[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
MEC at stowers.org
Thu Oct 1 21:59:15 CEST 2015
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....)
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