From: Andreas Leha <andreas.leha@med.uni-goettingen.de>
To: emacs-orgmode@gnu.org
Subject: Re: [babel] return file from R
Date: Thu, 17 Dec 2015 22:04:54 +0000 [thread overview]
Message-ID: <oluzix8iveh.fsf@med.uni-goettingen.de> (raw)
In-Reply-To: alpine.OSX.2.20.1512170851170.704@charles-berrys-macbook.local
Hi Chuck,
"Charles C. Berry" <ccberry@ucsd.edu> writes:
> On Thu, 17 Dec 2015, Andreas Leha wrote:
>
>> Hi all,
>>
>> I think there is a bug in the handling of results of R src blocks. What
>> is the suggested way to make an R block return a link to a file? The
>> obvious way appends a newline character to the file link (which is
>> broken because of that).
>>
>> Here is an example:
>> --8<---------------cut here---------------start------------->8---
>> #+NAME: TESTSRC
>> #+BEGIN_SRC R :results file
>> a <- file.path("junk", "test.org")
>> a
>> #+END_SRC
>>
>> #+RESULTS: TESTSRC
>> [[file:junk/test.org
>> ]]
>>
>> --8<---------------cut here---------------end--------------->8---
>
>
> That *is* the suggested way, and it will work in (say) emacs-lisp. The
> problem for `:results value' (the default) is that a newline is added
> to the result by `org-babel-R-evaluate-external-process'.
Thanks for the confirmation.
>
> This *might* be the fix, but I do not have time to check it thoroughly:
>
> diff --git a/lisp/ob-R.el b/lisp/ob-R.el
> index f72cd95..f660bbd 100644
> --- a/lisp/ob-R.el
> +++ b/lisp/ob-R.el
> @@ -397,7 +397,7 @@ last statement in BODY, as elisp."
> (org-babel-result-cond result-params
> (with-temp-buffer
> (insert-file-contents tmp-file)
> - (buffer-string))
> + (org-babel-chomp (buffer-string) "\n"))
> (org-babel-import-elisp-from-file tmp-file '(16)))
> column-names-p)))
> (output (org-babel-eval org-babel-R-command body))))
>
I'll try to test this in the next days.
>
> In the meanwhile, you can work around by using `:results output' and
> wrapping the result in cat().
Yes. But usually my source blocks are more noisy and produce some
messages, which would break this approach.
Thanks again,
Andreas
next prev parent reply other threads:[~2015-12-17 22:05 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-12-17 14:41 [babel] return file from R Andreas Leha
2015-12-17 17:00 ` Charles C. Berry
2015-12-17 22:04 ` Andreas Leha [this message]
2016-01-19 15:20 ` Andreas Leha
2016-01-20 4:40 ` Charles C. Berry
2016-01-20 6:26 ` Andreas Leha
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