Re: org tables into R?

[Andreas Leha <andreas.leha@med.uni-goettingen.de>]

Hi Rainer,

Thanks for chiming in.

Rainer M Krug <Rainer@krugs.de> writes:
> Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:
>
>> Hi Aaron and Nicolas,
>
> Sorry for coming so late to this topic - I should try to figure out what
> is causing the problem as I am the one responsible for this code...
>
>>
>> Thanks for partly fixing this issue.  Unfortunately, when working with
>> source block interactively the issue persists for me.  If in the same
>> sample file I view the source block via 'C-c C-v v' and step through the
>> generated code line-by-line, the table is again not split into columns.
>>
>> This time I immediately tried with 'emacs -Q' and I can reproduce the
>> issue.
>>
>> Here is the ecm again:
>>
>> * test
>> #+NAME: data
>> |   A |  B |  C |
>> |-----+----+----|
>> | 115 | 76 | 60 |
>> | 124 | 78 | 55 |
>> | 118 | 73 | 65 |
>> | 114 | 75 | 61 |
>> | 108 | 74 | 82 |
>>
>> and pass it into R like this, then evaluation (C-c C-c) works, but
>> stepping through the code generated for viewing (C-c C-v v) does not:
>>
>> #+BEGIN_SRC R :results output :exports both :session :var data.table=data
>>   names(data.table)
>>   head(data.table)
>> #+END_SRC
>>
>> #+results:
>> : [1] "A" "B" "C"
>> :     A  B  C
>> : 1 115 76 60
>> : 2 124 78 55
>> : 3 118 73 65
>> : 4 114 75 61
>> : 5 108 74 82
>>
>> #+begin_src emacs-lisp
>>   (concat
>>    (replace-regexp-in-string " on .*" "" (emacs-version))
>>    "\n"
>>    (replace-regexp-in-string " @.*" ")" (org-version nil t))
>>    "\n"
>>    (replace-regexp-in-string "].*" "]" (ess-version)))
>> #+end_src
>>
>> #+results:
>> : 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
>> : Org-mode version 8.3beta (release_8.3beta-717-ga8096c)
>> : ess-version: 14.05 [git: 4283f1304a54502c42707b6a4ba347703f0992dd]
>>
>
> ,----
> | #+RESULTS:
> | : GNU Emacs 24.4.1 (x86_64-apple-darwin14.0.0, Carbon Version 157 AppKit 1343.16)
> | :  of 2014-11-24
> | : Org-mode version 8.3beta (release_8.3beta-695-g390015)
> | : ess-version: 14.09 [svn: 6041 (2014-09-13)]
> `----
>
>
> I get the same in the preview, but it works for me. I do not use -q.
>
> ,----
> | > data.table <- local({
> | +      con <- textConnection(
> | +        "\"A\"	\"B\"	\"C\"
> | + \"115\"	\"76\"	\"60\"
> | + \"124\"	\"78\"	\"55\"
> | + \"118\"	\"73\"	\"65\"
> | + \"114\"	\"75\"	\"61\"
> | + \"108\"	\"74\"	\"82\""
> | +      )
> | +      res <- utils::read.table(
> | +        con,
> | +        header    = TRUE,
> | +        row.names = NULL,
> | +        sep       = "\t",
> | +        as.is     = TRUE
> | +      )
> | +      close(con)
> | +      res
> | +    })
> | >   names(data.table)
> | [1] "A" "B" "C"
> | >   head(data.table)
> |     A  B  C
> | 1 115 76 60
> | 2 124 78 55
> | 3 118 73 65
> | 4 114 75 61
> | 5 108 74 82
> | > 
> `----
>
>
>>
>> Here is what I see in the org babel preview:
>>
>
> This might be due to temail, but you don't have tabs (\t) between your
> entries below - could you verify if this is the case? If yes, this might
> be a locale issue (would be strange)?

Yes, there seem to be no tabs.  If there were tabs, R should parse the
table correctly, I guess.

(BTW: My custom filter replacing tabs with spaces is still disabled,
even though I pulled from master, which includes the recent

commit 70f965535b07c03a40792237de3a970d1cb57551
Author: Nicolas Goaziou <mail@nicolasgoaziou.fr>
Date:   Mon Jan 5 12:39:26 2015 +0100

    org-table: Ignore filters and hooks in radio tables
)


>
>> data.table <- local({
>>      con <- textConnection(
>>        "\"A\"   \"B\"   \"C\"
>> \"115\" \"76\"  \"60\"
>> \"124\" \"78\"  \"55\"
>> \"118\" \"73\"  \"65\"
>> \"114\" \"75\"  \"61\"
>> \"108\" \"74\"  \"82\""
>>      )
>>      res <- utils::read.table(
>>        con,
>>        header    = TRUE,
>>        row.names = NULL,
>>        sep       = "\t",
>>        as.is     = TRUE
>>      )
>>      close(con)
>>      res
>>    })
>> names(data.table)
>> head(data.table)
>
> One solution would be to insert (instead of the tab character) "\t" to
> separate the fields?
>
> You could try and modify the ob-R-transfer-variable-table-with-header -
> From the help:
>
> ,----
> | ob-R-transfer-variable-table-with-header is a variable defined in `ob-R.el'.
> | Its value is
> | "%s <- local({\n con <- textConnection(\n %S\n )\n res <-
> | utils::read.table(\n con,\n header = %s,\n row.names = %s,\n sep =
> | \"\\t\",\n as.is = TRUE\n )\n close(con)\n res\n })"
> | 
> |   This variable may be risky if used as a file-local variable.
> | 
> | Documentation:
> | R code used to transfer a table defined as a variable from org to R.
> | 
> | This function is used when the table contains a header.
> `----
>
> This is passed to the (format) function and one might be able to change
> something there.

Thanks for the hint.  Do I assume correctly, that this variable is used
when the code block is evaluated as well?  In that case, I am reluctant
to change it, as the evaluation now works.  The surprising thing is the
different behaviour for preview and evaluation.

I am extremely tight with my time right now, so that I won't be able to
do much experimentation/investigation right now, I am afraid.  But I
will try to still be helpful...

Thanks,
Andreas


>
> Cheers,
>
> Rainer
>
>>
>>
>> And finally, here is my R session, when I step through the code:
>>
>>
>> R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
>> Copyright (C) 2014 The R Foundation for Statistical Computing
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>>   Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE)
>>> data.table <- local({
>> +      con <- textConnection(
>> +        "\"A\"   \"B\"   \"C\"
>> + \"115\" \"76\"  \"60\"
>> + \"124\" \"78\"  \"55\"
>> + \"118\" \"73\"  \"65\"
>> + \"114\" \"75\"  \"61\"
>> + \"108\" \"74\"  \"82\""
>> +      )
>> +      res <- utils::read.table(
>> +        con,
>> +        header    = TRUE,
>> +        row.names = NULL,
>> +        sep       = "\t",
>> +        as.is     = TRUE
>> +      )
>> +      close(con)
>> +      res
>> +    })
>>> names(data.table)
>> [1] "A...B...C"
>>> head(data.table)
>>    A...B...C
>> 1 115 76  60
>> 2 124 78  55
>> 3 118 73  65
>> 4 114 75  61
>> 5 108 74  82
>>
>>
>> Regards,
>> Andreas
>>
>>
>>