* [ob-R] table variable passing broken
@ 2014-10-14 13:38 Andreas Leha
2014-10-14 16:36 ` Charles Berry
0 siblings, 1 reply; 4+ messages in thread
From: Andreas Leha @ 2014-10-14 13:38 UTC (permalink / raw)
To: emacs-orgmode
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---
This is on
- GNU Emacs 24.4.50.1 (x86_64-apple-darwin13.3.0, NS appkit-1265.21 Version 10.9.4 (Build 13E28)) of 2014-09-02 on mib106584i.local
- Org-mode version 8.3beta (release_8.3beta-470-g087f8e)
- ess-version: 14.05 [git: 4283f1304a54502c42707b6a4ba347703f0992dd]
Best,
Andreas
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [ob-R] table variable passing broken
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
0 siblings, 1 reply; 4+ messages in thread
From: Charles Berry @ 2014-10-14 16:36 UTC (permalink / raw)
To: emacs-orgmode
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
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [ob-R] table variable passing broken
2014-10-14 16:36 ` Charles Berry
@ 2014-10-14 19:03 ` Andreas Leha
2014-10-16 14:02 ` Andreas Leha
0 siblings, 1 reply; 4+ messages in thread
From: Andreas Leha @ 2014-10-14 19:03 UTC (permalink / raw)
To: emacs-orgmode
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
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [ob-R] table variable passing broken
2014-10-14 19:03 ` Andreas Leha
@ 2014-10-16 14:02 ` Andreas Leha
0 siblings, 0 replies; 4+ messages in thread
From: Andreas Leha @ 2014-10-16 14:02 UTC (permalink / raw)
To: emacs-orgmode
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:
>>
>>>
>>> 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
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2014-10-16 14:02 UTC | newest]
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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
2014-10-16 14:02 ` Andreas Leha
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