[babel] Working dir incorrect

[babel] Working dir incorrect

[Loris Bennett]

Hi,

In a file that used to work, when I now try to run some R code which
generates an image, I get the error:

  cannot open file './usage_users_historical_facet.pdf'

If I check the working directory for the R session I see

  getwd()
  [1] "/usr/share/emacs/site-lisp/ess"

instead of the directory in which my org file is located.

I am now running Org 9.0.5 on Emacs 25.1.1.  The last time things worked
I was definitely using an older version of Org and possibly Emacs 24.

Any thoughts?

Cheers,

Loris

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Re: [babel] Working dir incorrect

[Nick Dokos]

"Loris Bennett" <loris.bennett@fu-berlin.de> writes:

> Hi,
>
> In a file that used to work, when I now try to run some R code which
> generates an image, I get the error:
>
>   cannot open file './usage_users_historical_facet.pdf'
>
> If I check the working directory for the R session I see
>
>   getwd()
>   [1] "/usr/share/emacs/site-lisp/ess"
>
> instead of the directory in which my org file is located.
>
> I am now running Org 9.0.5 on Emacs 25.1.1.  The last time things worked
> I was definitely using an older version of Org and possibly Emacs 24.
>
> Any thoughts?
>

Can I make a plea for an ECM? If you provide one, I can spend five
minutes testing it, but without it I'll have to do real work to get an
example together and that's much more unlikely to happen.

-- 
Nick

Re: [babel] Working dir incorrect

[John Hendy]

On Mon, Mar 13, 2017 at 9:32 AM, Loris Bennett
<loris.bennett@fu-berlin.de> wrote:
> Hi,
>
> In a file that used to work, when I now try to run some R code which
> generates an image, I get the error:
>
>   cannot open file './usage_users_historical_facet.pdf'
>
> If I check the working directory for the R session I see
>
>   getwd()
>   [1] "/usr/share/emacs/site-lisp/ess"
>
> instead of the directory in which my org file is located.
>
> I am now running Org 9.0.5 on Emacs 25.1.1.  The last time things worked
> I was definitely using an older version of Org and possibly Emacs 24.
>
> Any thoughts?

I agree with Nick on an ECM. Just to start the ball rolling:

M-x org-version
Org mode version 9.0.5 (release_9.0.5-288-g4caad0 @
/home/jwhendy/.elisp/org/lisp/)

$ emacs --version
GNU Emacs 25.1.1

#+begin_src min-config

;; set load paths
(add-to-list 'load-path "~/.elisp/org.git/lisp/")
(add-to-list 'load-path "~/.elisp/org.git/contrib/lisp/")
(add-to-list 'load-path "~/.elisp/ess/lisp/")

(require 'ess-site)

;; setup babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)))

#+end_src

method:
- emacs -Q
- M-x load-file /path/to/min-config
- C-c C-c on both of these blocks and get the results as shown

;;;;;;;; file: ~/Desktop/test.org ;;;;;;;;;

* heading

#+begin_src R

getwd()

#+end_src

#+RESULTS:
: /home/jwhendy/Desktop

#+begin_src R :session r

getwd()

#+end_src

#+RESULTS:
: /home/jwhendy/Desktop

;;;;;;;;;;;;;;;;;


How does this go for you?
John

>
> Cheers,
>
> Loris
>
> --
> This signature is currently under construction.
>
>

Re: [babel] Working dir incorrect

[Eric S Fraga]

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On Monday, 13 Mar 2017 at 15:42, Nick Dokos wrote:

[...]

> Can I make a plea for an ECM? If you provide one, I can spend five
> minutes testing it, but without it I'll have to do real work to get an
> example together and that's much more unlikely to happen.

I've found that babel languages that start specific buffers that
persist (e.g. octave, gnuplot) will be started in a particular
directory based on a given org file.  If subsequently another org file,
in a different directory, is visited, babel won't change the directory
for existing babel buffers (and probably cannot easily do so in some
cases?).

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 26.0.50.1, Org release_9.0.4-242-g2c27b8

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Re: [babel] Working dir incorrect

[Loris Bennett]

Hi John,

John Hendy <jw.hendy@gmail.com> writes:

> On Mon, Mar 13, 2017 at 9:32 AM, Loris Bennett
> <loris.bennett@fu-berlin.de> wrote:
>> Hi,
>>
>> In a file that used to work, when I now try to run some R code which
>> generates an image, I get the error:
>>
>>   cannot open file './usage_users_historical_facet.pdf'
>>
>> If I check the working directory for the R session I see
>>
>>   getwd()
>>   [1] "/usr/share/emacs/site-lisp/ess"
>>
>> instead of the directory in which my org file is located.
>>
>> I am now running Org 9.0.5 on Emacs 25.1.1.  The last time things worked
>> I was definitely using an older version of Org and possibly Emacs 24.
>>
>> Any thoughts?
>
> I agree with Nick on an ECM. Just to start the ball rolling:
>
> M-x org-version
> Org mode version 9.0.5 (release_9.0.5-288-g4caad0 @
> /home/jwhendy/.elisp/org/lisp/)
>
> $ emacs --version
> GNU Emacs 25.1.1
>
> #+begin_src min-config
>
> ;; set load paths
> (add-to-list 'load-path "~/.elisp/org.git/lisp/")
> (add-to-list 'load-path "~/.elisp/org.git/contrib/lisp/")
> (add-to-list 'load-path "~/.elisp/ess/lisp/")
>
> (require 'ess-site)
>
> ;; setup babel languages
> (org-babel-do-load-languages
>  'org-babel-load-languages
>  '((R . t)))
>
> #+end_src
>
>
> method:
> - emacs -Q
> - M-x load-file /path/to/min-config
> - C-c C-c on both of these blocks and get the results as shown
>
> ;;;;;;;; file: ~/Desktop/test.org ;;;;;;;;;
>
> * heading
>
> #+begin_src R
>
> getwd()
>
> #+end_src
>
>
> #+RESULTS:
> : /home/jwhendy/Desktop
>
> #+begin_src R :session r
>
> getwd()
>
> #+end_src
>
> #+RESULTS:
> : /home/jwhendy/Desktop
>
> ;;;;;;;;;;;;;;;;;
>
>
> How does this go for you?

Thanks for doing most of the work for me.  Unfortunately for me, the ECM
works fine, so I'm going to have to do some work myself and debug my
crufty old .emacs.

Thanks again,

Loris

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Re: [babel] Working dir incorrect

[numbchild]

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Yes, it seems like this, I have a similar question at here:
https://lists.gnu.org/archive/html/emacs-orgmode/2017-03/msg00283.html

[stardiviner]           <Hack this world!>      GPG key ID: 47C32433
IRC(freeenode): stardiviner                     Twitter:  @numbchild
Key fingerprint = 9BAA 92BC CDDD B9EF 3B36  CB99 B8C4 B8E5 47C3 2433
Blog: http://stardiviner.github.io/

On Tue, Mar 14, 2017 at 3:28 PM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> On Monday, 13 Mar 2017 at 15:42, Nick Dokos wrote:
>
> [...]
>
> > Can I make a plea for an ECM? If you provide one, I can spend five
> > minutes testing it, but without it I'll have to do real work to get an
> > example together and that's much more unlikely to happen.
>
> I've found that babel languages that start specific buffers that
> persist (e.g. octave, gnuplot) will be started in a particular
> directory based on a given org file.  If subsequently another org file,
> in a different directory, is visited, babel won't change the directory
> for existing babel buffers (and probably cannot easily do so in some
> cases?).
>
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 26.0.50.1, Org release_9.0.4-242-g2c27b8
>

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Re: [babel] Working dir incorrect

[Loris Bennett]

Hi,

"Loris Bennett" <loris.bennett@fu-berlin.de> writes:

> Hi John,
>
> John Hendy <jw.hendy@gmail.com> writes:
>
>> On Mon, Mar 13, 2017 at 9:32 AM, Loris Bennett
>> <loris.bennett@fu-berlin.de> wrote:
>>> Hi,
>>>
>>> In a file that used to work, when I now try to run some R code which
>>> generates an image, I get the error:
>>>
>>>   cannot open file './usage_users_historical_facet.pdf'
>>>
>>> If I check the working directory for the R session I see
>>>
>>>   getwd()
>>>   [1] "/usr/share/emacs/site-lisp/ess"
>>>
>>> instead of the directory in which my org file is located.
>>>
>>> I am now running Org 9.0.5 on Emacs 25.1.1.  The last time things worked
>>> I was definitely using an older version of Org and possibly Emacs 24.
>>>
>>> Any thoughts?
>>
>> I agree with Nick on an ECM. Just to start the ball rolling:
>>
[snip (54 lines)]
>>
>> How does this go for you?
>
> Thanks for doing most of the work for me.  Unfortunately for me, the ECM
> works fine, so I'm going to have to do some work myself and debug my
> crufty old .emacs.

I finally got round to bisecting my .emacs and worked out the sequence
of events which lead me to shooting myself in the foot:

1. Installed Emacs 25 under /usr/local
2. Discovered that Emacs 25 couldn't find the ESS stuff
3. Defined a variable 'ess-directory' to be "/usr/share/emacs/site-lisp/ess/"
4. Used the variable in a function to add ESS to the load-path 

It turns out that variable 'ess-directory' already exists and is, according
to the documentation, "the directory ESS is run from".

Thus renaming the variable 'ess-directory' to
'non-in-the-foot-shooting-ess-directory' solves the problem.

Cheers,

Loris

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