From mboxrd@z Thu Jan 1 00:00:00 1970 From: Jeremie Subject: Re: Bug: R src blocks fail to produce link to graphics file [9.3 org-plus-contrib-20200127] Date: Mon, 27 Jan 2020 17:27:39 +0100 Message-ID: References: <38232967-8656-40be-89de-30a7fd180838@www.fastmail.com> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----QRU9ZN1CD1TIP9XO7EVQXPJJDBJDSF" Content-Transfer-Encoding: 7bit Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:60017) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1iw7FH-0005QA-Ek for emacs-orgmode@gnu.org; Mon, 27 Jan 2020 11:28:17 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1iw7FF-0006oH-Ho for emacs-orgmode@gnu.org; Mon, 27 Jan 2020 11:28:15 -0500 Received: from mail-wr1-x430.google.com ([2a00:1450:4864:20::430]:35208) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1iw7FF-0006gg-9X for emacs-orgmode@gnu.org; Mon, 27 Jan 2020 11:28:13 -0500 Received: by mail-wr1-x430.google.com with SMTP id g17so12099723wro.2 for ; Mon, 27 Jan 2020 08:28:13 -0800 (PST) In-Reply-To: <38232967-8656-40be-89de-30a7fd180838@www.fastmail.com> 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: emacs-orgmode@gnu.org, Tyler Smith Emacs Org-Mode Help ------QRU9ZN1CD1TIP9XO7EVQXPJJDBJDSF Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello, I don't have the lastest=2Eversion of org-mode so i can't confirm=2E But could you try with the option=20 :results output graphics :file test=2Epdf HTH, Jeremie On January 27, 2020 5:13:20 PM GMT+01:00, Tyler Smith wrote: >To reproduce: > >1=2E Start from `emacs -Q` > >2=2E 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 =2E t) > (R =2E t) > (shell =2E t))) >#+END_SRC > >#+RESULTS: > >#+begin_src R :results graphics :file test=2Ejpg >plot (1:10) >#+end_src >``` > >3=2E Evaluate the first code block (C-c C-c) to load ess and setup babel >to evaluate R code blocks > >4=2E Evaluate the second code block=2E > >What I expect:=20 > >A `#+RESULTS:` block is inserted, with a link to the file test=2Ejpg; > >What happens instead: > >A message appears in the minibuffer: 'Code block produced no output'=2E > >This worked previously=2E I'm not sure when it broke - sometime in the >last two months I think, as I demoed this feature for colleagues in >November=2E > >Emacs state provided below=2E > >Best, > >Tyler > >Emacs : GNU Emacs 28=2E0=2E50 (build 2, x86_64-pc-linux-gnu, GTK+ Versio= n >3=2E22=2E30) > of 2020-01-02 >Package: Org mode version 9=2E3 (release_9=2E3 @ >/home/smithty/=2Eemacs=2Ed/elpa/org-plus-contrib-20200127/) > >current state: >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >(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=01\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 =2E t) (R =2E t) (shell =2E t)) >org-src-lang-modes '(("redis" =2E redis) ("php" =2E php) ("arduino" =2E >arduino) ("C" =2E c) ("C++" =2E c++) > ("asymptote" =2E asy) ("bash" =2E sh) ("beamer" =2E latex) ("calc= " =2E >fundamental) > ("cpp" =2E c++) ("ditaa" =2E artist) ("dot" =2E fundamental) ("el= isp" >=2E emacs-lisp) > ("ocaml" =2E tuareg) ("screen" =2E shell-script) ("shell" =2E sh) >("sqlite" =2E 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\302=03Q!\207" ["news" browse-url ":"] 5 "\n\n(fn >URL)"]) > ("mailto" :follow > #[257 "\301\300\302=03Q!\207" ["mailto" browse-url ":"] 5 "\n\n(fn >URL)"]) > ("https" :follow > #[257 "\301\300\302=03Q!\207" ["https" 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) > ("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 > ) > > >--=20 >plantarum=2Eca ------QRU9ZN1CD1TIP9XO7EVQXPJJDBJDSF Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello,

I don't have the lastest=2Eversion o= f org-mode so i can't confirm=2E


But could you try with the opti= on

:results output graphics :file test=2Epdf

HTH,
Jeremie=


On January 27, 2020 5:13:20 PM GMT+0= 1:00, Tyler Smith <tyler@plantarum=2Eca> wrote:
To reproduce:

1=2E Start from `emacs -Q`
<=
br>2=2E open the following org file:

```
#+BEGIN_SRC elisp setup<=
br>(require 'package)
(setq package-load-list
      '((org-plus-contr=
ib t)
	(ess t)
	(julia-mode t)))
(package-initialize)
(require =
'org)
(require 'ess)

(org-babel-do-load-languages
 'org-babel-=
load-languages
 '((emacs-lisp =2E t)
   (R =2E t)
   (shell =2E t)=
))
#+END_SRC

#+RESULTS:

#+begin_src R :results graphics :f=
ile test=2Ejpg
plot (1:10)
#+end_src
```

3=2E Evaluate the =
first code block (C-c C-c) to load ess and setup babel to evaluate R code b=
locks

4=2E  Evaluate the second code block=2E

What I expect: =


A `#+RESULTS:` block is inserted, with a link to the file test=2Ejp=
g;

What happens instead:

A message appears in the minibuffer:=
   'Code block produced no output'=2E

This worked previously=2E I'm =
not sure when it broke - sometime in the last two months I think, as I demo=
ed this feature for colleagues in November=2E

Emacs state provided b=
elow=2E

Best,

Tyler

Emacs  : GNU Emacs 28=2E0=2E50 (bu=
ild 2, x86_64-pc-linux-gnu, GTK+ Version 3=2E22=2E30)
 of 2020-01-02
=
Package: Org mode version 9=2E3 (release_9=2E3 @ /home/smithty/=2Eemacs=2Ed=
/elpa/org-plus-contrib-20200127/)

current state:
(setq
 org-sr=
c-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-ed=
it-buffer)
 org-link-shell-confirm-function 'yes-or-no-p
 org-metadow=
n-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-ho=
ok 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=01\236A\207" [:title] 3 "\n\n(fn ENTRY)"]
 o=
rg-babel-pre-tangle-hook '(save-buffer)
 org-tab-first-hook '(org-babel-=
hide-result-toggle-maybe org-babel-header-arg-expand)
 org-babel-load-la=
nguages '((emacs-lisp =2E t) (R =2E t) (shell =2E t))
 org-src-lang-mode=
s '(("redis" =2E redis) ("php" =2E php) ("arduino" =2E arduino) ("C" =2E c)=
 ("C++" =2E c++)
		      ("asymptote" =2E asy) ("bash" =2E sh) ("beamer"=
 =2E latex) ("calc" =2E fundamental)
		      ("cpp" =2E c++) ("ditaa" =
=2E artist) ("dot" =2E fundamental) ("elisp" =2E emacs-lisp)
		      ("o=
caml" =2E tuareg) ("screen" =2E shell-script) ("shell" =2E sh) ("sqlite" =
=2E sql))
 org-occur-hook '(org-first-headline-recenter)
 org-cycle-h=
ook '(org-cycle-hide-archived-subtrees org-cycle-show-empty-lines
		  or=
g-optimize-window-after-visibility-change)
 org-speed-command-hook '(org=
-speed-command-activate org-babel-speed-command-activate)
 org-confirm-s=
hell-link-function 'yes-or-no-p
 org-link-parameters '(("attachment" :fo=
llow org-attach-open-link :export org-attach-export-link
			:complete or=
g-attach-complete-link)
		       ("id" :follow org-id-open) ("eww" :foll=
ow eww :store org-eww-store-link)
		       ("rmail" :follow org-rmail-op=
en :store org-rmail-store-link)
		       ("mhe" :follow org-mhe-open :st=
ore org-mhe-store-link)
		       ("irc" :follow org-irc-visit :store org=
-irc-store-link :export org-irc-export)
		       ("info" :follow org-inf=
o-open :export org-info-export :store
			org-info-store-link)
		     =
  ("gnus" :follow org-gnus-open :store org-gnus-store-link)
		       ("d=
ocview" :follow org-docview-open :export org-docview-export :store
			or=
g-docview-store-link)
		       ("bibtex" :follow org-bibtex-open :store =
org-bibtex-store-link)
		       ("bbdb" :follow org-bbdb-open :export or=
g-bbdb-export :complete
			org-bbdb-complete-link :store org-bbdb-store-=
link)
		       ("w3m" :store org-w3m-store-link) ("file+sys") ("file+ema=
cs")
		       ("shell" :follow org-link--open-shell)
		       ("news"=
 :follow
			#[257 "\301\300\302=03Q!\207" ["news" browse-url ":"] 5 "\n\=
n(fn URL)"])
		       ("mailto" :follow
			#[257 "\301\300\302=03Q!\2=
07" ["mailto" browse-url ":"] 5 "\n\n(fn URL)"])
		       ("https" :foll=
ow
			#[257 "\301\300\302=03Q!\207" ["https" browse-url ":"] 5 "\n\n(fn =
URL)"])
		       ("http" :follow
			#[257 "\301\300\302=03Q!\207" ["h=
ttp" 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)
		       ("file" :complete o=
rg-link-complete-file)
		       ("elisp" :follow org-link--open-elisp) (=
"doi" :follow org-link--open-doi))
 org-link-elisp-confirm-function 'yes=
-or-no-p
 )

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