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Re: [O] BUG: emacs orgmode ob-R.el function org-babel-R-evaluate-session
From: |
Charles C. Berry |
Subject: |
Re: [O] 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 14:56:57 -0700 |
User-agent: |
Alpine 2.20 (OSX 67 2015-01-07) |
On Thu, 1 Oct 2015, Cook, Malcolm wrote:
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
I'd try (for example):
#+BEGIN_SRC R :results value raw drawer :session
require(GenomicRanges)
capture.output(show(GRanges(seqnames=rep("a",100),
IRanges(start=1:100,width=1),strand=rep("*",100))))
#+END_SRC
rather than messing with the regexp.
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....
Just guessing that the things that `(setq ess-eval-visibly nil)' generates
(e.g., + + + + + > ) won't behave using your version.
HTH,
Chuck