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* BUG: table variable passing broken
@ 2014-12-05 13:25 Andreas Leha
  0 siblings, 0 replies; only message in thread
From: Andreas Leha @ 2014-12-05 13:25 UTC (permalink / raw)
  To: emacs-orgmode

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
>

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2014-12-05 13:25 BUG: table variable passing broken Andreas Leha

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