From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Tyler Smith" Subject: Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127] Date: Mon, 27 Jan 2020 11:58:10 -0500 Message-ID: <8ab8a7f4-e599-4207-ab65-4c4accc02cee@www.fastmail.com> References: <38232967-8656-40be-89de-30a7fd180838@www.fastmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=fd8703d132e147218f483cc01478029f Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:40635) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iw7jH-0005ph-1V for emacs-orgmode@gnu.org; Mon, 27 Jan 2020 11:59:17 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iw7jF-00019z-56 for emacs-orgmode@gnu.org; Mon, 27 Jan 2020 11:59:14 -0500 Received: from out4-smtp.messagingengine.com ([66.111.4.28]:34789) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1iw7jE-00018Z-QE for emacs-orgmode@gnu.org; Mon, 27 Jan 2020 11:59:13 -0500 In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane-mx.org@gnu.org Sender: "Emacs-orgmode" To: Jeremie , Emacs Org-Mode Help --fd8703d132e147218f483cc01478029f Content-Type: text/plain 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 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 "\n\n(fn URL)"]) >> ("help" :follow org-link--open-help) >> ("file" :complete org-link-complete-file) >> ("elisp" :follow org-link--open-elisp) ("doi" :follow org-link--open-doi)) >> org-link-elisp-confirm-function 'yes-or-no-p >> ) --fd8703d132e147218f483cc01478029f Content-Type: text/html Content-Transfer-Encoding: quoted-printable
Hi Jeremie,
=

I tried with `:results output graphics`, and w= ith the file as jpg, and also as pdf. In all cases I still get the same = result : no link is inserted.

I first notic= ed this with the org version that was released at the end of December, a= nd confirmed that the problem was still present in the latest version re= leased today.  I'm pretty confident that this worked prior to the D= ecember release.

Thanks,

=
Tyler

--
plantarum.ca
<= /div>



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, 2= 020 5:13:20 PM GMT+01:00, Tyler Smith <tyler@plantarum.ca> wrote:<= br>
To reproduce:

<=
/div>
1. Start from `emacs -Q`

2. open =
the following org file:

```
#=
+BEGIN_SRC elisp setup
(require 'package)
(s=
etq package-load-list
      '((org-plus-contrib t)
	(ess t)
	(julia-mode t)))
(package-i=
nitialize)
(require 'org)
(require 'ess)
=


(org-babel-do-load-languages
 'o=
rg-babel-load-languages
 '((emacs-lisp . t)
=
   (R . t)
   (shell . t)))
#+END_SRC

#+RESULTS:

#+begin_s=
rc R :results graphics :file test.jpg
plot (1:10)
#+end_src
```

3. Evalua=
te the first code block (C-c C-c) to load ess and setup babel to evaluat=
e R code blocks

4.  Evaluate the second cod=
e block.

What I expect: 

=

A `#+RESULTS:` block is inserted, with a link to the file tes=
t.jpg;

What happens instead:
=

A message appears in the minibuffer:   'Code block produc=
ed no output'.

This worked previously. I'm =
not sure when it broke - sometime in the last two months I think, as I d=
emoed this feature for colleagues in November.

<=
div>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 (rel=
ease_9.3 @ /home/smithty/.emacs.d/elpa/org-plus-contrib-20200127/)

current state:
(setq
 org-src-m=
ode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-ed=
it-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$\207"
		   [add-hook change-major-mode-hook or=
g-show-all append local] 5]
		 #[0 "\300\301\302\303\304$\=
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 'ye=
s-or-no-p
 org-agenda-before-write-hook '(org-agenda-add-e=
ntry-text)
 org-metaup-hook '(org-babel-load-in-session-ma=
ybe)
 org-bibtex-headline-format-function #[257 "\300=01\2=
36A\207" [:title] 3 "\n\n(fn ENTRY)"]
 org-babel-pre-tangl=
e-hook '(save-buffer)
 org-tab-first-hook '(org-babel-hide=
-result-toggle-maybe org-babel-header-arg-expand)
 org-bab=
el-load-languages '((emacs-lisp . t) (R . t) (shell . t))
=
 org-src-lang-modes '(("redis" . redis) ("php" . php) ("arduino" . ardui=
no) ("C" . c) ("C++" . c++)
		      ("asymptote" . asy) ("=
bash" . sh) ("beamer" . latex) ("calc" . fundamental)
		  =
    ("cpp" . c++) ("ditaa" . artist) ("dot" . fundamental) ("elisp" . em=
acs-lisp)
		      ("ocaml" . tuareg) ("screen" . shell-scr=
ipt) ("shell" . sh) ("sqlite" . sql))
 org-occur-hook '(or=
g-first-headline-recenter)
 org-cycle-hook '(org-cycle-hid=
e-archived-subtrees org-cycle-show-empty-lines
		  org-opt=
imize-window-after-visibility-change)
 org-speed-command-h=
ook '(org-speed-command-activate org-babel-speed-command-activate)
 org-confirm-shell-link-function 'yes-or-no-p
 or=
g-link-parameters '(("attachment" :follow org-attach-open-link :export o=
rg-attach-export-link
			:complete org-attach-complete-lin=
k)
		       ("id" :follow org-id-open) ("eww" :follow eww =
:store org-eww-store-link)
		       ("rmail" :follow org-r=
mail-open :store org-rmail-store-link)
		       ("mhe" :fo=
llow org-mhe-open :store org-mhe-store-link)
		       ("ir=
c" :follow org-irc-visit :store org-irc-store-link :export org-irc-expor=
t)
		       ("info" :follow org-info-open :export org-info=
-export :store
			org-info-store-link)
		   =
    ("gnus" :follow org-gnus-open :store org-gnus-store-link)
<=
div>		       ("docview" :follow org-docview-open :export org-docview-exp=
ort :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+sy=
s") ("file+emacs")
		       ("shell" :follow org-link--ope=
n-shell)
		       ("news" :follow
			#[257 "=
\301\300\302=03Q!\207" ["news" browse-url ":"] 5 "\n\n(fn URL)"])
		       ("mailto" :follow
			#[257 "\301\300\302=03=
Q!\207" ["mailto" browse-url ":"] 5 "\n\n(fn URL)"])
		   =
    ("https" :follow
			#[257 "\301\300\302=03Q!\207" ["ht=
tps" browse-url ":"] 5 "\n\n(fn URL)"])
		       ("http" :=
follow
			#[257 "\301\300\302=03Q!\207" ["http" browse-url=
 ":"] 5 "\n\n(fn URL)"])
		       ("ftp" :follow
=

			#[257 "\301\300\302=03Q!\207" ["ftp" browse-url ":"] 5 "\n\n(fn =
URL)"])
		       ("help" :follow org-link--open-help)
<=
/div>
		       ("file" :complete org-link-complete-file)
		       ("elisp" :follow org-link--open-elisp) ("doi" :follow org-li=
nk--open-doi))
 org-link-elisp-confirm-function 'yes-or-no=
-p
 )
=
--fd8703d132e147218f483cc01478029f--