* Re: [babel] return file from R
2015-12-17 17:00 ` Charles C. Berry
@ 2015-12-17 22:04 ` Andreas Leha
2016-01-19 15:20 ` Andreas Leha
1 sibling, 0 replies; 6+ messages in thread
From: Andreas Leha @ 2015-12-17 22:04 UTC (permalink / raw)
To: emacs-orgmode
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
^ permalink raw reply [flat|nested] 6+ messages in thread* Re: [babel] return file from R
2015-12-17 17:00 ` Charles C. Berry
2015-12-17 22:04 ` Andreas Leha
@ 2016-01-19 15:20 ` Andreas Leha
2016-01-20 4:40 ` Charles C. Berry
1 sibling, 1 reply; 6+ messages in thread
From: Andreas Leha @ 2016-01-19 15:20 UTC (permalink / raw)
To: emacs-orgmode
Hi Chuck,
Thanks for following that up. And sorry for the long delay.
"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'.
>
> 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))))
>
>
> In the meanwhile, you can work around by using `:results output' and
> wrapping the result in cat().
>
Using the ':results output' work around won't work on most of my code
blocks as these are typically longer and more verbose. So, that really
is just a work-around.
I've tested your patch and it seems to work. But it does seem to need
an analogous change in org-babel-R-evaluate-session to also cure blocks
with ':session'.
--8<---------------cut here---------------start------------->8---
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index f72cd95..193548e 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))))
@@ -431,7 +431,7 @@ 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
--8<---------------cut here---------------end--------------->8---
Regards,
Andreas
^ permalink raw reply related [flat|nested] 6+ messages in thread