using variables defined by org mode table in R leads to invalid function error on remote host

using variables defined by org mode table in R leads to invalid function error on remote host

[Johannes Meisig]

Hi,

adding to this question:

http://lists.gnu.org/archive/html/emacs-orgmode/2012-06/msg00677.html

I have the following problem. If I define a table in an .org file and 
then try to use it in R as a variable, it's no problem on the local 
host. However, remotely I get the error:

Invalid function: with-parsed-tramp-file-name

The following code lines are sort of a minmal example for the behavior: 
(leave the first line away for local execution)

#+PROPERTY: dir /foo@bar://home/user

#+TBLNAME: genes
| names              |
|--------------------|
| ENSMUSG00000000031 |
| ENSMUSG00000063856 |
| ENSMUSG00000006056 |


#+BEGIN_SRC R :session :var genes=genes
print(genes[,1])
#+END_SRC

Any ideas? Thanks a lot,

Johannes

Re: using variables defined by org mode table in R leads to invalid function error on remote host

[Eric Schulte]

Johannes Meisig <j.meisig@biologie.hu-berlin.de> writes:

> Hi,
>
> adding to this question:
>
> http://lists.gnu.org/archive/html/emacs-orgmode/2012-06/msg00677.html
>
> I have the following problem. If I define a table in an .org file and 
> then try to use it in R as a variable, it's no problem on the local 
> host. However, remotely I get the error:
>
> Invalid function: with-parsed-tramp-file-name
>

On my system that function is provided by tramp.el, so maybe adding

  (require 'tramp)

to your .emacs will solve this problem.

Best,

>
> The following code lines are sort of a minmal example for the
>behavior:
> (leave the first line away for local execution)
>
> #+PROPERTY: dir /foo@bar://home/user
>
> #+TBLNAME: genes
> | names              |
> |--------------------|
> | ENSMUSG00000000031 |
> | ENSMUSG00000063856 |
> | ENSMUSG00000006056 |
>
>
> #+BEGIN_SRC R :session :var genes=genes
> print(genes[,1])
> #+END_SRC
>
> Any ideas? Thanks a lot,
>
> Johannes
>

-- 
Eric Schulte
http://cs.unm.edu/~eschulte

Re: using variables defined by org mode table in R leads to invalid function error on remote host

[Johannes Meisig]

Hi Eric,

No, (require 'tramp) doesn't solve the problem. However,
commenting out

(declare-function with-parsed-tramp-file-name "tramp" (filename var 
&rest body))

in ob.el does the job. However, this can hardly be the solution (Also, 
it doesn't get rid of the error message in the minibuffer).

Johannes

On 07/08/2012 03:37 PM, Eric Schulte wrote:
> Johannes Meisig <j.meisig@biologie.hu-berlin.de> writes:
>
>> Hi,
>>
>> adding to this question:
>>
>> http://lists.gnu.org/archive/html/emacs-orgmode/2012-06/msg00677.html
>>
>> I have the following problem. If I define a table in an .org file and
>> then try to use it in R as a variable, it's no problem on the local
>> host. However, remotely I get the error:
>>
>> Invalid function: with-parsed-tramp-file-name
>>
> On my system that function is provided by tramp.el, so maybe adding
>
>    (require 'tramp)
>
> to your .emacs will solve this problem.
>
> Best,
>
>> The following code lines are sort of a minmal example for the
>> behavior:
>> (leave the first line away for local execution)
>>
>> #+PROPERTY: dir /foo@bar://home/user
>>
>> #+TBLNAME: genes
>> | names              |
>> |--------------------|
>> | ENSMUSG00000000031 |
>> | ENSMUSG00000063856 |
>> | ENSMUSG00000006056 |
>>
>>
>> #+BEGIN_SRC R :session :var genes=genes
>> print(genes[,1])
>> #+END_SRC
>>
>> Any ideas? Thanks a lot,
>>
>> Johannes
>>