Re: [O] [ob-R] table variable passing broken

[Andreas Leha]

Andreas Leha <address@hidden> writes:
> Charles Berry <address@hidden> 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

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