From: Andreas Leha <andreas.leha@med.uni-goettingen.de>
To: emacs-orgmode@gnu.org
Subject: Re: [ob-R] table variable passing broken
Date: Tue, 14 Oct 2014 20:03:50 +0100 [thread overview]
Message-ID: <olu1tqafp7t.fsf@med.uni-goettingen.de> (raw)
In-Reply-To: loom.20141014T174815-640@post.gmane.org
Charles Berry <ccberry@ucsd.edu> writes:
> 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.
I agree. Saving the table as tsv (via org-table-export) results
in a file that cannot be read from R either.
>
> Did you actually revert to the earlier version of ob-R.el to confirm that
> this would have run correctly?
I did not revert. But that org file used to work. I won't be able
to bisect any time soon.
>
> 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:
>
>
> #+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"
>
exactly. That also causes the org-table-export to fail.
>
> #+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 |
>
> 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.
>
I am the wrong person to answer that. But it looks to me to be an
issue for org-table.el.
Thanks for your better analysis.
Regards,
Andreas
next prev parent reply other threads:[~2014-10-14 19:04 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
2014-10-14 19:03 ` Andreas Leha [this message]
2014-10-16 14:02 ` Andreas Leha
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