2kmjl1SarMIW96hqWmfWXKeJV4qGhz7k6dhLXOl1LyDrfCC9+pIgBvB+p/kJg== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; spf=pass (aspmx1.migadu.com: domain of emacs-orgmode-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=emacs-orgmode-bounces@gnu.org X-Migadu-Spam-Score: -2.41 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of emacs-orgmode-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=emacs-orgmode-bounces@gnu.org X-Migadu-Queue-Id: BCB792DA31 X-Spam-Score: -2.41 X-Migadu-Scanner: scn0.migadu.com X-TUID: h1tzCcb/YmoX 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% - # 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% - # 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% - # 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% - # 1 0% - gui-backend-selection-exists-p 1 0% - apply 1 0% # 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% - # 5 4% - # 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% - # 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% - # 1 0% - apply 1 0% - # 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% - # 1 0% - completion-basic-try-completion 1 0% - try-completion 1 0% - # 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