From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp10.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id EKDyOb/ggWIECAEAbAwnHQ (envelope-from ) for ; Mon, 16 May 2022 07:27:28 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp10.migadu.com with LMTPS id iNTsOL/ggWItgQAAG6o9tA (envelope-from ) for ; Mon, 16 May 2022 07:27:27 +0200 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 7E7D215AF1 for ; Mon, 16 May 2022 07:27:27 +0200 (CEST) Received: from localhost ([::1]:57750 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nqTGQ-00037G-De for larch@yhetil.org; Mon, 16 May 2022 01:27:26 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:40364) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nqTDr-0001sx-SW for emacs-orgmode@gnu.org; Mon, 16 May 2022 01:24:47 -0400 Received: from gallois.livando.com ([31.170.109.33]:51002) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nqTDp-0005xx-VO for emacs-orgmode@gnu.org; Mon, 16 May 2022 01:24:47 -0400 X-PDA-ORIGIN: gallois.livando.com Received: (qmail 921581 invoked from network); 16 May 2022 05:24:44 -0000 Received: by simscan 1.4.0 ppid: 921564, pid: 921577, t: 0.1601s scanners: clamav: 0.103.6/m:62/d:26542 Received: from unknown (HELO ?192.168.0.77?) (christian@gladbachcity.de@95.90.192.16) by 0 with SMTP; 16 May 2022 05:24:44 -0000 Message-ID: <3b0aba2f26c9fd8d36476e660ca444c6f8df9bca.camel@gladbachcity.de> Subject: Re: Bug: ob-R.el breaks when :session is specified From: Christian Heinrich To: emacs-orgmode@gnu.org Date: Mon, 16 May 2022 07:24:43 +0200 In-Reply-To: <871qwu30a3.fsf@gmail.com> References: <877d6n2p6t.fsf@localhost> <87wnemg9ts.fsf@gmail.com> <4c9235234536450d7bece1b3043008d96da3a504.camel@gladbachcity.de> <871qwu30a3.fsf@gmail.com> Content-Type: multipart/signed; micalg="pgp-sha512"; protocol="application/pgp-signature"; boundary="=-Bd83mXrHRPViLF2Xx/P3" User-Agent: Evolution 3.42.3-1 MIME-Version: 1.0 Received-SPF: none client-ip=31.170.109.33; envelope-from=com-orgmode-mailinglist@gladbachcity.de; helo=gallois.livando.com 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, SPF_HELO_NONE=0.001, SPF_NONE=0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: emacs-orgmode@gnu.org X-Mailman-Version: 2.1.29 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 X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1652678847; 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:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post; bh=bR2Ch6KMDXYgdgiQhAzTb5EzF08mTMiNzKw5RqdEb8E=; b=Q1iYRAY/DVPtLIwwSXhLf/sSieqZSRQVu0Z+5ftPr8/SdZ2sV+jNld/uYUVi9JYoh4vohA VwEjqjC8CdAIZ+0p+hrWqBE9If5dAZhByu88G30ZKvm4z878HXh27Kp+S63GRua2Jy7nPC BsIeoti6HDLyK17krDcdPDXlhqaW3mCQpeEYMP/xQgnIQ+wrucrMg/jTrtEqT+cUHqU3pU ObU+e+ChBT0SKgsyDCCllWuPWu/56NFlcnIFqslkjUR4FC44TF/1dJBD14bOA70LUDRQH6 qzN3uPv58knI57YcwdHXSOwlXMBLwPiSwwiVkMyt/MSDsQXbVVCRU9BAduxoYg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652678847; a=rsa-sha256; cv=none; b=V3tPdbUYvzAsC+5bg9ewFfdCwrzvKK7ffEARKrtUzJcfjRmwxw8JTNKE1FrdGGy4kQV925 zN02HCWtcH/nD/H/NrKyNoI3IBH/iFheaGpT+cqSSIarnn+kCDEI1SiiLWtUHyYRahZj6o 7BffEFO8AEQmxxDHDruEwpqt9+J4VvVQSKOqzXFmtEoj23yDLq37628QFj4ifR2KWN+79z GXEZ9N+eujMWJKQ8YzmQ9NzEux853TIrBy+zeQUe4+d1uaDewPVkEbG1ItjcwTjupdWqAY TIkrOZy65cWKJEEaRt2ToV5Q8ERLm+eAW4463nyqJImW9u8lGQLxzSiUfqAbDA== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "emacs-orgmode-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="emacs-orgmode-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: -4.93 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of "emacs-orgmode-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="emacs-orgmode-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 7E7D215AF1 X-Spam-Score: -4.93 X-Migadu-Scanner: scn1.migadu.com X-TUID: NP+DZnVM5JeT --=-Bd83mXrHRPViLF2Xx/P3 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Jeremie, thank you for providing this example! The ess that was found in the load path was years old and once updated, all= issues were resolved. In fact, my so-called minimum init still used (require 'package) and I didn't = even think about ESS causing this trouble. It's now a bit clearer how to build a real minimum init - thank you! This is hence resolved. Best regards Christian On Mon, 2022-05-16 at 00:21 +0200, Jeremie Juste wrote: >=20 > Hello Christian >=20 > On Sunday, 15 May 2022 at 20:06, Christian Heinrich wrote: > > I just tested with > >=20 > > =C2=A0Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @ > > /home/heinrich/.emacs.d/straight/repos/org/lisp/) > >=20 > > using > >=20 > > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cai= ro version 1.16.0) of > > 2021- > > 11-27, modified by Debian >=20 >=20 > Many thanks for reporting back.=C2=A0 I updated to gcdbb1c and it is stil= l working fine. >=20 > My minimum working example is the following. From the org-mode root direc= tory, >=20 > $ emacs -Q -L ./lisp -l org=C2=A0 -l ~/ess-barebone.el >=20 > where ~/ess-barebone.el is the following: >=20 > #+begin_src=C2=A0 elisp > (add-to-list 'load-path "/home/djj/.emacs.d/elpa/ess-20220125.2207/") > (require 'ess-r-mode) >=20 > =C2=A0(org-babel-do-load-languages > =C2=A0=C2=A0 'org-babel-load-languages > =C2=A0=C2=A0 '((R . t))) >=20 > (setq org-confirm-babel-evaluate nil) > #+end_src >=20 > Note that I'm still using a rather old ess version. Could you please try > with the above configuration? Note that I am using a rather old ess > version but the I haven't experienced issues with the newer one. >=20 > Best regards > Jeremie >=20 >=20 > > Hi Jeremie, > >=20 > > I just tested with > >=20 > > =C2=A0Org mode version 9.5.3 (release_9.5.3-504-gcdbb1c @ > > /home/heinrich/.emacs.d/straight/repos/org/lisp/) > >=20 > > using > >=20 > > GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.30, cai= ro version 1.16.0) of > > 2021- > > 11-27, modified by Debian > >=20 > > I am on Debian Testing and that is the default emacs version. > >=20 > > Using the unmodified org (git hash from above) I get the following mess= ages when executing a src > > block with R: > >=20 > > =C2=A0=C2=A0 executing R code block... > > =C2=A0=C2=A0 Loading =E2=80=98ess-bugs-l=E2=80=99: unescaped character = literals `?(', `?)' detected, `?\(', `?\)' > > expected! > > =C2=A0=C2=A0 Type C-h m for help on ESS version 15.09 > > =C2=A0=C2=A0 ess-tracebug mode enabled > > =C2=A0=C2=A0 Quit > > =C2=A0=C2=A0 Package cl is deprecated > >=20 > > Note that the "Quit" is me pressing Ctrl-g after a few seconds. > >=20 > > Removing the commit in question makes the block return instantaneously: > >=20 > > =C2=A0=C2=A0 executing R code block... > > =C2=A0=C2=A0 Loading =E2=80=98ess-bugs-l=E2=80=99: unescaped character = literals `?(', `?)' detected, `?\(', `?\)' > > expected! > > =C2=A0=C2=A0 Type C-h m for help on ESS version 15.09 > > =C2=A0=C2=A0 ess-tracebug mode enabled > > =C2=A0=C2=A0 Code block evaluation complete. > > =C2=A0=C2=A0 Package cl is deprecated > >=20 > > I anticipated that this would not be obvious, since this feature is use= d too much to go > > unnoticed for > > two years - but I am clueless as to how I should continue with debuggin= g... > >=20 > > Thanks for your help! > > Christian > >=20 > > On Sun, 2022-05-15 at 16:16 +0200, Jeremie Juste wrote: > > >=20 > > > Hello Christian, > > >=20 > > > Thanks for reporting but I cannot reproduce the bug with the org and > > > emacs version below. > > >=20 > > > Org mode version 9.5.3 (release_9.5.3-467-g2bd34e @ > > > /home/djj/src/org-mode/lisp/) > > > GNU Emacs 27.2 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.24) o= f > > > 2022-01-16 > > >=20 > > > Can you please let me know which version of org-mode you are actually > > > using? > > >=20 > > > Ihor, many thanks for checking. > > >=20 > > > Best regards, > > > Jeremie > > >=20 > > > On Sunday, 15 May 2022 at 16:08, Ihor Radchenko wrote: > > > > Christian Heinrich writes= : > > > >=20 > > > > > I got back to an org file after upgrading to the latest release o= f org-mode and tried > > > > > executing the > > > > > contained R source blocks. Unfortunately, emacs got stuck in the = execution and was > > > > > blocked; I > > > > > had to > > > > > exit using C-g. > > > > >=20 > > > > > Here's a minimal example src block that causes emacs to get stuck= : > > > > >=20 > > > > > #+begin_src R :results output :session *R* :exports both > > > > > =C2=A0 a <- 10 > > > > > =C2=A0 a > > > > > #+end_src > > > > >=20 > > > > > R itself does start and the code is also executed correctly. Howe= ver, the output from that > > > > > session > > > > > is apparently not returned to emacs or the buffer. > > > >=20 > > > > I tried you example using Emacs >=3D26 and it works just fine. > > > >=20 > > > > Best, > > > > Ihor >=20 --=-Bd83mXrHRPViLF2Xx/P3 Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEE+9lGLw1S8YBUC27di84V01FvzDwFAmKB4BsACgkQi84V01Fv zDx+uw//UZdD6K6/Pp1/93D1Hz4NgcKD0OjXX/x22wAl6Oc2J32yZ8j5bXoo6dys 6SJL879VDzIhWxMhZM+MnWzkorxv7qYgVYXsjUM+CeY3IuavVHmk0P9eTg3gj+Ef N3+/iFB+++TTSp0VtLTbQzNZJPMF1m0kOwBBJ89FJGIiGFD02s9FizOvIlv6PoZ9 AJSYJDY/iZsx6bi7biizDBn7V32yfdnQw5lTdZqjw9y66+WMvjb8OdlfGqS+bPWv Fy4S7t3dHRaepnmK21djX7SJtk6+Sj4wlzVgsYqGPDSPq5nZ6H51MgWIMfa/EPS5 iQzTr6gnsIr/TPadn2LV+ZAqZBNCscDkax9QXxhYKVimHcMPkZIjma5nGGTj1ZIx /qCtoll7WkDTFT5LtFZ6xTC7y2n9/yTF1N+QCmXlXIUFTuTMlq6WNd7zSgelAfId ygJ75k4X+EPRcvypwsL6sE6Lv094tA0kMymnMOoPFp9cE/CmA5IYjpLWoM2clqtf fBcX7bjuibZUj9PGhmzjUAuO4oEjl1emsKKZ/tmS2Wpud2unEmMFbsXQK0EmDT98 oEeKZ1ykhpx/75Pt7IgIPhxVMMOn/cCsnxdpC917RC96Bc8l6M+BLinRWwtGYq/9 JPpybwCSaaJDzE6INaOlq3pq3WN0ZkVVIb0SPps2A0JM5pX9aiA= =KHpC -----END PGP SIGNATURE----- --=-Bd83mXrHRPViLF2Xx/P3--