From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Cook, Malcolm" Subject: BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session over aggressively performs "; ; cleanup extra prompts left in output" and a possible workaround Date: Thu, 1 Oct 2015 19:59:15 +0000 Message-ID: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Return-path: Content-Language: en-US List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: r-devel-bounces@r-project.org Sender: "R-devel" To: "emacs-orgmode@gnu.org" Cc: "bioc-devel@r-project.org" , "r-devel@r-project.org" List-Id: emacs-orgmode.gnu.org Hello , I am not sure what the best solution is, but, in my hands using Org-mode version 8.3.2-elpa org-20150929 the reg-expt used to "cleanup extra prompts left in output" is over-aggressive and will trim session :output at lines consisting exclusively of blanks and periods such as produced when printing a BioConductor 'Views' object which wants to appear as #+RESULTS: #+begin_example Views on a 23011544-letter DNAString subject subject: CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATA...TATCTTTCAAATTTTGATGACCCCCACTAGCAAAAAATGCGAAAATTAACCCAAATAATGATTTCCCTAAATCCTTCCAAAAGTAAATATTAACTTTTTGGCAAAATCCATTTTCCCAAATTTCGGTCATTAAATAATCAGTTTTTTGCCACAACTTTTAAAATAATTGTCTGAAAATGGAATGTCATATCTCGATGAGCTCATAATTAAATTTACAATCAAACTGTGTTCGAAAAAGAGAAAACTAACATTTTTTTGGCATATTTGCAAATTTTGATGAACCCCCCTTTCAAA views: start end width [1] 344766 344773 8 [CATGAGGC] [2] 563564 563571 8 [CATGAGGC] [3] 641027 641034 8 [CATGAGGC] [4] 656168 656175 8 [CATGAGGC] [5] 709112 709119 8 [CATGAGGC] ... ... ... ... ... [141] 22209984 22209991 8 [CATGAGGC] [142] 22371543 22371550 8 [CATGAGGC] [143] 22554991 22554998 8 [CATGAGGC] [144] 22618578 22618585 8 [CATGAGGC] [145] 22897728 22897735 8 [CATGAGGC] #+end_example But alas rather appears as: #+RESULTS: #+begin_example ... ... ... ... ... [141] 22209984 22209991 8 [CATGAGGC] [142] 22371543 22371550 8 [CATGAGGC] [143] 22554991 22554998 8 [CATGAGGC] [144] 22618578 22618585 8 [CATGAGGC] [145] 22897728 22897735 8 [CATGAGGC] #+end_example I offer as a possible workaround the following: So far, I have had good success having removed provision for allowing leading whitespace by changing the regexp org-babel-R-evaluate-session from "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" to "^\\([>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" But I don't know all the test cases so, YMMV.... HTH, ~Malcolm (who, FWIW, has never really liked the way ob-R communicated with the inferior R session in the first place....)