[BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)]

[BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)]

[Sam Crawford]

When running an R session for org babel, if the working directory of
that session is different to the directory of the org file, then source
blocks with :results (output) graphics file will not work correctly. I
believe this is due to the fact that
org-babel-R-construct-graphics-device-call uses a relative filename.

I'm not sure what the best way to fix this is. My workaround was to
replace out-file with (file-name-concat default-directory out-file) in
the call to format at the end of 
org-babel-R-construct-graphics-device-call, but I'm not convinced this
is the best way to do things.


Emacs : GNU Emacs 30.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.42, cairo version 1.18.0)
of 2024-06-21
Package: Org mode version 9.8-pre (release_9.7.4-80-g7fa169 @ /var/home/sam/.emacs.d/straight/build/org/)

Re: [BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)]

[Ihor Radchenko]

Sam Crawford <sam@crawf.uk> writes:

> When running an R session for org babel, if the working directory of
> that session is different to the directory of the org file, then source
> blocks with :results (output) graphics file will not work correctly. I
> believe this is due to the fact that
> org-babel-R-construct-graphics-device-call uses a relative filename.

May you please create a reproducer?

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

[POLL] ob-R, ob-julia: Should we force-disable ess-ask-for-ess-directory? (was: [BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)])

[Ihor Radchenko]

[ Adding Org mailing list back to CC to keep the conversation public ]

Sam Crawford <sam@crawf.uk> writes:

>>  May you please create a reproducer?
>
> Sure: evaluating the following code cell
>
> #+begin_src R :session R :async yes :results file graphics :file test.png
>   plot(iris$Sepal.Length, iris$Sepal.Width)
> #+end_src
>
> will call run-ess-r, which gives a prompt asking for the "R starting directory". Selecting any directory other than the directory the org file is located in will cause the issue.

I can reproduce, but I am not sure if this is something we are supposed
to fix.

The Org mode manual says the following about :dir header argument in
code blocks:

    The ‘dir’ header argument specifies the default directory during code
    block execution.  If it is absent, then the directory associated with
    the current buffer is used.
    ...
       When ‘dir’ is used with ‘session’, Org sets the starting directory
    for a new session.  But Org does not alter the directory of an already
    existing session.

ob-R currently does not obey what the manual says, and, when :dir is
omitted, allows the session directory to be set via prompt rather than
keeping the Org buffer's directory.

I'd like to hear from ob-R/ob-julia users whether the current behavior
is something they rely on. If not, I'd prefer to follow the conventions
we introduce in the manual and suppress the ESS's directory prompt.

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>

Re: [POLL] ob-R, ob-julia: Should we force-disable ess-ask-for-ess-directory? (was: [BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)])

[Rudolf Adamkovič]

Ihor Radchenko <yantar92@posteo.net> writes:

> I'd like to hear from ob-R/ob-julia users whether the current behavior
> is something they rely on. If not, I'd prefer to follow the conventions
> we introduce in the manual and suppress the ESS's directory prompt.

+1 from me; I have always found that ESS prompt annoying.

Rudy
-- 
"Chop your own wood and it will warm you twice."
--- Henry Ford; Francis Kinloch, 1819; Henry David Thoreau, 1854

Rudolf Adamkovič <rudolf@adamkovic.org> [he/him]
http://adamkovic.org

Re: [POLL] ob-R, ob-julia: Should we force-disable ess-ask-for-ess-directory? (was: [BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)])

[Christian Moe]

Rudolf Adamkovič writes:

> Ihor Radchenko <yantar92@posteo.net> writes:
>
>> I'd like to hear from ob-R/ob-julia users whether the current behavior
>> is something they rely on. If not, I'd prefer to follow the conventions
>> we introduce in the manual and suppress the ESS's directory prompt.
>
> +1 from me; I have always found that ESS prompt annoying.
>
> Rudy

+1; same, and I (rightly or wrongly) never rely on it for anything

Christian

Re: [POLL] ob-R, ob-julia: Should we force-disable ess-ask-for-ess-directory?

[Suhail Singh]

Ihor Radchenko <yantar92@posteo.net> writes:

> I'd like to hear from ob-R/ob-julia users whether the current behavior
> is something they rely on.

It's a (minor) nuisance, but one I'd be happy to have fixed.

-- 
Suhail

Re: [POLL] ob-R, ob-julia: Should we force-disable ess-ask-for-ess-directory? (was: [BUG] Relative filenames for graphics output in ob-R.el [9.8-pre (release_9.7.4-80-g7fa169)])

[Ihor Radchenko]

Ihor Radchenko <yantar92@posteo.net> writes:

> I'd like to hear from ob-R/ob-julia users whether the current behavior
> is something they rely on. If not, I'd prefer to follow the conventions
> we introduce in the manual and suppress the ESS's directory prompt.

The responses expressed no objections to the change.
So, ob-R and ob-julia now obey the working directory conventions common
for the rest of babel backends - use default-directory or :dir; no
queries.

Closed.
https://git.savannah.gnu.org/cgit/emacs/org-mode.git/commit/?id=62b88d613e

-- 
Ihor Radchenko // yantar92,
Org mode contributor,
Learn more about Org mode at <https://orgmode.org/>.
Support Org development at <https://liberapay.com/org-mode>,
or support my work at <https://liberapay.com/yantar92>