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(christian@gladbachcity.de@95.90.192.16) by 0 with SMTP; 16 May 2022 05:23:38 -0000 Message-ID: Subject: Re: Bug: ob-R.el breaks when :session is specified From: Christian Heinrich To: emacs-orgmode@gnu.org Date: Mon, 16 May 2022 07:23:38 +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="=-6Zg36bYI/PpDAdXqjSa3" User-Agent: Evolution 3.42.3-1 MIME-Version: 1.0 Received-SPF: none client-ip=31.170.109.33; envelope-from=christian@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=1652678700; 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=hbE+nArzUT/6m1rMiHB2Nb4af1puyHfmfOh8HWW16Vg=; b=AhUtbltf9774MAqp8IBykhNuXdfY3Mvq8ckZmZz6710zRLC8Mt4guSDE+pSAauS54sFgzk eRceln5txPBIQs4hAXdrk58rB3nzK0FodglorQJQhol4irgqgsUh2KBb4E9Gpvwm8EaEdd moenvR1vlLshBQOwsR8cJa5xRhLz6hsf/469Jp9eGQEurAmKjZ8Ciu/btPVithDtcP+nRS 4xEBC68BjcIxstI1gD1PDk5VEhf18wyXhPmtqW+ZjECnLIicUcJkb64gJBMe+/WpcSVf6L byFt5K1mnRz9QjGuFoKudefY9QULuzWxcAToZMXkI+1NVJsoTTDOWwzkWot61g== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1652678700; a=rsa-sha256; cv=none; b=G7jCzuft57aAxbW5BD43QYPHkkx6cBUTiCh7MU7MTJjPwAwK1xKDye3D+v5Xi8AZkd9JmC pVBNSYCtWXw6O9/jIIo0v96ALdlCRbyRBeO+dvapIrjnwWeuZHU4V2BRbxspYVxYb3Cxry yvoOgrlU5XQ/600hrIqqT7CvkuSWfDOtoNADcKRm40h6W2nBTGLk4WTm61UkON+hUiIX6Z IqhUSDG9HoTdZ881QL8XdkvHSufOzmBfocUpQrCxFInrVtJutEG1oKJVFVjMt8v+0XOMd8 sHwlZrbgLCXKx3Hl2nyL0IKu9cW6z87gF4t+zatdplhInq+u8fUsX9EvEG7Ptg== 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: 36A15159F7 X-Spam-Score: -4.93 X-Migadu-Scanner: scn1.migadu.com X-TUID: QLAVjsUIGjst --=-6Zg36bYI/PpDAdXqjSa3 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 --=-6Zg36bYI/PpDAdXqjSa3 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+9lGLw1S8YBUC27di84V01FvzDwFAmKB39oACgkQi84V01Fv zDwgtA/8Dbwmy8Df6x+pK8GyZlKNczeVaHK95iDv/YOP7RV42prHfGAcYJOse8ne ux+kNC8AQKI57B5HGUtL3UJ75nU/FBOQSxls9ssjCOwhfu4UXxE/F3wdmIgdKf26 uRWY9x7JpGMWqWnFt2jFmbfnWYPSQfok9oGz3hNdjaZ/LicXilo2D7vpIG0G2rRE tLApFHB8677xFPOfL2Hxz3Wr3hGt8Txops2eKi3YnpyUopMy0XFFoL/otJxwaJbN UXrJZSgGiXCMgRg/PpVijodbTincmfq7qW2qise1xGTzyhU8vRN90ubCk2hpGdZD 0NylyzOpkafemRa/b35zUdks7RtgiWkDKDy9O1tSZ1DZTwUIBdBCJKq1MrVCL+g+ VzGNftDhY6bAWQkzo2fN2TnjYU6AG+UNwc6J1vr7E1LxlweRdbURIBMnqmNkVNMw nyf1FYuRSzhY55Lqrxzgq5vWTPX9YVRhca4IOIIugTKTSJHxINdKxA8QY4Ko94YT lMC4JBQuG3Akd8jb56gKSD1QTTKK66R4sixpIpzKP3ADU9QQPuR/t8E/sDrfmMIL /ahbQMq4cPFwqDov3O+PS8tC4LdAPnS/yP0y+0SnDTFG13lB5goYefKqjR4GkCs+ csXw2N3Bc5Er2H0DTkVZLbr4CaAo+HrvrBHjri3RHn7OSJq1/KA= =Kjep -----END PGP SIGNATURE----- --=-6Zg36bYI/PpDAdXqjSa3--