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From: Charles Berry <ccberry@ucsd.edu>
To: emacs-orgmode@gnu.org
Subject: Re: [ob-R] table variable passing broken
Date: Tue, 14 Oct 2014 16:36:01 +0000 (UTC)	[thread overview]
Message-ID: <loom.20141014T174815-640@post.gmane.org> (raw)
In-Reply-To: olud29ug49l.fsf@med.uni-goettingen.de

Andreas Leha <andreas.leha <at> med.uni-goettingen.de> writes:

> 
> Hi all,
> 
> There seems to be a bug in table passing as variables now using the
> tangle-friendly version of passing variables.
> 
> Here is an example (I get an error also with emacs -Q):
> 
> --8<---------------cut here---------------start------------->8---
> * test
> #+name: testtab
> | variable              | display                       | unit  |
> |-----------------------+-------------------------------+-------|
> | num_cells             | Number of Cells in Well       |       |
> | cell_area             | Cell Area                     | μm²   |
> | nucleus_area          | Nucleus Area                  | μm²   |
> | roundness             | Cell Roundness                |       |
> | ratio_w2l             | Cell Width to Length Ratio    |       |
> | inten_nuc_dapi_median | Intensity Nucleus DAPI Median |       |
> | dapi_median           | Intensity Nucleus DAPI Median |       |
> | edu_median            | Intensity edu Median          |       |
> | oct4_median           | Intensity oct4 Median         |       |
> | clump_size            | Clump Size                    | cells |
> | short_name            | Cell Line                     |       |
> | p_col                 | Column                        |       |
> | batch                 | Batch                         |       |
> | concentration         | Fibronectin Concentration     | ugml  |
> | Residual              | Residual                      |       |
> | evaluation_guid       | Plate                         |       |
> | donor                 | Genotype                      |       |
> 
> #+BEGIN_SRC R :session *test* :var test=testtab
>   test
> #+END_SRC
> 
> #+RESULTS:
> --8<---------------cut here---------------end--------------->8---
> 
> I see this in my R session:
> 
> --8<---------------cut here---------------start------------->8---
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, 
> na.strings,  (from
> testorg.org!917613Wp#22) : 
>   line 17 did not have 3 elements
> --8<---------------cut here---------------end--------------->8---
> 

I think this is the wrong diagnosis.

Did you actually revert to the earlier version of ob-R.el to confirm that 
this would have run correctly? 

The reason I ask is that I just tried this with org-babel-R-assign-elisp
from 

  org-mode-a5686d87786b1d6514ec85959a2188f703346a06/lisp/ob-R.el

and got the same error. Note this:

--8<---------------cut here---------------start------------->8---

#+name: testtab2
| variable | display  | unit |
|----------+----------+------|
| donor    | Genotype |      |

  
#+BEGIN_SRC emacs-lisp :var test=testtab2
(orgtbl-to-tsv test '(:fmt org-babel-R-quote-tsv-field))
#+END_SRC

#+RESULTS:
: "donor"	"Genotype"


#+BEGIN_SRC emacs-lisp :var value=testtab2
;; from org-babel-R-assign-elisp
(mapcar 'length (org-remove-if-not 'sequencep value))
#+END_SRC

#+RESULTS:
| 3 |

--8<---------------cut here---------------end--------------->8---

In particular, the empty table cells are omitted even though 

`value' or `test' has all lengths as 3. This results in 
calling read.table ( ..., fill=FALSE) implicitly.

Not sure if the fix is to retool org-babel-R-assign-elisp or something
in org-table.el.

HTH,

Chuck

next prev parent reply	other threads:[~2014-10-14 16:36 UTC|newest]

Thread overview: 4+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2014-10-14 13:38 [ob-R] table variable passing broken Andreas Leha
2014-10-14 16:36 ` Charles Berry [this message]
2014-10-14 19:03   ` Andreas Leha
2014-10-16 14:02     ` Andreas Leha

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