Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Damien Cassou]

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Hi,

it seems that, if a cell within a table contains a space, the
corresponding value passed as parameter to a R script will be
wrong. Please find a very simple org file attached to this email. I
expect the length of the variable to be 2 (which is the length of '("A
B" "C") and not 3. Apparently, R receives this array instead: '("A B"
"C" nil).

Emacs  : GNU Emacs 27.1 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.21, cairo version 1.16.0)
Package: Org mode version 9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)


-- 
Damien Cassou

"Success is the ability to go from one failure to another without
losing enthusiasm." --Winston Churchill

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#+name: table
|     | 2014 |
|-----+------|
| A C |    1 |
| C   |    2 |


#+name: linechart
#+begin_src R :results value :var accounts="" :exports none
length(accounts)
#+end_src

#+call: linechart(accounts=table[,0])

#+RESULTS:
: 3

Re: Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Berry, Charles via General discussions about Org-mode.]

> On Sep 6, 2020, at 4:32 AM, Damien Cassou <damien@cassou.me> wrote:
> 
> 
> Hi,
> 
> it seems that, if a cell within a table contains a space, the
> corresponding value passed as parameter to a R script will be
> wrong.


Not exactly. Your ECM has one column, and using both columns removes the issue.

Here is another ECM that illustrates the bug:

#+begin_src R :results output :var accounts=(identity '("A B" "C")) 
print(accounts)
#+end_src


The bug is in `org-babel-R-assign-elisp' which attempts to get the number of elements in each line of a table, but when the table has just one row or column it gets this wrong.


> Please find a very simple org file attached to this email. I
> expect the length of the variable to be 2 (which is the length of '("A
> B" "C") and not 3. Apparently, R receives this array instead: '("A B"
> "C" nil).
> 

Actually the length should be 1, i.e. a data.frame with a single column of two elements.

BTW, C-c C-v C-v with point in the src block will show you what R `receives'.

Unfortunately, there are other cases where the variable assignment does not work seamlessly for R src blocks.  There are workarounds, but they are ungainly - like using a src block for another language to render the table and then using a noweb reference to it to import the data. 

HTH,
Chuck

Re: Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Bastien]

Hi Charles,

"Berry, Charles" via "General discussions about Org-mode."
<emacs-orgmode@gnu.org> writes:

> Here is another ECM that illustrates the bug:

I'm just confirming this bug with X-Woof-Bug: confirmed so that it
appears on https://updates.orgmode.org.

Best,

-- 
 Bastien

Re: Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Bastien]

Bastien <bzg@gnu.org> writes:

> I'm just confirming this bug with X-Woof-Bug: confirmed so that it
> appears on https://updates.orgmode.org.

Of course, the first time I mention "X-Woof-Bug: confirmed" in the
body of the email, I forgot to add it as a mail header.

-- 
 Bastien

Re: Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Jeremie Juste]

Hello,

Apologies for the late reply and thanks for pointing out this bug.
|| On Sunday,  6 Sep 2020 at 13:32, Damien Cassou wrote:

#+name: table
|     | 2014 |
|-----+------|
| A C |    1 |
| C   |    2 |

#+name: linechart
#+begin_src R :results value :var accounts="" :exports none
length(accounts)
#+end_src

#+call: linechart(accounts=table[,0])

#+RESULTS:
: 3

Currently there are no support for vectors. So it is either a
data.frame or an object of length 1. 

|| On Sun, 06 Sep 2020 18:23:19  Berry, Charles" wrote
> Actually the length should be 1, i.e. a data.frame with a single column of two elements.

Indeed with the current handling the length should be 1 but it is
not. Even with the previous case solved, it might still be an
unexpected behavior for a typical R user who would expect a vector. Do you
think it is reasonable?

The following patch will at least harmonize the results towards the
data.frame. 

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 420b8ccbc..81693d157 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -236,11 +236,11 @@ This function is called by `org-babel-execute-src-block'."
 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
   "Construct R code assigning the elisp VALUE to a variable named NAME."
   (if (listp value)
-      (let* ((value (if (listp (car value)) value (list value)))
-            (lengths (mapcar 'length (cl-remove-if-not 'sequencep value)))
+      (let* ((lengths (mapcar 'length (cl-remove-if-not 'sequencep value)))
             (max (if lengths (apply 'max lengths) 0))
             (min (if lengths (apply 'min lengths) 0)))
         ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
+        (unless (listp (car value)) (setq value (list value)))
        (let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
              (header (if (or (eq (nth 1 value) 'hline) colnames-p)
                          "TRUE" "FALSE"))


so the following will return a data.frame

#+begin_src R :results output :var accounts=(identity '("A B" "C")) 
print(accounts)
#+end_src

#+RESULTS:
:    V1 V2
: 1 A B  C


I will add support for selection of 1 single column as a
vector soon.

Best regards,
Jeremie

PS: I am a newbie maintainer so feel free to comment if there you find
room for improvements ;-)

Re: Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Bastien]

Hi Damien and Jeremie,

Jeremie Juste <jeremiejuste@gmail.com> writes:

> The following patch will at least harmonize the results towards the
> data.frame. 

I see the patch has been applied - thanks!

I'm marking this bug as resolved right now, feel free to reopen it if
I'm wrong.

Thanks,

-- 
 Bastien

Re: Bug: Babel+R handles spaces wrongly in tables [9.3.6 (release_9.3.6 @ /home/cassou/.emacs.d/lib/org/lisp/)]

[Jeremie Juste]

Hello Bastien,

Many thanks, I was waiting for feedback but it seems that nobody
complained. 

On Sunday,  2 May 2021 at 05:52, Bastien wrote:
> Hi Damien and Jeremie,
>
> Jeremie Juste <jeremiejuste@gmail.com> writes:
>
>> The following patch will at least harmonize the results towards the
>> data.frame. 
>
> I see the patch has been applied - thanks!
>
> I'm marking this bug as resolved right now, feel free to reopen it if
> I'm wrong.
>
Thanks, feel free to reopen if you face any issue.


Best regards
-- 
Jeremie Juste