[babel] return file from R

[babel] return file from R

[Andreas Leha]

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---

Regards,
Andreas

Re: [babel] return file from R

[Charles C. Berry]

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().

HTH,

Chuck

Re: [babel] return file from R

[Andreas Leha]

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

Re: [babel] return file from R

[Andreas Leha]

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

Re: [babel] return file from R

[Charles C. Berry]

On Tue, 19 Jan 2016, Andreas Leha wrote:

> Hi Chuck,
>

[snip]

> 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'.
>

Correct. I committed a patch like this and added a test

Thanks,

Chuck

Re: [babel] return file from R

[Andreas Leha]

Hi Chuck,

"Charles C. Berry" <ccberry@ucsd.edu> writes:
> On Tue, 19 Jan 2016, Andreas Leha wrote:
>
>> Hi Chuck,
>>
>
> [snip]
>
>> 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'.
>>
>
> Correct. I committed a patch like this and added a test
>

Thanks!

Andreas