From: Andreas Leha <andreas.leha@med.uni-goettingen.de>
To: emacs-orgmode@gnu.org
Subject: BUG: table variable passing broken
Date: Fri, 05 Dec 2014 13:25:38 +0000 [thread overview]
Message-ID: <olulhmmtei5.fsf@med.uni-goettingen.de> (raw)
Hi,
This issue is still open. And I do not seem to be able to find this
thread on gmane for some reason.
So, I resend the last message as a summary.
EDIT:
I just tried to answer to that thread but the message again did not come
through. So, another try (with a slightly adapted title).
Best,
Andreas
Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:
>> Charles Berry <ccberry@ucsd.edu> writes:
>>> Andreas Leha <andreas.leha <at> med.uni-goettingen.de> writes:
>>>
>>>>=20
>>>> Hi all,
>>>>=20
>>>> There seems to be a bug in table passing as variables now using the
>>>> tangle-friendly version of passing variables.
>>>>=20
>>>> Here is an example (I get an error also with emacs -Q):
>>>>=20
>>>> --8<---------------cut here---------------start------------->8---
>>>> * test
>>>> #+name: testtab
>>>> | variable | display | unit |
>>>> |-----------------------+-------------------------------+-------|
>>>> | num_cells | Number of Cells in Well | |
>>>> | cell_area | Cell Area | =CE=BCm=C2=B2=
> |
>>>> | nucleus_area | Nucleus Area | =CE=BCm=C2=B2=
> |
>>>> | 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 | |
>>>>=20
>>>> #+BEGIN_SRC R :session *test* :var test=3Dtesttab
>>>> test
>>>> #+END_SRC
>>>>=20
>>>> #+RESULTS:
>>>> --8<---------------cut here---------------end--------------->8---
>>>>=20
>>>> I see this in my R session:
>>>>=20
>>>> --8<---------------cut here---------------start------------->8---
>>>> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,=20
>>>> na.strings, (from
>>>> testorg.org!917613Wp#22) :=20
>>>> line 17 did not have 3 elements
>>>> --8<---------------cut here---------------end--------------->8---
>>>>=20
>>>
>>> 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 tha=
>t=20
>>> this would have run correctly?=20
>>
>> 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=20
>>>
>>> org-mode-a5686d87786b1d6514ec85959a2188f703346a06/lisp/ob-R.el
>>>
>>> and got the same error. Note this:
>>>
>>>
>>> #+name: testtab2
>>> | variable | display | unit |
>>> |----------+----------+------|
>>> | donor | Genotype | |
>>>
>>>=20=20=20
>>> #+BEGIN_SRC emacs-lisp :var test=3Dtesttab2
>>> (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=3Dtesttab2
>>> ;; 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=20
>>>
>>> `value' or `test' has all lengths as 3. This results in=20
>>> calling read.table ( ..., fill=3DFALSE) 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
>
>To keep this issue going, here a quick thought:
>
>Since orgtbl-to-csv seems to work, a temporary fix on ob-R's side would
>be to use that for passing of tables.
>
>Andreas
>
reply other threads:[~2014-12-05 13:25 UTC|newest]
Thread overview: [no followups] expand[flat|nested] mbox.gz Atom feed
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