cannot execute org-mode code from the front page tutorial.

cannot execute org-mode code from the front page tutorial.

[jenia.ivlev]

Hello.

I'm trying to go through the org-mode tutorial on its official page.

However, I have trouble execute the code there"


    #+NAME: tbl-example-data()
    #+BEGIN_SRC R :results value  
    runif(n=5, min=0, max=1)
    #+END_SRC
    
    #+RESULTS: tbl-example-data
    |  0.565871287835762 |
    |  0.457158328965306 |
    | 0.0498181856237352 |
    |  0.988381117349491 |
    |  0.898329895688221 |
    
    
    
    #+NAME: R-mean(x)
    #+BEGIN_SRC R :var x=tbl-example-data
    mean(x)
    #+END_SRC
    
    
    
    
    #+call: R-mean(x=tbl-example-data)


It returns me:



     Reference 'R-mean' not found in this buffer.


Can someone please tell me how can I fix this error?

Thanks in advance for your time and kind help.

Jenia.

Re: cannot execute org-mode code from the front page tutorial.

[Thomas S. Dye]

Aloha Jenia,

jenia.ivlev@gmail.com (jenia.ivlev) writes:

> Hello.
>
> I'm trying to go through the org-mode tutorial on its official page.
>
> However, I have trouble execute the code there"
>
>
>     #+NAME: tbl-example-data()
>     #+BEGIN_SRC R :results value  
>     runif(n=5, min=0, max=1)
>     #+END_SRC
>     
>     #+RESULTS: tbl-example-data
>     |  0.565871287835762 |
>     |  0.457158328965306 |
>     | 0.0498181856237352 |
>     |  0.988381117349491 |
>     |  0.898329895688221 |
>     
>     
>     
>     #+NAME: R-mean(x)
>     #+BEGIN_SRC R :var x=tbl-example-data
>     mean(x)
>     #+END_SRC
>     
>     
>     
>     
>     #+call: R-mean(x=tbl-example-data)
>
>
> It returns me:
>
>
>
>      Reference 'R-mean' not found in this buffer.
>

FWIW, this code doesn't work for me, either, using a recent Org-mode from
git.


For others able to help, the "org-mode tutorial on its official page"
that Jenia refers to is
http://orgmode.org/worg/org-contrib/babel/intro.html#spreadsheet

hth,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: cannot execute org-mode code from the front page tutorial.

[Nick Dokos]

tsd@tsdye.com (Thomas S. Dye) writes:

> Aloha Jenia,
>
> jenia.ivlev@gmail.com (jenia.ivlev) writes:
>
>> Hello.
>>
>> I'm trying to go through the org-mode tutorial on its official page.
>>
>> However, I have trouble execute the code there"
>>
>>
>>     #+NAME: tbl-example-data()
>>     #+BEGIN_SRC R :results value  
>>     runif(n=5, min=0, max=1)
>>     #+END_SRC
>>     
>>     #+RESULTS: tbl-example-data
>>     |  0.565871287835762 |
>>     |  0.457158328965306 |
>>     | 0.0498181856237352 |
>>     |  0.988381117349491 |
>>     |  0.898329895688221 |
>>     
>>     
>>     
>>     #+NAME: R-mean(x)
>>     #+BEGIN_SRC R :var x=tbl-example-data
>>     mean(x)
>>     #+END_SRC
>>     
>>     
>>     
>>     
>>     #+call: R-mean(x=tbl-example-data)
>>
>>
>> It returns me:
>>
>>
>>
>>      Reference 'R-mean' not found in this buffer.
>>
>
> FWIW, this code doesn't work for me, either, using a recent Org-mode from
> git.
>
>
> For others able to help, the "org-mode tutorial on its official page"
> that Jenia refers to is
> http://orgmode.org/worg/org-contrib/babel/intro.html#spreadsheet
>

I simplified the org file that leads to the error:

--8<---------------cut here---------------start------------->8---
#+name: tbl-example-data
|               foo |
|-------------------|
| 0.996612656628713 |
| 0.148018079344183 |
| 0.560482589527965 |
| 0.329234286677092 |
|  0.99839389254339 |
    
    
    
#+BEGIN_SRC R :var x=tbl-example-data
   mean(x)
#+END_SRC

#+RESULTS:
: nil
--8<---------------cut here---------------end--------------->8---

Running it in the debugger, I think what it does is the equivalent of

--8<---------------cut here---------------start------------->8---

x <- local({con <- textConnection("0.996612656628713
0.148018079344183
0.560482589527965
0.329234286677092
0.99839389254339")
		res <- read.table(
				  con,
				  header    = FALSE,
				  row.names = NULL,
				  sep       = "\t",
				  as.is     = TRUE
				  )
		close(con)
		res})

mean(x)
--8<---------------cut here---------------end--------------->8---

and trying this on the command line, I get an error:

,----
| > x <- local({con <- textConnection("0.996612656628713
| 0.148018079344183
| 0.560482589527965
| 0.329234286677092
| 0.99839389254339")
| 		res <- read.table(
| 				  con,
| 				  header    = FALSE,
| 				  row.names = NULL,
| 				  sep       = "\t",
| 				  as.is     = TRUE
| 				  )
| 		close(con)
| 		res})
| 
| + + + + + + + + + + + + + > > x
|          V1
| 1 0.9966127
| 2 0.1480181
| 3 0.5604826
| 4 0.3292343
| 5 0.9983939
| > mean(x)
| [1] NA
| Warning message:
| In mean.default(x) : argument is not numeric or logical: returning NA
`----

[Disclaimer: from this point on, I'm mostly talking about R - I know
nothing about R]

Fumbling around with typeof(x) and help(list), I stumbled upon unlist()
and used it in the evaluation of x:

,----
| > x <- local({con <- textConnection("0.996612656628713
| 0.148018079344183
| 0.560482589527965
| 0.329234286677092
| 0.99839389254339")
| 		res <- read.table(
| 				  con,
| 				  header    = FALSE,
| 				  row.names = NULL,
| 				  sep       = "\t",
| 				  as.is     = TRUE
| 				  )
| 		close(con)
| 		unlist(res)})
| + + + + + + + + + + + + + > x
|       V11       V12       V13       V14       V15 
| 0.9966127 0.1480181 0.5604826 0.3292343 0.9983939 
| > mean(x)
| [1] 0.6065483
| > 
`----

Seems to work.

Based on this purely empirical observation, I applied this patch
to org:

--8<---------------cut here---------------start------------->8---
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 9f4eb4b..f3338cb 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -106,7 +106,7 @@ this variable.")
        as.is     = TRUE
      )
      close(con)
-     res
+     unlist(res)
    })"
   "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.")
@@ -126,7 +126,7 @@ This function is used when the table contains a header.")
        col.names = paste(\"V\", seq_len(%d), sep =\"\")
      )
      close(con)
-     res
+     unlist(res)
    })"
   "R code used to transfer a table defined as a variable from org to R.
 This function is used when the table does not contain a header.")
--8<---------------cut here---------------end--------------->8---

and the org file at the top works. But this clearly needs to be vetted
by an R expert.

The original example needs some changes to work, mainly simplification
of the #+names:

--8<---------------cut here---------------start------------->8---
    #+NAME: tbl-example-data
    #+BEGIN_SRC R :results value  
    runif(n=5, min=0, max=1)
    #+END_SRC
    
    #+NAME: R-mean
    #+BEGIN_SRC R :var x=tbl-example-data
    mean(x)
    #+END_SRC

    #+call: R-mean(x=tbl-example-data)
--8<---------------cut here---------------end--------------->8---

And assuming this is correct, the worg page will need to be corrected
too.

--
Nick

Re: cannot execute org-mode code from the front page tutorial.

[jenia.ivlev]

I can't make the changes - apply the your path - because my ob-R.el file
is completly different, its a elisp file and doesnt contain any R code.

The file is located at /usr/share/emacs/24.3/lisp/org/ob-R.el

Can you tell me how do I proceed to apply our changes to my emacs?

Thanks again for your help.

Jenia.

Re: cannot execute org-mode code from the front page tutorial.

[Nick Dokos]

jenia.ivlev@gmail.com (jenia.ivlev) writes:

> I can't make the changes - apply the your path - because my ob-R.el file
> is completly different, its a elisp file and doesnt contain any R code.
>
> The file is located at /usr/share/emacs/24.3/lisp/org/ob-R.el
>
> Can you tell me how do I proceed to apply our changes to my emacs?
>
> Thanks again for your help.
>

Sorry, I tested latest org (and wrongly assumed that that's what you are
using). Can you post the results of

        M-x org-version

here? I'll try to take a look at what goes wrong in that version.

For the record, the patch modifies the initialization of two
lisp constants that ob-R.el defines in its latest incarnation. This
change was introduced by Rainer Krug on June 23 with commit
4c415f38a5c71b45409faf9b59030ee7cee6abad. Before that, the values were
transmitted through temporary files. I hope Rainer (cc'ed) takes a look
at this thread: he is clearly the R expert here.

-- 
Nick

Re: cannot execute org-mode code from the front page tutorial.

[Nick Dokos]

jenia.ivlev@gmail.com (jenia.ivlev) writes:

> I can't make the changes - apply the your path - because my ob-R.el file
> is completly different, its a elisp file and doesnt contain any R code.
>
> The file is located at /usr/share/emacs/24.3/lisp/org/ob-R.el
>
> Can you tell me how do I proceed to apply our changes to my emacs?
>
> Thanks again for your help.
>
> Jenia.
>
>
>

Sorry, I tested latest org (and wrongly assumed that that's what you are
using). Can you post the results of

        M-x org-version

here? I'll try to take a look at what goes wrong in that version.

For the record, the patch modifies the initialization of two lisp
constants that ob-R.el defines in its latest incarnation. This change
was introduced by Rainer Krug on June 23 with commit
4c415f38a5c71b45409faf9b59030ee7cee6abad. Before that, the values were
transmitted through temporary files. I hope Rainer takes a look at this
thread: he is clearly the R expert here.

-- 
Nick

-- 
Nick

Re: cannot execute org-mode code from the front page tutorial.

[Charles Berry]

Nick Dokos <ndokos <at> gmail.com> writes:

> 
> tsd <at> tsdye.com (Thomas S. Dye) writes:
> 
> > Aloha Jenia,
> >
> > jenia.ivlev <at> gmail.com (jenia.ivlev) writes:
> >
> >> Hello.
> >>
> >> I'm trying to go through the org-mode tutorial on its official page.
> >>

[discussion showing that (if (listp value)...) generates a data.frame 
deleted]

[delete patch turning a data.frame into a vector]

> And assuming this is correct, the worg page will need to be corrected
> too.
>

No patch is needed.

The point of the code in  org-babel-R-assign-elisp is to create a data.frame
when `value' is a list.

The patch adding `unlist(res)' turns it into an ordinary vector.

This will break almost all uses of :var in R scr blocks.

I don't think this example could have worked for a long while - turning
elisp lists into R data.frames has been a feature for a good while. 
Also, note the use of `sbe' vs `org-sbe' in the formula.

#+TBLFM: @2$1='(sbe "R-mean" (x "tbl-example-data()"))


Use `colMeans(x)' to fix the worg page.

HTH,

Chuck

Re: cannot execute org-mode code from the front page tutorial.

[Thomas S. Dye]

Charles Berry <ccberry@ucsd.edu> writes:

> Nick Dokos <ndokos <at> gmail.com> writes:
>
>> 
>> tsd <at> tsdye.com (Thomas S. Dye) writes:
>> 
>> > Aloha Jenia,
>> >
>> > jenia.ivlev <at> gmail.com (jenia.ivlev) writes:
>> >
>> >> Hello.
>> >>
>> >> I'm trying to go through the org-mode tutorial on its official page.
>> >>
>
> [discussion showing that (if (listp value)...) generates a data.frame 
> deleted]
>
> [delete patch turning a data.frame into a vector]
>
>> And assuming this is correct, the worg page will need to be corrected
>> too.
>>
>
> No patch is needed.
>
> The point of the code in  org-babel-R-assign-elisp is to create a data.frame
> when `value' is a list.
>
> The patch adding `unlist(res)' turns it into an ordinary vector.
>
> This will break almost all uses of :var in R scr blocks.
>
> I don't think this example could have worked for a long while - turning
> elisp lists into R data.frames has been a feature for a good while. 
> Also, note the use of `sbe' vs `org-sbe' in the formula.
>
> #+TBLFM: @2$1='(sbe "R-mean" (x "tbl-example-data()"))
>
>
> Use `colMeans(x)' to fix the worg page.

Also, it appears that babel no longer supports passing variables through
the #+name: line.  I don't use this syntax and can't remember now
whether support for it was removed, or if it just withered away.

At any rate, if I use the #+header: syntax then I can get the example
working partially.  It is possible then to get the OP's desired result
with the #+call: line.  Changing (sbe ...) to (org-sbe ...) in the table
calculates the mean, but doesn't yield a real table.  The initial "|" on
the last line is missing. 

#+NAME: tbl-example-data
#+BEGIN_SRC R :results value  
runif(n=5, min=0, max=1)
#+END_SRC

#+RESULTS: tbl-example-data
|   0.850588989211246 |
|   0.138243367196992 |
|   0.382761054905131 |
| 0.00688096368685365 |
|   0.394350948277861 |

#+NAME: R-mean
#+header: :var x=""
#+header: :results output
#+BEGIN_SRC R 
colMeans(x)
#+END_SRC

#+call: R-mean(x=tbl-example-data)

#+results:
:        V1 
: 0.4273072 

#+tblname: summaries
| mean |
|------|
| V1   |
0.2574993|
#+TBLFM: @2$1='(org-sbe "R-mean" (x "tbl-example-data()"))

hth,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: cannot execute org-mode code from the front page tutorial.

[Nick Dokos]

Charles Berry <ccberry@ucsd.edu> writes:

> Nick Dokos <ndokos <at> gmail.com> writes:
>
>> 
>> tsd <at> tsdye.com (Thomas S. Dye) writes:
>> 
>> > Aloha Jenia,
>> >
>> > jenia.ivlev <at> gmail.com (jenia.ivlev) writes:
>> >
>> >> Hello.
>> >>
>> >> I'm trying to go through the org-mode tutorial on its official page.
>> >>
>
> [discussion showing that (if (listp value)...) generates a data.frame 
> deleted]
>

Ah, that's what's happening!

> [delete patch turning a data.frame into a vector]
>
>> And assuming this is correct, the worg page will need to be corrected
>> too.
>>
>
> No patch is needed.
>
> The point of the code in  org-babel-R-assign-elisp is to create a data.frame
> when `value' is a list.
>
> The patch adding `unlist(res)' turns it into an ordinary vector.
>
> This will break almost all uses of :var in R scr blocks.
>
> I don't think this example could have worked for a long while - turning
> elisp lists into R data.frames has been a feature for a good while. 
> Also, note the use of `sbe' vs `org-sbe' in the formula.
>
> #+TBLFM: @2$1='(sbe "R-mean" (x "tbl-example-data()"))
>
> Use `colMeans(x)' to fix the worg page.
>

Thanks! As penance, I'll try to fix the worg page (unless somebody beats
me to it of cource).

-- 
Nick