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* BUG variable expansion with table
@ 2014-06-25 19:55 Rainer M Krug
  2014-06-26 23:25 ` Andreas Leha
  2014-07-28 15:46 ` Bastien
  0 siblings, 2 replies; 4+ messages in thread
From: Rainer M Krug @ 2014-06-25 19:55 UTC (permalink / raw)
  To: emacs-orgmode; +Cc: schulte.eric

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Hi

there seems to be a bug in the table transfer. The org file below
evaluates as shown, i.e. the TABLE_BLOCK contains one column less then
it should as the first column is discarded and the second one used as
the row names. This only occurs when there is a second variable
defined. When the second variable is not passed, the code works (see
second example below).

I did not get far when debugging, only that in the function
org-babel-R-assign-elisp when assigning TABLE_FILE the rownames are
missing in the =value=.

Rainer

First example:
--8<---------------cut here---------------start------------->8---
#+PROPERTY: rownames yes
#+PROPERTY: colnames yes

#+NAME: TABLE
|          | name         | description        |
|----------+--------------+--------------------|
| annee    | year         | Year of simulation |
| id       | ipoints_Qdiv | Point Number       |
| iespece  | species      | species number     |
| scenario | scenario     | Type of forest     |
#+PROPERTY: var TABLE_FILE=TABLE
#+PROPERTY: var+ float=123.45

* Data Assessment Results
#+HEADERS: :var TABLE_BLOCK=TABLE
#+HEADERS: :rownames yes
#+HEADERS: :colnames yes
#+begin_src R :results output wrap
TABLE_FILE
TABLE_BLOCK
#+end_src

#+RESULTS:
:RESULTS:
                 name        description
annee            year Year of simulation
id       ipoints_Qdiv       Point Number
iespece       species     species number
scenario     scenario     Type of forest
             Year.of.simulation
ipoints_Qdiv       Point Number
species          species number
scenario         Type of forest
:END:
--8<---------------cut here---------------end--------------->8---

Second example:

--8<---------------cut here---------------start------------->8---
#+PROPERTY: rownames yes
#+PROPERTY: colnames yes

#+NAME: TABLE
|          | name         | description        |
|----------+--------------+--------------------|
| annee    | year         | Year of simulation |
| id       | ipoints_Qdiv | Point Number       |
| iespece  | species      | species number     |
| scenario | scenario     | Type of forest     |
#+PROPERTY: var TABLE_FILE=TABLE
#+ PROPERTY: var+ float=123.45

* Data Assessment Results
#+HEADERS: :var TABLE_BLOCK=TABLE
#+HEADERS: :rownames yes
#+HEADERS: :colnames yes
#+begin_src R :results output wrap
TABLE_FILE
TABLE_BLOCK
#+end_src

#+RESULTS:
:RESULTS:
                 name        description
annee            year Year of simulation
id       ipoints_Qdiv       Point Number
iespece       species     species number
scenario     scenario     Type of forest
                 name        description
annee            year Year of simulation
id       ipoints_Qdiv       Point Number
iespece       species     species number
scenario     scenario     Type of forest
:END:
--8<---------------cut here---------------end--------------->8---





-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]

^ permalink raw reply	[flat|nested] 4+ messages in thread

* Re: BUG variable expansion with table
  2014-06-25 19:55 BUG variable expansion with table Rainer M Krug
@ 2014-06-26 23:25 ` Andreas Leha
  2014-06-27  9:48   ` Rainer M Krug
  2014-07-28 15:46 ` Bastien
  1 sibling, 1 reply; 4+ messages in thread
From: Andreas Leha @ 2014-06-26 23:25 UTC (permalink / raw)
  To: emacs-orgmode

Hi Rainer,

Rainer M Krug <Rainer@krugs.de> writes:

> Hi
>
> there seems to be a bug in the table transfer. The org file below
> evaluates as shown, i.e. the TABLE_BLOCK contains one column less then
> it should as the first column is discarded and the second one used as
> the row names. This only occurs when there is a second variable
> defined. When the second variable is not passed, the code works (see
> second example below).
>
> I did not get far when debugging, only that in the function
> org-babel-R-assign-elisp when assigning TABLE_FILE the rownames are
> missing in the =value=.
>
> Rainer
>
> First example:
>
> #+PROPERTY: rownames yes
> #+PROPERTY: colnames yes
>
> #+NAME: TABLE
> |          | name         | description        |
> |----------+--------------+--------------------|
> | annee    | year         | Year of simulation |
> | id       | ipoints_Qdiv | Point Number       |
> | iespece  | species      | species number     |
> | scenario | scenario     | Type of forest     |
> #+PROPERTY: var TABLE_FILE=TABLE
> #+PROPERTY: var+ float=123.45
>
> * Data Assessment Results
> #+HEADERS: :var TABLE_BLOCK=TABLE
> #+HEADERS: :rownames yes
> #+HEADERS: :colnames yes
> #+begin_src R :results output wrap
> TABLE_FILE
> TABLE_BLOCK
> #+end_src
>
> #+RESULTS:
> :RESULTS:
>                  name        description
> annee            year Year of simulation
> id       ipoints_Qdiv       Point Number
> iespece       species     species number
> scenario     scenario     Type of forest
>              Year.of.simulation
> ipoints_Qdiv       Point Number
> species          species number
> scenario         Type of forest
> :END:
>
>
> Second example:
>
> #+PROPERTY: rownames yes
> #+PROPERTY: colnames yes
>
> #+NAME: TABLE
> |          | name         | description        |
> |----------+--------------+--------------------|
> | annee    | year         | Year of simulation |
> | id       | ipoints_Qdiv | Point Number       |
> | iespece  | species      | species number     |
> | scenario | scenario     | Type of forest     |
> #+PROPERTY: var TABLE_FILE=TABLE
> #+ PROPERTY: var+ float=123.45
>
> * Data Assessment Results
> #+HEADERS: :var TABLE_BLOCK=TABLE
> #+HEADERS: :rownames yes
> #+HEADERS: :colnames yes
> #+begin_src R :results output wrap
> TABLE_FILE
> TABLE_BLOCK
> #+end_src
>
> #+RESULTS:
> :RESULTS:
>                  name        description
> annee            year Year of simulation
> id       ipoints_Qdiv       Point Number
> iespece       species     species number
> scenario     scenario     Type of forest
>                  name        description
> annee            year Year of simulation
> id       ipoints_Qdiv       Point Number
> iespece       species     species number
> scenario     scenario     Type of forest
> :END:


FWIW, I think that bug was reported some while back [fn:1] --
unfortunately without a fix .... ;-)

- Andreas



Footnotes:

[fn:1] http://article.gmane.org/gmane.emacs.orgmode/82295/match=

^ permalink raw reply	[flat|nested] 4+ messages in thread

* Re: BUG variable expansion with table
  2014-06-26 23:25 ` Andreas Leha
@ 2014-06-27  9:48   ` Rainer M Krug
  0 siblings, 0 replies; 4+ messages in thread
From: Rainer M Krug @ 2014-06-27  9:48 UTC (permalink / raw)
  To: Andreas Leha; +Cc: emacs-orgmode

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Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:

> Hi Rainer,
>
> Rainer M Krug <Rainer@krugs.de> writes:
>
>> Hi
>>
>> there seems to be a bug in the table transfer. The org file below
>> evaluates as shown, i.e. the TABLE_BLOCK contains one column less then
>> it should as the first column is discarded and the second one used as
>> the row names. This only occurs when there is a second variable
>> defined. When the second variable is not passed, the code works (see
>> second example below).
>>
>> I did not get far when debugging, only that in the function
>> org-babel-R-assign-elisp when assigning TABLE_FILE the rownames are
>> missing in the =value=.
>>
>> Rainer
>>
>> First example:
>>
>> #+PROPERTY: rownames yes
>> #+PROPERTY: colnames yes
>>
>> #+NAME: TABLE
>> |          | name         | description        |
>> |----------+--------------+--------------------|
>> | annee    | year         | Year of simulation |
>> | id       | ipoints_Qdiv | Point Number       |
>> | iespece  | species      | species number     |
>> | scenario | scenario     | Type of forest     |
>> #+PROPERTY: var TABLE_FILE=TABLE
>> #+PROPERTY: var+ float=123.45
>>
>> * Data Assessment Results
>> #+HEADERS: :var TABLE_BLOCK=TABLE
>> #+HEADERS: :rownames yes
>> #+HEADERS: :colnames yes
>> #+begin_src R :results output wrap
>> TABLE_FILE
>> TABLE_BLOCK
>> #+end_src
>>
>> #+RESULTS:
>> :RESULTS:
>>                  name        description
>> annee            year Year of simulation
>> id       ipoints_Qdiv       Point Number
>> iespece       species     species number
>> scenario     scenario     Type of forest
>>              Year.of.simulation
>> ipoints_Qdiv       Point Number
>> species          species number
>> scenario         Type of forest
>> :END:
>>
>>
>> Second example:
>>
>> #+PROPERTY: rownames yes
>> #+PROPERTY: colnames yes
>>
>> #+NAME: TABLE
>> |          | name         | description        |
>> |----------+--------------+--------------------|
>> | annee    | year         | Year of simulation |
>> | id       | ipoints_Qdiv | Point Number       |
>> | iespece  | species      | species number     |
>> | scenario | scenario     | Type of forest     |
>> #+PROPERTY: var TABLE_FILE=TABLE
>> #+ PROPERTY: var+ float=123.45
>>
>> * Data Assessment Results
>> #+HEADERS: :var TABLE_BLOCK=TABLE
>> #+HEADERS: :rownames yes
>> #+HEADERS: :colnames yes
>> #+begin_src R :results output wrap
>> TABLE_FILE
>> TABLE_BLOCK
>> #+end_src
>>
>> #+RESULTS:
>> :RESULTS:
>>                  name        description
>> annee            year Year of simulation
>> id       ipoints_Qdiv       Point Number
>> iespece       species     species number
>> scenario     scenario     Type of forest
>>                  name        description
>> annee            year Year of simulation
>> id       ipoints_Qdiv       Point Number
>> iespece       species     species number
>> scenario     scenario     Type of forest
>> :END:
>
>
> FWIW, I think that bug was reported some while back [fn:1] --
> unfortunately without a fix .... ;-)

Pity - I will work around it then.

Thanks,

Rainer

>
> - Andreas
>
>
>
> Footnotes:
>
> [fn:1] http://article.gmane.org/gmane.emacs.orgmode/82295/match=
>
>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]

^ permalink raw reply	[flat|nested] 4+ messages in thread

* Re: BUG variable expansion with table
  2014-06-25 19:55 BUG variable expansion with table Rainer M Krug
  2014-06-26 23:25 ` Andreas Leha
@ 2014-07-28 15:46 ` Bastien
  1 sibling, 0 replies; 4+ messages in thread
From: Bastien @ 2014-07-28 15:46 UTC (permalink / raw)
  To: Rainer M Krug; +Cc: emacs-orgmode, schulte.eric

Hi Rainer,

Rainer M Krug <Rainer@krugs.de> writes:

> I did not get far when debugging, only that in the function
> org-babel-R-assign-elisp when assigning TABLE_FILE the rownames are
> missing in the =value=.

Did you have a chance to debug this further?

Thanks,

-- 
 Bastien

^ permalink raw reply	[flat|nested] 4+ messages in thread

end of thread, other threads:[~2014-07-28 17:25 UTC | newest]

Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2014-06-25 19:55 BUG variable expansion with table Rainer M Krug
2014-06-26 23:25 ` Andreas Leha
2014-06-27  9:48   ` Rainer M Krug
2014-07-28 15:46 ` Bastien

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