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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