[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>

The ob-R :results graphics file :dir "images" :file "plot.png" specified directory not working

[stardiviner]

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This seems not working, I have following example:

In Org mode file "~/Org/Programming/R/test.org"

#+begin_src R :results graphics file :dir "images" :file "hist_rnorm.png"
x <- rnorm(100)
print(mean(x))
hist(x)
#+end_src

#+RESULTS[(2025-01-14 11:19:59) 2387108d2b01bf63b1eac4044a7430ea7ba87466]:
[[file:images/hist_rnorm.png]]

The generated plot image "images/hist_rnorm.png" is NOT in
"~/Org/Programming/R/images/hist_rnorm.png". It's in "~/Org/hist_rnorm.png".

My environment:
- Emacs version: GNU Emacs 31.0.50 (commit nil)
- Org mode version: 9.8-pre (using branch "main" latest commit "c2d57df0e")

[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, Aug 6, 2024 at 4:42 PM Ihor Radchenko <yantar92@posteo.net> wrote:

> 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>
>
>

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Re: The ob-R :results graphics file :dir "images" :file "plot.png" specified directory not working

[stardiviner]

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I tested using org-mode's `make repro` clean Emacs & org-mode environment
instance. It works fine. I double checked my Emacs init file about R
settings. Have not found suspicious config.
Here is my reproduce test.


[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, Jan 14, 2025 at 1:10 PM stardiviner <numbchild@gmail.com> wrote:

> This seems not working, I have following example:
>
> In Org mode file "~/Org/Programming/R/test.org"
>
> #+begin_src R :results graphics file :dir "images" :file "hist_rnorm.png"
> x <- rnorm(100)
> print(mean(x))
> hist(x)
> #+end_src
>
> #+RESULTS[(2025-01-14 11:19:59) 2387108d2b01bf63b1eac4044a7430ea7ba87466]:
> [[file:images/hist_rnorm.png]]
>
> The generated plot image "images/hist_rnorm.png" is NOT in
> "~/Org/Programming/R/images/hist_rnorm.png". It's in
> "~/Org/hist_rnorm.png".
>
> My environment:
> - Emacs version: GNU Emacs 31.0.50 (commit nil)
> - Org mode version: 9.8-pre (using branch "main" latest commit "c2d57df0e")
>
> [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, Aug 6, 2024 at 4:42 PM Ihor Radchenko <yantar92@posteo.net> wrote:
>
>> 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>
>>
>>

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* test org-mode

#+begin_src sh
# open a clean Emacs & Org mode instance.
make repro
#+end_src

* load ESS

#+begin_src emacs-lisp
(package-initialize)
#+end_src

#+begin_src emacs-lisp
(use-package ess
  :ensure t
  :defer t
  :mode (("\\.[rR]\\'" . R-mode)
         ("\\.Rd\\'" . Rd-mode) ; R documentation
         ("\\.Rprofile\\'" . R-mode)
         ("\\.Renviron\\'" . R-mode)
         ("\\.S\\'" . S-mode))
  :commands (R run-ess-r)
  :custom ((ess-ask-for-ess-directory nil) ; suppress ESS from prompting for session directory
           (ess-R-readline nil) ; whether start REPL with `--no-readline' argument?
           ;; (inferior-ess-primary-prompt "ℝ> ") ; customized R prompt
           ;; (inferior-S-prompt "[]a-zA-Z0-9.[]*\\(?:[>+.] \\)*ℝ+> ") ; handle the custom ℝ prompt
           (ess-use-ido nil)
           (ess-describe-at-point-method 'tooltip)
           (ess-eval-visibly nil) ; speedup eval without show the eval commands.
           (ess-use-company t)
           (ess-use-auto-complete nil))
  :init
  (add-to-list 'display-buffer-alist '("\\*R[:*:*]?\\*" . (display-buffer-below-selected)))
  (add-to-list 'display-buffer-alist '("\\*help\\[R\\]\\(.*\\)\\*" . (display-buffer-below-selected)))
  (add-to-list 'display-buffer-alist '("\\*ess-apropos\\[R\\]\\(.*\\)\\*" . (display-buffer-below-selected)))
  :config
  ;; auto start ESS inferior process
  ;; (add-hook 'ess-mode-hook #'ess-force-buffer-current)

  ;; quickly insert assign operator: <-
  (with-eval-after-load 'ess-mode
    (define-key ess-mode-map (kbd "C-c =") (lambda () (interactive) (insert " <- ")))))
#+end_src

#+RESULTS:
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R-mode) (\.gpg\(~\|\.~[0-9]+~\)?\' nil epa-file) (\.elc\' . elisp-byte-code-mode) (\.zst\' nil jka-compr) (\.dz\' nil jka-compr) (\.xz\' nil jka-compr) (\.lzma\' nil jka-compr) (\.lz\' nil jka-compr) (\.g?z\' nil jka-compr) (\.bz2\' nil jka-compr) (\.Z\' nil jka-compr) (\.vr[hi]?\' . vera-mode) (\(?:\.\(?:rbw?\|ru\|rake\|thor\|axlsx\|jbuilder\|rabl\|gemspec\|podspec\)\|/\(?:Gem\|Rake\|Cap\|Thor\|Puppet\|Berks\|Brew\|Fast\|Vagrant\|Guard\|Pod\)file\)\' . ruby-mode) (\.re?st\' . rst-mode) (/\(?:Pipfile\|\.?flake8\)\' . conf-mode) (\(?:\.\(?:p\(?:th\|y[iw]?\)\)\|/\(?:SCons\(?:\(?:crip\|truc\)t\)\)\)\' . python-mode) (\.m\' . octave-maybe-mode) (\.less\' . less-css-mode) (\.editorconfig\' . editorconfig-conf-mode) (\.scss\' . scss-mode) (\.cs\' . csharp-mode) (\.awk\' . awk-mode) (\.\(u?lpc\|pike\|pmod\(\.in\)?\)\' . pike-mode) (\.idl\' . idl-mode) (\.java\' . java-mode) (\.m\' . objc-mode) (\.ii\' . c++-mode) (\.i\' . c-mode) (\.lex\' . c-mode) (\.y\(acc\)?\' . c-mode) (\.h\' . c-or-c++-mode) (\.c\' . c-mode) (\.\(CC?\|HH?\)\' . c++-mode) (\.[ch]\(pp\|xx\|\+\+\)\' . c++-mode) (\.\(cc\|hh\)\' . c++-mode) (\.\(bat\|cmd\)\' . bat-mode) (\.[sx]?html?\(\.[a-zA-Z_]+\)?\' . mhtml-mode) (\.svgz?\' . image-mode) (\.svgz?\' . xml-mode) (\.x[bp]m\' . image-mode) (\.x[bp]m\' . c-mode) (\.p[bpgn]m\' . image-mode) (\.tiff?\' . image-mode) (\.gif\' . image-mode) (\.png\' . image-mode) (\.jpe?g\' . image-mode) (\.webp\' . image-mode) (\.te?xt\' . text-mode) (\.[tT]e[xX]\' . tex-mode) (\.ins\' . tex-mode) (\.ltx\' . latex-mode) (\.dtx\' . doctex-mode) (\.org\' . org-mode) (\.dir-locals\(?:-2\)?\.el\' . lisp-data-mode) (\.eld\' . lisp-data-mode) (eww-bookmarks\' . lisp-data-mode) (tramp\' . lisp-data-mode) (/archive-contents\' . lisp-data-mode) (places\' . lisp-data-mode) (\.emacs-places\' . lisp-data-mode) (\.el\' . emacs-lisp-mode) (Project\.ede\' . emacs-lisp-mode) (\(?:\.\(?:scm\|sls\|sld\|stk\|ss\|sch\)\|/\.guile\)\' . scheme-mode) (\.l\' . lisp-mode) (\.li?sp\' . 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. sh-mode) (/PKGBUILD\' . sh-mode) (\(/\|\`\)\.\(bash_\(profile\|history\|log\(in\|out\)\)\|z?log\(in\|out\)\)\' . sh-mode) (\(/\|\`\)\.\(shrc\|zshrc\|m?kshrc\|bashrc\|t?cshrc\|esrc\)\' . sh-mode) (\(/\|\`\)\.\([kz]shenv\|xinitrc\|startxrc\|xsession\)\' . sh-mode) (\.m?spec\' . sh-mode) (\.m[mes]\' . nroff-mode) (\.man\' . nroff-mode) (\.sty\' . latex-mode) (\.cl[so]\' . latex-mode) (\.bbl\' . latex-mode) (\.bib\' . bibtex-mode) (\.bst\' . bibtex-style-mode) (\.sql\' . sql-mode) (\(acinclude\|aclocal\|acsite\)\.m4\' . autoconf-mode) (\.m[4c]\' . m4-mode) (\.mf\' . metafont-mode) (\.mp\' . metapost-mode) (\.vhdl?\' . vhdl-mode) (\.article\' . text-mode) (\.letter\' . text-mode) (\.i?tcl\' . tcl-mode) (\.exp\' . tcl-mode) (\.itk\' . tcl-mode) (\.icn\' . icon-mode) (\.sim\' . simula-mode) (\.mss\' . scribe-mode) (\.f9[05]\' . f90-mode) (\.f0[38]\' . f90-mode) (\.indent\.pro\' . fundamental-mode) (\.\(pro\|PRO\)\' . idlwave-mode) (\.srt\' . srecode-template-mode) (\.prolog\' . prolog-mode) (\.tar\' . tar-mode) (\.\(arc\|zip\|lzh\|lha\|zoo\|[jew]ar\|xpi\|rar\|cbr\|7z\|squashfs\|ARC\|ZIP\|LZH\|LHA\|ZOO\|[JEW]AR\|XPI\|RAR\|CBR\|7Z\|SQUASHFS\)\' . archive-mode) (\.oxt\' . archive-mode) (\.\(deb\|[oi]pk\)\' . archive-mode) (\`/tmp/Re . text-mode) (/Message[0-9]*\' . text-mode) (\`/tmp/fol/ . text-mode) (\.oak\' . scheme-mode) (\.sgml?\' . sgml-mode) (\.x[ms]l\' . xml-mode) (\.dbk\' . xml-mode) (\.dtd\' . sgml-mode) (\.ds\(ss\)?l\' . dsssl-mode) (\.js[mx]?\' . javascript-mode) (\.har\' . javascript-mode) (\.json\' . js-json-mode) (\.[ds]?va?h?\' . verilog-mode) (\.by\' . bovine-grammar-mode) (\.wy\' . wisent-grammar-mode) (\.erts\' . erts-mode) ([:/\]\..*\(emacs\|gnus\|viper\)\' . emacs-lisp-mode) (\`\..*emacs\' . emacs-lisp-mode) ([:/]_emacs\' . emacs-lisp-mode) (/crontab\.X*[0-9]+\' . shell-script-mode) (\.ml\' . lisp-mode) (\.ld[si]?\' . ld-script-mode) (ld\.?script\' . ld-script-mode) (\.xs\' . c-mode) (\.x[abdsru]?[cnw]?\' . ld-script-mode) (\.zone\' . dns-mode) (\.soa\' . dns-mode) (\.asd\' . lisp-mode) (\.\(asn\|mib\|smi\)\' . snmp-mode) (\.\(as\|mi\|sm\)2\' . snmpv2-mode) (\.\(diffs?\|patch\|rej\)\' . diff-mode) (\.\(dif\|pat\)\' . diff-mode) (\.[eE]?[pP][sS]\' . ps-mode) (\.\(?:PDF\|EPUB\|CBZ\|FB2\|O?XPS\|DVI\|OD[FGPST]\|DOCX\|XLSX?\|PPTX?\|pdf\|epub\|cbz\|fb2\|o?xps\|djvu\|dvi\|od[fgpst]\|docx\|xlsx?\|pptx?\)\' . doc-view-mode-maybe) (configure\.\(ac\|in\)\' . autoconf-mode) (\.s\(v\|iv\|ieve\)\' . sieve-mode) (BROWSE\' . ebrowse-tree-mode) (\.ebrowse\' . ebrowse-tree-mode) (#\*mail\* . mail-mode) (\.g\' . antlr-mode) (\.mod\' . m2-mode) (\.ses\' . ses-mode) (\.docbook\' . sgml-mode) (\.com\' . dcl-mode) (/config\.\(?:bat\|log\)\' . fundamental-mode) (/\.?\(authinfo\|netrc\)\' . authinfo-mode) (\.\(?:[iI][nN][iI]\|[lL][sS][tT]\|[rR][eE][gG]\|[sS][yY][sS]\)\' . conf-mode) (\.la\' . conf-unix-mode) (\.ppd\' . conf-ppd-mode) (java.+\.conf\' . conf-javaprop-mode) (\.properties\(?:\.[a-zA-Z0-9._-]+\)?\' . conf-javaprop-mode) (\.toml\' . conf-toml-mode) (\.desktop\' . conf-desktop-mode) (/\.redshift\.conf\' . conf-windows-mode) (\`/etc/\(?:DIR_COLORS\|ethers\|.?fstab\|.*hosts\|lesskey\|login\.?de\(?:fs\|vperm\)\|magic\|mtab\|pam\.d/.*\|permissions\(?:\.d/.+\)?\|protocols\|rpc\|services\)\' . conf-space-mode) (\`/etc/\(?:acpid?/.+\|aliases\(?:\.d/.+\)?\|default/.+\|group-?\|hosts\..+\|inittab\|ksysguarddrc\|opera6rc\|passwd-?\|shadow-?\|sysconfig/.+\)\' . conf-mode) ([cC]hange[lL]og[-.][-0-9a-z]+\' . change-log-mode) (/\.?\(?:gitconfig\|gnokiirc\|hgrc\|kde.*rc\|mime\.types\|wgetrc\)\' . conf-mode) (/\.mailmap\' . conf-unix-mode) (/\.\(?:asound\|enigma\|fetchmail\|gltron\|gtk\|hxplayer\|mairix\|mbsync\|msmtp\|net\|neverball\|nvidia-settings-\|offlineimap\|qt/.+\|realplayer\|reportbug\|rtorrent\.\|screen\|scummvm\|sversion\|sylpheed/.+\|xmp\)rc\' . conf-mode) (/\.\(?:gdbtkinit\|grip\|mpdconf\|notmuch-config\|orbital/.+txt\|rhosts\|tuxracer/options\)\' . conf-mode) (/\.?X\(?:default\|resource\|re\)s\> . conf-xdefaults-mode) (/X11.+app-defaults/\|\.ad\' . conf-xdefaults-mode) (/X11.+locale/.+/Compose\' . conf-colon-mode) (/X11.+locale/compose\.dir\' . conf-javaprop-mode) (\.~?[0-9]+\.[0-9][-.0-9]*~?\' nil t) (\.\(?:orig\|in\|[bB][aA][kK]\)\' nil t) ([/.]c\(?:on\)?f\(?:i?g\)?\(?:\.[a-zA-Z0-9._-]+\)?\' . conf-mode-maybe) (\.[1-9]\' . nroff-mode) (\.art\' . image-mode) (\.avs\' . image-mode) (\.bmp\' . image-mode) (\.cmyk\' . image-mode) (\.cmyka\' . image-mode) (\.crw\' . image-mode) (\.dcr\' . image-mode) (\.dcx\' . image-mode) (\.dng\' . image-mode) (\.dpx\' . image-mode) (\.fax\' . image-mode) (\.heic\' . image-mode) (\.hrz\' . image-mode) (\.icb\' . image-mode) (\.icc\' . image-mode) (\.icm\' . image-mode) (\.ico\' . image-mode) (\.icon\' . image-mode) (\.jbg\' . image-mode) (\.jbig\' . image-mode) (\.jng\' . image-mode) (\.jnx\' . image-mode) (\.miff\' . image-mode) (\.mng\' . image-mode) (\.mvg\' . image-mode) (\.otb\' . image-mode) (\.p7\' . image-mode) (\.pcx\' . image-mode) (\.pdb\' . image-mode) (\.pfa\' . image-mode) (\.pfb\' . image-mode) (\.picon\' . image-mode) (\.pict\' . image-mode) (\.rgb\' . image-mode) (\.rgba\' . image-mode) (\.tga\' . image-mode) (\.wbmp\' . image-mode) (\.webp\' . image-mode) (\.wmf\' . image-mode) (\.wpg\' . image-mode) (\.xcf\' . image-mode) (\.xmp\' . image-mode) (\.xwd\' . image-mode) (\.yuv\' . image-mode) (\.tgz\' . tar-mode) (\.tbz2?\' . tar-mode) (\.txz\' . tar-mode) (\.tzst\' . tar-mode))

* load ob-R

#+begin_src emacs-lisp
(use-package ob-R
  :defer t
  :after org
  :init
  (add-to-list 'org-babel-load-languages '(R . t))
  (org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)
  (add-to-list 'org-src-lang-modes '("R" . R)) ; `ess-r-mode'
  (add-to-list 'org-babel-tangle-lang-exts '("R" . "R"))
  :config
  (setq org-babel-default-header-args:R
        '((:session . "*R*")
          (:exports . "both")
          (:results . "replace")
          ;; customize R plot window
          ;; (:width . 640)
          ;; (:height . 640)
          ;; (:bg . "white")
          ;; (:type . :any)
          )))
#+end_src

#+RESULTS:
: t

* test ob-R

#+begin_src R :results graphics file :dir "images" :file "hist_rnorm.png"
x <- rnorm(100)
print(mean(x))
hist(x)
#+end_src

#+RESULTS:
[[file:images/hist_rnorm.png]]

Re: The ob-R :results graphics file :dir "images" :file "plot.png" specified directory not working

[sam--- via General discussions about Org-mode.]

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On 2025-01-14 05:29, stardiviner wrote:

> I tested using org-mode's `make repro` clean Emacs & org-mode 
> environment instance. It works fine. I double checked my Emacs init 
> file about R settings. Have not found suspicious config.

So to confirm, you *cannot* reproduce the error with a clean config?

> Here is my reproduce test.

I tried running this, and it seems to work as expected.

>> The generated plot image "images/hist_rnorm.png" is NOT in
>> "~/Org/Programming/R/images/hist_rnorm.png". It's in 
>> "~/Org/hist_rnorm.png".

Some relevant settings that may be altered by your config are 
`ess-startup-directory` and `ess-startup-directory-function`. It might 
be, for example, that one of these is forcibly changing the R process' 
working directory to a project root ("~/Org", in this instance)

By the way, setting `:dir` changes the *working* directory, which you 
might not want to be "images". There is a separate header argument, 
`:output-dir` that can be used for this purpose.

Sam

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Re: The ob-R :results graphics file :dir "images" :file "plot.png" specified directory not working

[stardiviner]

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Finally found the real reason: package `project-rootfile` -> (add-to-list
'project-find-functions #'project-rootfile-try-detect t)
I don't know why project-rootfile involved in the Org mode Babel source
block execution path.
I checked out the source code of `project-rootfile`. Have not found any
clue.
Anyone have thoughts on this weird problem?


[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, Jan 14, 2025 at 6:49 PM <sam@crawf.uk> wrote:

> On 2025-01-14 05:29, stardiviner wrote:
>
> I tested using org-mode's `make repro` clean Emacs & org-mode environment
> instance. It works fine. I double checked my Emacs init file about R
> settings. Have not found suspicious config.
>
>
> So to confirm, you *cannot* reproduce the error with a clean config?
>
> Here is my reproduce test.
>
>
> I tried running this, and it seems to work as expected.
>
> The generated plot image "images/hist_rnorm.png" is NOT in
> "~/Org/Programming/R/images/hist_rnorm.png". It's in
> "~/Org/hist_rnorm.png".
>
>
> Some relevant settings that may be altered by your config are
> `ess-startup-directory` and `ess-startup-directory-function`. It might be,
> for example, that one of these is forcibly changing the R process' working
> directory to a project root ("~/Org", in this instance)
>
> By the way, setting `:dir` changes the *working* directory, which you
> might not want to be "images". There is a separate header argument,
> `:output-dir` that can be used for this purpose.
>
> Sam
>

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Re: The ob-R :results graphics file :dir "images" :file "plot.png" specified directory not working

[stardiviner]

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> Some relevant settings that may be altered by your config are
`ess-startup-directory` and `ess-startup-directory-function`. It might be,
for example, that one of these is forcibly changing the R process' working
directory to a project root ("~/Org", in this instance)

Yes, I found the reason `project-rootfile` changed the directory when babel
source block execution.

> By the way, setting `:dir` changes the *working* directory, which you
might not want to be "images". There is a separate header argument,
`:output-dir` that can be used for this purpose.

Thanks for your tips.


[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, Jan 14, 2025 at 6:49 PM <sam@crawf.uk> wrote:

> On 2025-01-14 05:29, stardiviner wrote:
>
> I tested using org-mode's `make repro` clean Emacs & org-mode environment
> instance. It works fine. I double checked my Emacs init file about R
> settings. Have not found suspicious config.
>
>
> So to confirm, you *cannot* reproduce the error with a clean config?
>
> Here is my reproduce test.
>
>
> I tried running this, and it seems to work as expected.
>
> The generated plot image "images/hist_rnorm.png" is NOT in
> "~/Org/Programming/R/images/hist_rnorm.png". It's in
> "~/Org/hist_rnorm.png".
>
>
> Some relevant settings that may be altered by your config are
> `ess-startup-directory` and `ess-startup-directory-function`. It might be,
> for example, that one of these is forcibly changing the R process' working
> directory to a project root ("~/Org", in this instance)
>
> By the way, setting `:dir` changes the *working* directory, which you
> might not want to be "images". There is a separate header argument,
> `:output-dir` that can be used for this purpose.
>
> Sam
>

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Re: The ob-R :results graphics file :dir "images" :file "plot.png" specified directory not working

[William Denton]

On Tuesday, January 14th, 2025 at 11:04, stardiviner <numbchild@gmail.com> wrote:

> Finally found the real reason: package `project-rootfile` -> (add-to-list 'project-find-functions #'project-rootfile-try-detect t)
> I don't know why project-rootfile involved in the Org mode Babel source block execution path.
> I checked out the source code of `project-rootfile`. Have not found any clue.
> Anyone have thoughts on this weird problem?

I think you've identified the same kind of problem I have.  I have some Org files with R code that I run in a session, and I want the working directory to be the directory the files are in (.) but it is one up (..).  I couldn't figure out why it happened, because it wasn't happening with "make repro" tests.  But now that I look at it, this happens in files that are in projects or Git repositories.  I don't use the package you do, though, just built-in projects.el.  Still, maybe it's the same thing?

Bill

--
William Denton
https://www.miskatonic.org/
Librarian, artist and licensed private investigator.
Toronto, Canada