From: "Cook, Malcolm" <MEC@stowers.org>
To: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Cc: "bioc-devel@r-project.org" <bioc-devel@r-project.org>,
"r-devel@r-project.org" <r-devel@r-project.org>
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 [thread overview]
Message-ID: <e23d5e509a6740f19e355d07757c30d7@exchsrv2.sgc.loc> (raw)
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....)
next reply other threads:[~2015-10-01 19:59 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-10-01 19:59 Cook, Malcolm [this message]
2015-10-01 21:56 ` 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 Charles C. Berry
2015-10-01 23:15 ` Cook, Malcolm
2015-10-08 19:24 ` Charles C. Berry
2015-10-08 20:41 ` Cook, Malcolm
2015-11-05 12:57 ` Nicolas Goaziou
2015-11-06 23:11 ` Charles C. Berry
2015-11-07 21:30 ` Charles C. Berry
2015-11-07 21:41 ` Nicolas Goaziou
2015-11-07 23:22 ` Cook, Malcolm
2015-11-08 0:32 ` Charles C. Berry
2015-11-09 20:04 ` Cook, Malcolm
2015-11-09 20:56 ` Charles C. Berry
2015-11-09 22:11 ` Cook, Malcolm
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://www.orgmode.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=e23d5e509a6740f19e355d07757c30d7@exchsrv2.sgc.loc \
--to=mec@stowers.org \
--cc=bioc-devel@r-project.org \
--cc=emacs-orgmode@gnu.org \
--cc=r-devel@r-project.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).