Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
You're welcome! I think the examples could use refreshing/restructuring, but I'm not sure when I'll have time to get to that. Best, Tyler -- plantarum.ca On Mon, Feb 17, 2020, at 12:40 PM, Jack Kamm wrote: > Hi Tyler, > > >> The documentation for ob-R is now incorrect: > >> > >> https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html > > > > Yes, also that page could use some other updates, e.g. there are some > > dead links in there. > > Just saw that you updated the docs a few days ago. Thanks for taking > care of this! > > Best, > Jack >
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
Hi Tyler, >> The documentation for ob-R is now incorrect: >> >> https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html > > Yes, also that page could use some other updates, e.g. there are some > dead links in there. Just saw that you updated the docs a few days ago. Thanks for taking care of this! Best, Jack
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
> Is the rationale explained anywhere? After a bit of poking around, it looks > like using the `:file` flag without a `file` argument to results doesn't do > anything (no file is created), nor does the reverse. That is, unless you use > both the `file` argument and the `:file` option, nothing happens. Is there a > situation where you can use `:file` to do something that doesn't require a > `file` argument to `:results`? The specific commit where it happened was 26ed66b23335eb389f1f2859e409f46f66279e15, which says: "Deducing the results from some other arguments is not obvious. Moreover, it prevents users from setting, e.g., :file-ext, in a node property, as every block would then create a file." The commit also links to this thread: http://lists.gnu.org/r/emacs-orgmode/2018-05/msg00469.html I wasn't involved in that discussion, but I think the idea is that you could create a subtree with many named source blocks each creating a PNG file, set the :file-ext parameter at the subtree level, and have the file names auto-created from the source block names. > The documentation for ob-R is now incorrect: > > https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html Yes, also that page could use some other updates, e.g. there are some dead links in there.
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
On Mon, Jan 27, 2020, at 12:29 PM, Jack Kamm wrote: > > It should now be ":results graphics file". This behavior changed in Org > 9.3, see https://orgmode.org/Changes.html (:file header argument no > longer assume "file" :results). > That fixes it, thanks! The documentation for ob-R is now incorrect: https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-R.html Is the rationale explained anywhere? After a bit of poking around, it looks like using the `:file` flag without a `file` argument to results doesn't do anything (no file is created), nor does the reverse. That is, unless you use both the `file` argument and the `:file` option, nothing happens. Is there a situation where you can use `:file` to do something that doesn't require a `file` argument to `:results`? Best, Tyler -- plantarum.ca
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
> #+begin_src R :results graphics :file test.jpg > plot (1:10) > #+end_src It should now be ":results graphics file". This behavior changed in Org 9.3, see https://orgmode.org/Changes.html (:file header argument no longer assume "file" :results).
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
On 27 January 2020, Tyler Smith wrote: #+begin_src R :results graphics :file test.jpg plot (1:10) #+end_src ":results file graphics" should do it. Bill -- William Denton :: Toronto, Canada --- Listening to Art: https://listeningtoart.org/ https://www.miskatonic.org/ --- GHG.EARTH: https://ghg.earth/ Caveat lector. --- STAPLR: https://staplr.org/
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
Hi Jeremie,
I tried with `:results output graphics`, and with the file as jpg, and also as
pdf. In all cases I still get the same result : no link is inserted.
I first noticed this with the org version that was released at the end of
December, and confirmed that the problem was still present in the latest
version released today. I'm pretty confident that this worked prior to the
December release.
Thanks,
Tyler
--
plantarum.ca
On Mon, Jan 27, 2020, at 11:27 AM, Jeremie wrote:
> Hello,
>
> I don't have the lastest.version of org-mode so i can't confirm.
>
>
> But could you try with the option
>
> :results output graphics :file test.pdf
>
> HTH,
> Jeremie
>
>
> On January 27, 2020 5:13:20 PM GMT+01:00, Tyler Smith
> wrote:
>> To reproduce:
>>
>> 1. Start from `emacs -Q`
>>
>> 2. open the following org file:
>>
>> ```
>> #+BEGIN_SRC elisp setup
>> (require 'package)
>> (setq package-load-list
>> '((org-plus-contrib t)
>> (ess t)
>> (julia-mode t)))
>> (package-initialize)
>> (require 'org)
>> (require 'ess)
>>
>> (org-babel-do-load-languages
>> 'org-babel-load-languages
>> '((emacs-lisp . t)
>>(R . t)
>>(shell . t)))
>> #+END_SRC
>>
>> #+RESULTS:
>>
>> #+begin_src R :results graphics :file test.jpg
>> plot (1:10)
>> #+end_src
>> ```
>>
>> 3. Evaluate the first code block (C-c C-c) to load ess and setup babel to
>> evaluate R code blocks
>>
>> 4. Evaluate the second code block.
>>
>> What I expect:
>>
>> A `#+RESULTS:` block is inserted, with a link to the file test.jpg;
>>
>> What happens instead:
>>
>> A message appears in the minibuffer: 'Code block produced no output'.
>>
>> This worked previously. I'm not sure when it broke - sometime in the last
>> two months I think, as I demoed this feature for colleagues in November.
>>
>> Emacs state provided below.
>>
>> Best,
>>
>> Tyler
>>
>> Emacs : GNU Emacs 28.0.50 (build 2, x86_64-pc-linux-gnu, GTK+ Version
>> 3.22.30)
>> of 2020-01-02
>> Package: Org mode version 9.3 (release_9.3 @
>> /home/smithty/.emacs.d/elpa/org-plus-contrib-20200127/)
>>
>> current state:(setq
>> org-src-mode-hook '(org-src-babel-configure-edit-buffer
>> org-src-mode-configure-edit-buffer)
>> org-link-shell-confirm-function 'yes-or-no-p
>> org-metadown-hook '(org-babel-pop-to-session-maybe)
>> org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>> org-mode-hook '(org-eldoc-load
>> #[0 "\300\301\302\303\304$\207"
>> [add-hook change-major-mode-hook org-show-all append local]
>> 5]
>> #[0 "\300\301\302\303\304$\207"
>> [add-hook change-major-mode-hook org-babel-show-result-all
>> append local] 5]
>> org-babel-result-hide-spec org-babel-hide-all-hashes)
>> org-archive-hook '(org-attach-archive-delete-maybe)
>> org-confirm-elisp-link-function 'yes-or-no-p
>> org-agenda-before-write-hook '(org-agenda-add-entry-text)
>> org-metaup-hook '(org-babel-load-in-session-maybe)
>> org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3
>> "\n\n(fn ENTRY)"]
>> org-babel-pre-tangle-hook '(save-buffer)
>> org-tab-first-hook '(org-babel-hide-result-toggle-maybe
>> org-babel-header-arg-expand)
>> org-babel-load-languages '((emacs-lisp . t) (R . t) (shell . t))
>> org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" . arduino)
>> ("C" . c) ("C++" . c++)
>>("asymptote" . asy) ("bash" . sh) ("beamer" . latex)
>> ("calc" . fundamental)
>>("cpp" . c++) ("ditaa" . artist) ("dot" . fundamental)
>> ("elisp" . emacs-lisp)
>>("ocaml" . tuareg) ("screen" . shell-script) ("shell" .
>> sh) ("sqlite" . sql))
>> org-occur-hook '(org-first-headline-recenter)
>> org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
>>org-optimize-window-after-visibility-change)
>> org-speed-command-hook '(org-speed-command-activate
>> org-babel-speed-command-activate)
>> org-confirm-shell-link-function 'yes-or-no-p
>> org-link-parameters '(("attachment" :follow org-attach-open-link :export
>> org-attach-export-link
>> :complete org-attach-complete-link)
>> ("id" :follow org-id-open) ("eww" :follow eww :store
>> org-eww-store-link)
>> ("rmail" :follow org-rmail-open :store
>> org-rmail-store-link)
>> ("mhe" :follow org-mhe-open :store org-mhe-store-link)
>> ("irc" :follow org-irc-visit :store org-irc-store-link
>> :export org-irc-export)
>> ("info" :follow org-info-open :export org-info-export
>> :store
>> org-info-store-link)
>> ("gnus" :follow org-gnus-open :store org-gnus-store-link)
>> ("docview" :follow org-docview-open :export
>> org-docview-export :store
>> org-docview-store-link)
>> ("bibtex" :follow
Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
Hello,
I don't have the lastest.version of org-mode so i can't confirm.
But could you try with the option
:results output graphics :file test.pdf
HTH,
Jeremie
On January 27, 2020 5:13:20 PM GMT+01:00, Tyler Smith
wrote:
>To reproduce:
>
>1. Start from `emacs -Q`
>
>2. open the following org file:
>
>```
>#+BEGIN_SRC elisp setup
>(require 'package)
>(setq package-load-list
> '((org-plus-contrib t)
> (ess t)
> (julia-mode t)))
>(package-initialize)
>(require 'org)
>(require 'ess)
>
>(org-babel-do-load-languages
> 'org-babel-load-languages
> '((emacs-lisp . t)
> (R . t)
> (shell . t)))
>#+END_SRC
>
>#+RESULTS:
>
>#+begin_src R :results graphics :file test.jpg
>plot (1:10)
>#+end_src
>```
>
>3. Evaluate the first code block (C-c C-c) to load ess and setup babel
>to evaluate R code blocks
>
>4. Evaluate the second code block.
>
>What I expect:
>
>A `#+RESULTS:` block is inserted, with a link to the file test.jpg;
>
>What happens instead:
>
>A message appears in the minibuffer: 'Code block produced no output'.
>
>This worked previously. I'm not sure when it broke - sometime in the
>last two months I think, as I demoed this feature for colleagues in
>November.
>
>Emacs state provided below.
>
>Best,
>
>Tyler
>
>Emacs : GNU Emacs 28.0.50 (build 2, x86_64-pc-linux-gnu, GTK+ Version
>3.22.30)
> of 2020-01-02
>Package: Org mode version 9.3 (release_9.3 @
>/home/smithty/.emacs.d/elpa/org-plus-contrib-20200127/)
>
>current state:
>==
>(setq
>org-src-mode-hook '(org-src-babel-configure-edit-buffer
>org-src-mode-configure-edit-buffer)
> org-link-shell-confirm-function 'yes-or-no-p
> org-metadown-hook '(org-babel-pop-to-session-maybe)
> org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
> org-mode-hook '(org-eldoc-load
>#[0 "\300\301\302\303\304$\207"
> [add-hook change-major-mode-hook org-show-all append local]
> 5]
>#[0 "\300\301\302\303\304$\207"
> [add-hook change-major-mode-hook org-babel-show-result-all
> append
>local] 5]
>org-babel-result-hide-spec org-babel-hide-all-hashes)
> org-archive-hook '(org-attach-archive-delete-maybe)
> org-confirm-elisp-link-function 'yes-or-no-p
> org-agenda-before-write-hook '(org-agenda-add-entry-text)
> org-metaup-hook '(org-babel-load-in-session-maybe)
>org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3
>"\n\n(fn ENTRY)"]
> org-babel-pre-tangle-hook '(save-buffer)
>org-tab-first-hook '(org-babel-hide-result-toggle-maybe
>org-babel-header-arg-expand)
> org-babel-load-languages '((emacs-lisp . t) (R . t) (shell . t))
>org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" .
>arduino) ("C" . c) ("C++" . c++)
> ("asymptote" . asy) ("bash" . sh) ("beamer" . latex)
> ("calc" .
>fundamental)
> ("cpp" . c++) ("ditaa" . artist) ("dot" . fundamental)
> ("elisp"
>. emacs-lisp)
> ("ocaml" . tuareg) ("screen" . shell-script) ("shell" .
> sh)
>("sqlite" . sql))
> org-occur-hook '(org-first-headline-recenter)
>org-cycle-hook '(org-cycle-hide-archived-subtrees
>org-cycle-show-empty-lines
> org-optimize-window-after-visibility-change)
>org-speed-command-hook '(org-speed-command-activate
>org-babel-speed-command-activate)
> org-confirm-shell-link-function 'yes-or-no-p
>org-link-parameters '(("attachment" :follow org-attach-open-link
>:export org-attach-export-link
> :complete org-attach-complete-link)
> ("id" :follow org-id-open) ("eww" :follow eww :store
>org-eww-store-link)
> ("rmail" :follow org-rmail-open :store
> org-rmail-store-link)
> ("mhe" :follow org-mhe-open :store org-mhe-store-link)
> ("irc" :follow org-irc-visit :store org-irc-store-link
> :export
>org-irc-export)
> ("info" :follow org-info-open :export org-info-export
> :store
> org-info-store-link)
> ("gnus" :follow org-gnus-open :store org-gnus-store-link)
> ("docview" :follow org-docview-open :export
> org-docview-export
>:store
> org-docview-store-link)
> ("bibtex" :follow org-bibtex-open :store
>org-bibtex-store-link)
> ("bbdb" :follow org-bbdb-open :export org-bbdb-export
>:complete
> org-bbdb-complete-link :store org-bbdb-store-link)
> ("w3m" :store org-w3m-store-link) ("file+sys")
> ("file+emacs")
> ("shell" :follow org-link--open-shell)
> ("news" :follow
> #[257 "\301\300\302Q!\207" ["news" browse-url ":"] 5
> "\n\n(fn
>URL)"])
> ("mailto" :follow
> #[257 "\301\300\302Q!\207" ["mailto" browse-url ":"] 5
> "\n\n(fn
>URL)"])
> ("https" :follow
>
Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127]
To reproduce:
1. Start from `emacs -Q`
2. open the following org file:
```
#+BEGIN_SRC elisp setup
(require 'package)
(setq package-load-list
'((org-plus-contrib t)
(ess t)
(julia-mode t)))
(package-initialize)
(require 'org)
(require 'ess)
(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . t)
(R . t)
(shell . t)))
#+END_SRC
#+RESULTS:
#+begin_src R :results graphics :file test.jpg
plot (1:10)
#+end_src
```
3. Evaluate the first code block (C-c C-c) to load ess and setup babel to
evaluate R code blocks
4. Evaluate the second code block.
What I expect:
A `#+RESULTS:` block is inserted, with a link to the file test.jpg;
What happens instead:
A message appears in the minibuffer: 'Code block produced no output'.
This worked previously. I'm not sure when it broke - sometime in the last two
months I think, as I demoed this feature for colleagues in November.
Emacs state provided below.
Best,
Tyler
Emacs : GNU Emacs 28.0.50 (build 2, x86_64-pc-linux-gnu, GTK+ Version 3.22.30)
of 2020-01-02
Package: Org mode version 9.3 (release_9.3 @
/home/smithty/.emacs.d/elpa/org-plus-contrib-20200127/)
current state:
==
(setq
org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
org-link-shell-confirm-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
org-mode-hook '(org-eldoc-load
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-show-all append local]
5]
#[0 "\300\301\302\303\304$\207"
[add-hook change-major-mode-hook org-babel-show-result-all
append local] 5]
org-babel-result-hide-spec org-babel-hide-all-hashes)
org-archive-hook '(org-attach-archive-delete-maybe)
org-confirm-elisp-link-function 'yes-or-no-p
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-metaup-hook '(org-babel-load-in-session-maybe)
org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3 "\n\n(fn
ENTRY)"]
org-babel-pre-tangle-hook '(save-buffer)
org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
org-babel-load-languages '((emacs-lisp . t) (R . t) (shell . t))
org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" . arduino)
("C" . c) ("C++" . c++)
("asymptote" . asy) ("bash" . sh) ("beamer" . latex)
("calc" . fundamental)
("cpp" . c++) ("ditaa" . artist) ("dot" . fundamental)
("elisp" . emacs-lisp)
("ocaml" . tuareg) ("screen" . shell-script) ("shell" .
sh) ("sqlite" . sql))
org-occur-hook '(org-first-headline-recenter)
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
org-optimize-window-after-visibility-change)
org-speed-command-hook '(org-speed-command-activate
org-babel-speed-command-activate)
org-confirm-shell-link-function 'yes-or-no-p
org-link-parameters '(("attachment" :follow org-attach-open-link :export
org-attach-export-link
:complete org-attach-complete-link)
("id" :follow org-id-open) ("eww" :follow eww :store
org-eww-store-link)
("rmail" :follow org-rmail-open :store
org-rmail-store-link)
("mhe" :follow org-mhe-open :store org-mhe-store-link)
("irc" :follow org-irc-visit :store org-irc-store-link
:export org-irc-export)
("info" :follow org-info-open :export org-info-export
:store
org-info-store-link)
("gnus" :follow org-gnus-open :store org-gnus-store-link)
("docview" :follow org-docview-open :export
org-docview-export :store
org-docview-store-link)
("bibtex" :follow org-bibtex-open :store
org-bibtex-store-link)
("bbdb" :follow org-bbdb-open :export org-bbdb-export
:complete
org-bbdb-complete-link :store org-bbdb-store-link)
("w3m" :store org-w3m-store-link) ("file+sys")
("file+emacs")
("shell" :follow org-link--open-shell)
("news" :follow
#[257 "\301\300\302Q!\207" ["news" browse-url ":"] 5
"\n\n(fn URL)"])
("mailto" :follow
#[257 "\301\300\302Q!\207" ["mailto" browse-url ":"] 5
"\n\n(fn URL)"])
("https" :follow
#[257 "\301\300\302Q!\207" ["https" browse-url ":"] 5
"\n\n(fn URL)"])
("http" :follow
#[257 "\301\300\302Q!\207" ["http" browse-url ":"] 5
"\n\n(fn URL)"])
("ftp" :follow
#[257 "\301\300\302Q!\207" ["ftp" browse-url ":"] 5
