From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.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 qDiSD1EaiWNsXwAAbAwnHQ (envelope-from ) for ; Thu, 01 Dec 2022 22:19:13 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id QOZqD1EaiWPZIgEAauVa8A (envelope-from ) for ; Thu, 01 Dec 2022 22:19:13 +0100 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 0F2BFFA19 for ; Thu, 1 Dec 2022 22:19:13 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p0qwr-0001uT-5X; Thu, 01 Dec 2022 16:18:25 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p0qwi-0001u7-Cz for emacs-orgmode@gnu.org; Thu, 01 Dec 2022 16:18:17 -0500 Received: from mx0a-00395d01.pphosted.com ([148.163.133.170]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p0qwf-00048q-Ee for emacs-orgmode@gnu.org; Thu, 01 Dec 2022 16:18:16 -0500 Received: from pps.filterd (m0173170.ppops.net [127.0.0.1]) by mx0a-00395d01.pphosted.com (8.17.1.19/8.17.1.19) with ESMTP id 2B1Kpcl8023194; Thu, 1 Dec 2022 13:18:05 -0800 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=ucsd.edu; h=from : to : cc : subject : date : message-id : references : in-reply-to : content-type : content-id : content-transfer-encoding : mime-version; s=campus; bh=09IfYByu0IjAf5GgAY97YMF2UmckNxxIfhHS9drWVQc=; b=hzEZtIo2uajgMFAMvHh2Xd/ChLnrNPGTtf41ckfpI5d4YnOEvk3jl7Mm0KBIqndAMpgg R5/RUeHQ0aqZoBcXSCKj6i9zFB//pChmccBv3NBspZdavEXJx3IlHkwMkP0qE4PhCtLc cLTNIrgdJMP+D1mVcRu2HWy91JH4KLJZg8oRNpDtVXS+Bb+IFVUIrgEUm33uKg2lkXTd hnz7AWPo2X843YCSn7aScRxdnhaD3Ded9PqHxZk5+f/5o5t+tvOHO9fwybmsam8tpIhT jC2+pDhiSprz0OG6eXg4tfW/l1yL+pICxKRdx3md7+d6SnzfpBEEA3Ii3Wg0TRC/CP/8 Cg== Received: from secdlpezp03.ucsd.edu ([40.112.251.180]) by mx0a-00395d01.pphosted.com (PPS) with ESMTPS id 3m73nyr26r-1 (version=TLSv1.2 cipher=ECDHE-RSA-AES256-GCM-SHA384 bits=256 verify=NOT); Thu, 01 Dec 2022 13:18:05 -0800 ARC-Seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=jPNAArB7L8rcbJ9UDFOP0RMKILLbBb6SmGaA/MSXAPZ2FkbP9UEl1KGtsZbEzlMCmVcb35v42El293r7o9bxZZJL2pGfEM5QcEgfDgZtKDkkrgJIHLQivvoc2O08VeQ3J1j1qjWBWDLoxFGMWc6Ldri2GhKIcdI0PDbh51s7NTb5KL926c6wlFXtUepI8hVESkTA4jUZgOoKopP06k9n//PzuWYxfCQvPd8du4Ml5AclknHeAwqhQNMvgnCKGjDQn8bNEMi+GIir8buFt8I4+dJa3Qiies9I4CtbvxZL0BVyS8EoAmNYsQhqlScOI80XK7B8VbJQmiz7LXPOlg9sfQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-AntiSpam-MessageData-ChunkCount:X-MS-Exchange-AntiSpam-MessageData-0:X-MS-Exchange-AntiSpam-MessageData-1; bh=09IfYByu0IjAf5GgAY97YMF2UmckNxxIfhHS9drWVQc=; b=MuGlkWYYpLPcqSVwzSxBGE/kJjZjl6gdZkbrZcYA584p6gLp/zmgIfuB2Ju93Uqt9KxrrAV5jb6YvsoBe1HFUHU+7HpCG+ZsIhbaB7EMtKe0y/QTVUk4ut0FvqfDf/t4h7YBDjOglRjBEIYimVdjsQ4xgWHAjJ8QlXr3B9ZZ10tN6mKRtfgLOxH4mZTsUSzWrkNlt9v2Zx8XJENy3cRjmlblazT2BI5GYZ/dKygAElnbpPfJqJ0PeJd48Sx6L1YQhClRzSmpAkTUgMpB0o0p0YRHQcjdABtoKWB57IFy9lt+XRWTot06t0tzz4Lr/3P7bnyQuTbQMzWq2mv9SkJw5g== ARC-Authentication-Results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=health.ucsd.edu; dmarc=pass action=none header.from=health.ucsd.edu; dkim=pass header.d=health.ucsd.edu; arc=none DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=ucsdhs.onmicrosoft.com; s=selector2-ucsdhs-onmicrosoft-com; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=09IfYByu0IjAf5GgAY97YMF2UmckNxxIfhHS9drWVQc=; b=Hl4nqHMGXybBB7s3uFixl41WTqWopumeKKvvT4iICAzfUWV/QysK3pwx569jEyc/EB4fKY9fDLpMZ6lKorrimH90iZH4JqVUlCdW56rytxlHcOwHWgyUDI7t3I+tm8cXLPuTYqwZh/gRHtkUAPApGwQRxegICoGP6T01oCRZYe8= From: "Berry, Charles" To: Ihor Radchenko CC: William Denton , =?iso-8859-1?Q?Fr=E9d=E9ric_Santos?= , "emacs-orgmode@gnu.org" Subject: Re: [BUG] ob-R: session evaluation returns empty ouputs with Org 9.6 [9.6 ( @ /home/fsantos/.emacs.d/elpa/org-9.6/)] Thread-Topic: [BUG] ob-R: session evaluation returns empty ouputs with Org 9.6 [9.6 ( @ /home/fsantos/.emacs.d/elpa/org-9.6/)] Thread-Index: AQHZBcplTMToJYKpi0a6GXPHfTIfWw== Date: Thu, 1 Dec 2022 21:18:02 +0000 Message-ID: <68952C61-AD16-4863-BB46-24ECDA46AE8C@health.ucsd.edu> References: <877czca7oj.fsf@u-bordeaux.fr> <87y1rr1xpc.fsf@localhost> <87fsdzuc61.fsf@localhost> In-Reply-To: <87fsdzuc61.fsf@localhost> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-ms-publictraffictype: Email x-ms-traffictypediagnostic: BYAPR19MB2581:EE_|BL3PR19MB6538:EE_ x-ms-office365-filtering-correlation-id: 01d2389a-5114-4ca9-1780-08dad3e187f2 x-ms-exchange-senderadcheck: 1 x-ms-exchange-antispam-relay: 0 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255; CTRY:; LANG:en; SCL:1; SRV:; IPV:NLI; SFV:NSPM; H:BYAPR19MB2581.namprd19.prod.outlook.com; PTR:; CAT:NONE; SFS:(13230022)(4636009)(376002)(136003)(396003)(39860400002)(366004)(346002)(451199015)(6506007)(71200400001)(53546011)(186003)(2616005)(6512007)(8936002)(54906003)(66556008)(122000001)(64756008)(6486002)(66476007)(66446008)(6916009)(33656002)(75432002)(8676002)(4326008)(86362001)(83380400001)(786003)(38100700002)(316002)(66946007)(38070700005)(76116006)(2906002)(478600001)(41300700001)(41320700001)(5660300002)(45980500001); DIR:OUT; SFP:1102; x-ms-exchange-antispam-messagedata-chunkcount: 1 x-ms-exchange-antispam-messagedata-0: =?iso-8859-1?Q?ssMw4Vyh9kYppFzBfaHXMB5ahACUXpEHgAH41Mvz2t0Gl67+mnalJ9VtXD?= =?iso-8859-1?Q?kcrrJAObn73FEKSM4w+CveI8sqkYFZYj/5tLaohjZEEGDNQnxohLf4N57B?= =?iso-8859-1?Q?pCj+Aq5tJ64xXKIEPOEEVrBqu5DrahOGJjrgJindeXkdb/S1Mkvlbh50/7?= =?iso-8859-1?Q?ZU7F6tXksxCz52Kj/Qi4sIhicQVLAS1dLuTLG5saDO/FuPo3KixOMTpAgC?= =?iso-8859-1?Q?zZXtzwudEST4ZKREOyWwdMqXed+IFHk/bS9v+8SZwi8qElz6q/3mqCiYAb?= =?iso-8859-1?Q?ff5/p8Cy2OiriIxtrnzyYAJ7T5jb1an8vID03yI6otJl6jPlQuhAWniLJy?= =?iso-8859-1?Q?wQnNT1XIRSGJBALi6rNVwvwrvXDFR/ofg9MvLiC6Oc01CU7bAIIT96cFQV?= =?iso-8859-1?Q?4D2lmZ5xViW1uYcPQMUqKNKVaPwHCucNsEC94KCdIyDZRBxzqfzuBTy5gM?= =?iso-8859-1?Q?yUwYRKQAMl+hBAyJp3fpZyTOHdBuRU3U4ciqmNgGXyQ7E0X2XE35Fc01ND?= =?iso-8859-1?Q?eubsfDuZLQXNNsP+8U3M8ftdPSpuveQuac72058wlWwwFd5M0faEV0qzHb?= =?iso-8859-1?Q?AU8Xt+VMPScIzNO/g+iiVBKE+3pZIWTeQ+R/C5++ru78iux+Q+729R3ye8?= =?iso-8859-1?Q?wOrLIXjNv2oUnwc5W0nA7NZHjyNocnZXE2RnBvPVvwC68fk5xDJxOdmfYF?= =?iso-8859-1?Q?D9NMn/+IcAMhLPakIEUcOb1fURquJZpucNsR+7N+BG8AKOEQAfhccfhwbK?= =?iso-8859-1?Q?4/TGyaisZYmuNQA+RtsQOe/5nhagPdrvYaKT446WcYBeAQhtGA7d40pW2p?= =?iso-8859-1?Q?XmSYqg2w0ssAR57uHk479LVeMI60o/3q4fGBmcQESbXtX6HOzvBKkoht7S?= =?iso-8859-1?Q?ZUNW3iuEhau8j6uz4kiI8Afh5//8gDLMvSei1hct2bn0vGKG3SPKSi8p/r?= =?iso-8859-1?Q?MLWzeF1XyD8CUFQ6eW/m7MVGX4e42FBctqVGSHmx3yWQ77aS0k2ZmZv6Y9?= =?iso-8859-1?Q?FH1cZLDfy/gX/c4AXNX3U//DLy5Z0MdRt4wRInbzUDz3NoCIukSivHNaYl?= =?iso-8859-1?Q?F8dtr2XcM7HTR+TzCmO+jaDrd7uCXNQM1WSaG6SDIhCUxkhOTaKO+MzSyy?= =?iso-8859-1?Q?F2XrW1YCzyk2uXkH7SJFZW7+lteqpShKViuNAB0iO/j4efShAnfd3JyqRU?= =?iso-8859-1?Q?VUc8lC+4jDaC2rKtQz1Q+zwWlh50xRcuhfo+g7peh3+5HwevPPpIHsRKSl?= =?iso-8859-1?Q?hzJ7uIsfdyTZFm4SpCpfZ6ff17sMCreCPhSiK3sTUbUIkMWHH65+PKcJlh?= =?iso-8859-1?Q?tFmSbtbovVqGXwG8L6X4JafuV2mD4hwZZv+A4p2bV00JyxdAgAxAMPcJKj?= =?iso-8859-1?Q?hH3vhG4YYwDKuTHOYpAgPx3YdZMVA4zjC1fSQrKDS2TdBGg6Bx6wXaQkRO?= =?iso-8859-1?Q?PhDUzy4XzxHk1SUt0+0O0Mt8HFhPoSpA8u05PlthYwWGGOdVd9rn7csJMu?= =?iso-8859-1?Q?EYBh0mjLR7EKVeBuMT/DprLQ+Yo6De9fRtX3PG/4USkCLzlf7miky+oZ+j?= =?iso-8859-1?Q?zY6xjgTYKiAONvbRq/M8GZt14yLLYl8t1MQ+xxbMLCSmfAiHt9dS8zlv89?= =?iso-8859-1?Q?R0Rsgu6Nr2dO+3zg5Qaeu+4dzaa0DLUalGVA+f890pIoCa3uvRNkpG/guh?= =?iso-8859-1?Q?oEXd0OXeVZaSGsW7csG+yssbBrKhdtggfQfjAzk8aFD2M9q0E4leBgj11G?= =?iso-8859-1?Q?sX6w=3D=3D?= Content-Type: text/plain; charset="iso-8859-1" Content-ID: <331DCAAB1F71FE41AFF0D81701DC5B1C@namprd19.prod.outlook.com> Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-MS-Exchange-AntiSpam-ExternalHop-MessageData-ChunkCount: 1 X-MS-Exchange-AntiSpam-ExternalHop-MessageData-0: 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 X-OriginatorOrg: health.ucsd.edu X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: BYAPR19MB2581.namprd19.prod.outlook.com X-MS-Exchange-CrossTenant-Network-Message-Id: 01d2389a-5114-4ca9-1780-08dad3e187f2 X-MS-Exchange-CrossTenant-originalarrivaltime: 01 Dec 2022 21:18:02.7613 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: e470d736-e7f7-41a8-8eab-dad544b2b579 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: L5k9KFSP8cewniVfmSwRQd7GGygXufZVvvMHbq2f3MROU38yyPAvbjxBBNyOCBRcPv5TtG0Jq8cL3Lb7dpaSOg== X-MS-Exchange-Transport-CrossTenantHeadersStamped: BL3PR19MB6538 X-Proofpoint-GUID: 2lZeQlZzF6P-xwSo_L1sCX63IPE6yOXR X-Proofpoint-ORIG-GUID: 2lZeQlZzF6P-xwSo_L1sCX63IPE6yOXR X-Proofpoint-Virus-Version: vendor=baseguard engine=ICAP:2.0.219,Aquarius:18.0.923,Hydra:6.0.545,FMLib:17.11.122.1 definitions=2022-12-01_14,2022-12-01_01,2022-06-22_01 X-Proofpoint-Spam-Details: rule=outbound_notspam policy=outbound score=0 lowpriorityscore=0 clxscore=1011 bulkscore=0 mlxlogscore=999 adultscore=0 suspectscore=0 phishscore=0 priorityscore=1501 impostorscore=0 mlxscore=0 spamscore=0 malwarescore=0 classifier=spam adjust=0 reason=mlx scancount=1 engine=8.12.0-2210170000 definitions=main-2212010163 Received-SPF: pass client-ip=148.163.133.170; envelope-from=ccberry@health.ucsd.edu; helo=mx0a-00395d01.pphosted.com X-Spam_score_int: -19 X-Spam_score: -2.0 X-Spam_bar: -- X-Spam_report: (-2.0 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_EF=-0.1, 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: 2.1.29 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-bounces+larch=yhetil.org@gnu.org X-TUID: /VIncdZhLngn > On Nov 30, 2022, at 5:48 PM, Ihor Radchenko wrote: >=20 > William Denton writes: >=20 >> I tried that, but it didn't fix it. :( >=20 > Ok. I was able to reproduce on my side. >=20 >> With a minimal setup, running the R block with a :session makes it ask w= here the=20 >> working directory should be (the default in the prompt is the directory = the test=20 >> Org file is in). Setting ess-startup-directory to 'default-directory do= esn't=20 >> change that, or the output problem. >=20 > It looks like there is something wrong with comint-prompt-regexp in R > buffers. It somehow does not match the prompt. >=20 > I will need to look further. >=20 The older (commit bed47b437d8cde7a98bafdb07996e248b40f70e6e) version of org= -babel-comint-with-output used comint-prompt-regexp and works fine. I don't really follow how `org-babel-comint-prompt-separator` gets set to s= omething useful in the current version.=20 Reverting org-babel-comint-with-output to that older commit (and eval-ing t= he defun for org-babel-R-evaluate-session) seems to fix this case for those= who need `:results output` in R src blocks till this gets sorted out. HTH, Chuck=