From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id 6AcpAEZlSV+bFQAA0tVLHw (envelope-from ) for ; Fri, 28 Aug 2020 20:12:54 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id dgyfN0VlSV8HDQAA1q6Kng (envelope-from ) for ; Fri, 28 Aug 2020 20:12:53 +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 743879403A9 for ; Fri, 28 Aug 2020 20:12:53 +0000 (UTC) Received: from localhost ([::1]:58222 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kBkjz-00022P-Dd for larch@yhetil.org; Fri, 28 Aug 2020 16:12:51 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:52436) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kBkjb-000229-B1 for emacs-orgmode@gnu.org; Fri, 28 Aug 2020 16:12:27 -0400 Received: from aibo.runbox.com ([91.220.196.211]:34748) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kBkjZ-0001hi-4u for emacs-orgmode@gnu.org; Fri, 28 Aug 2020 16:12:27 -0400 Received: from [10.9.9.73] (helo=submission02.runbox) by mailtransmit03.runbox with esmtp (Exim 4.86_2) (envelope-from ) id 1kBkjQ-0006Dj-O2 for emacs-orgmode@gnu.org; Fri, 28 Aug 2020 22:12:16 +0200 Received: by submission02.runbox with esmtpsa [Authenticated alias (611856)] (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) id 1kBkj7-0002vU-6p for emacs-orgmode@gnu.org; Fri, 28 Aug 2020 22:11:57 +0200 User-agent: mu4e 1.4.3; emacs 26.3 From: Dylan Schwilk To: emacs-orgmode@gnu.org Subject: Help debugging R source code block output problem with :session Date: Fri, 28 Aug 2020 15:11:55 -0500 Message-ID: <87r1rqled0.fsf@havana> MIME-Version: 1.0 Content-Type: text/plain; format=flowed Received-SPF: pass client-ip=91.220.196.211; envelope-from=dylan@schwilk.org; helo=aibo.runbox.com X-detected-operating-system: by eggs.gnu.org: First seen = 2020/08/28 16:12:17 X-ACL-Warn: Detected OS = ??? X-Spam_score_int: -25 X-Spam_score: -2.6 X-Spam_bar: -- X-Spam_report: (-2.6 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H3=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, T_SPF_PERMERROR=0.01 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-Scanner: scn0 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-Spam-Score: -0.51 X-TUID: QWw5nTuWhdhF I returned to an org file this week and found that I am getting some strange source code block output for R code when I use the :session header. I have been able to duplicate this with a minimal init file. I strongly suspect it is some problem at my end but perhaps folks here can help me know here to look? It occurs with a minimal emacs initialization. First, here is a small org file example of the problem. In the second results block the ">" appears to be treated as a prompt line to strip from output but only when a session is started. This happens with any ">" in output when the :session header occurs. the problem is dramatic when printing tibbles where the column modes are enclosed in angle brackets. test.org >>> ** Test org babel R output prompt problem #+begin_src R :results output print(" ") print("one three") print("end") #+end_src #+RESULTS: : [1] " " : [1] "one three" : [1] "end" #+begin_src R :results output :session "NEW" print(" ") print("one three") print("end") #+end_src #+RESULTS: : [1] "< : < : " : [1] "one < : three" : [1] "end" <<< The second block produces the bad output. This occurs with a minimal setup. I start emacs with > emacs -Q -l "~/debugorg.el" where debugorg.el is: >> require 'package) add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/") t) add-to-list 'package-archives '("org" . "https://orgmode.org/elpa/") t) package-initialize) require 'ess-site) (org-babel-do-load-languages 'org-babel-load-languages '((R . t))) << emacs version 26.3 org-mode version 9.3.7 ess version 18.10.3snapshot --