From MEC at stowers.org  Thu Oct  1 21:59:15 2015
From: MEC at stowers.org (Cook, Malcolm)
Date: Thu, 1 Oct 2015 19:59:15 +0000
Subject: [Rd] 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
Message-ID: <e23d5e509a6740f19e355d07757c30d7@exchsrv2.sgc.loc>

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....)



[Rd] 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
Cook, Malcolm