Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

[Uwe Brauer]

hello

Please look at the following example



\documentclass[addpoints,12pt]{exam}

\begin{document}




% [[file:~/ALLES/tex/vorlesungen/HGBioQuim/Examen+geogebra/Examen2/README.org::*Overview][Overview]]

\begin{questions}  


% [[file:~/ALLES/tex/vorlesungen/HGBioQuim/Examen+geogebra/Examen2/README.org::*Overview][Overview]]

\end{questions}

`org-open-at-point' opens the first link, but not the one in the
environment questions.

regards

Uwe Brauer 



Emacs  : GNU Emacs 25.1.50.1 (i686-pc-linux-gnu, GTK+ Version 2.20.1)
 of 2016-01-19
Package: Org-mode version 8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)

current state:
==============
(setq
 org-entities-user '(("implies" "\\Rightarrow" t "⇒" "=>" "=>" "⇒")
		     ("iff" "\\iff" t "&hArr;" "<=>" "<=>" "⇔"))
 org-ref-cite-onclick-function 'org-ref-cite-click-helm
 outline-mode-hook '(hide-body)
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe)
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-pretty-entities t
 org-html-format-inlinetask-function 'org-html-format-inlinetask-default-function
 org-odt-preferred-output-format "doc"
 org-shiftleft-hook '(#[nil "\300\301!\207" [org-ref-swap-citation-link -1] 2])
 org-tab-first-hook '(org-hide-block-toggle-maybe org-babel-hide-result-toggle-maybe
		      org-babel-header-arg-expand)
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-cycle-hook '(org-ref-show-biblinks org-cycle-hide-archived-subtrees org-cycle-hide-drawers
		  org-cycle-show-empty-lines org-optimize-window-after-visibility-change)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-ref-notes-function '(lambda (thekey)
			  (let*
			   ((results (org-ref-get-bibtex-key-and-file thekey)) (key (car results))
			    (bibfile (cdr results)))
			   (save-excursion
			    (with-temp-buffer (insert-file-contents bibfile)
			     (bibtex-set-dialect (parsebib-find-bibtex-dialect) t) (bibtex-search-entry key)
			     (org-ref-open-bibtex-notes))
			    )
			   )
			  )
 org-ref-open-notes-function '(lambda nil (org-show-entry) (show-branches) (show-children)
			       (org-cycle (quote (64))) (recenter-top-bottom 0))
 org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook)
 org-export-with-toc nil
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-ref-insert-cite-function 'org-ref-helm-insert-cite-link
 org-ref-open-pdf-function 'org-ref-open-pdf-at-point
 org-odt-convert-processes '(("LibreOffice"
			      "/opt/libreoffice4.3/program/soffice --headless --convert-to %f%x %i")
			     )
 org-babel-pre-tangle-hook '(save-buffer)
 org-return-follows-link t
 org-occur-hook '(org-ref-show-biblinks org-first-headline-recenter)
 org-shiftright-hook '(#[nil "\300\301!\207" [org-ref-swap-citation-link 1] 2])
 org-latex-default-packages-alist '(("AUTO" "inputenc" t) ("T1" "fontenc" t) ("" "fixltx2e" nil)
				    ("" "graphicx" t) ("" "grffile" t) ("" "longtable" nil) ("" "wrapfig" nil)
				    ("" "rotating" nil) ("normalem" "ulem" t) ("" "amsmath" t)
				    ("" "textcomp" t) ("" "amssymb" t) ("" "capt-of" nil) ("" "hyperref" nil)
				    ("" "a4wide" nil) ("" "comment" nil))
 org-html-format-headline-function 'org-html-format-headline-default-function
 org-structure-template-alist '(("d" "#+OPTIONS: d:nil\n") ("C" "#+begin_comment\n?\n#+end_comment")
				("s" "#+begin_src matlab :results output\n\n#+end_src")
				("e" "#+BEGIN_EXAMPLE\n?\n#+END_EXAMPLE")
				("q" "#+BEGIN_QUOTE\n?\n#+END_QUOTE") ("v" "#+BEGIN_VERSE\n?\n#+END_VERSE")
				("V" "#+BEGIN_VERBATIM\n?\n#+END_VERBATIM")
				("c" "#+BEGIN_CENTER\n?\n#+END_CENTER") ("l" "#+BEGIN_LaTeX\n?\n#+END_LaTeX")
				("L" "#+LaTeX: ") ("h" "#+BEGIN_HTML\n?\n#+END_HTML")
				("H" "#+ATTR_HTML: border=\"2\" rules=\"all\" frame=\"border\"")
				("a" "#+BEGIN_ASCII\n?\n#+END_ASCII") ("A" "#+ASCII: ") ("i" "#+INDEX: ?")
				("I" "#+INCLUDE: %file ?"))
 org-html-table-default-attributes '(:border "2" :cellspacing "0" :cellpadding "6" :rules "all" :frame
				     "border")
 org-ref-clean-bibtex-entry-hook '(orcb-key-comma org-ref-replace-nonascii orcb-& orcb-%
				   org-ref-title-case-article orcb-clean-year orcb-key orcb-clean-doi
				   orcb-clean-pages org-ref-sort-bibtex-entry)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-capture-templates '(("r" "Reply" entry (file+headline "~/Mail/TODO-email.org" "Emails") "** REPLY %a %?"
			  :gnus-attachments t)
			 ("l" "EmacsLisp(headline)" entry
			  (file+headline
			   (expand-file-name (read-file-name "Name of file (curr dir;table format)!: "))
			   "EmacsLisp")
			  "* TODO %?, Link: %A")
			 ("j" "Journal(datatree)" entry
			  (file+datetree
			   (expand-file-name (read-file-name "Name of file (curr dir;table format)!: ")))
			  "* %?\nEntered on %U\n %i\n %a")
			 ("G" "Generic README.org file (table format)" table-line
			  (file+headline
			   (expand-file-name (read-file-name "Name of file (curr dir;table format)!: "))
			   "Overview")
			  "|%f| %U|%A|" :prepend t)
			 )
 org-latex-format-drawer-function '(lambda (name contents) contents)
 org-load-hook '(my-link-keys)
 org-format-latex-options '(:foreground default :background default :scale 1 :html-foreground "Black"
			    :html-background "Transparent" :html-scale 1 :matchers
			    ("begin" "$1" "$" "$$" "\\(" "\\["))
 org-highlight-latex-and-related '(latex)
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-ref-insert-label-function 'org-ref-helm-insert-label-link
 org-agenda-include-diary t
 org-html-with-latex 'imagemagick
 org-mode-hook '(turn-on-diff-hl-mode my-org-keys turn-on-flyspell turn-on-auto-capitalize-mode
		 org-auctex-keys-minor-mode org-ref-org-menu
		 #[nil "\300\301\302\303#\210\304\305\306\307#\207"
		   [advice-add org-activate-bracket-links :after org-ref-make-org-link-cite-key-visible
		    font-lock-add-keywords nil
		    ((org-ref-match-next-cite-link (0 (quote org-ref-cite-face) t))
		     (org-ref-match-next-label-link (0 (quote org-ref-label-face) t))
		     (org-ref-match-next-ref-link (0 (quote org-ref-ref-face) t))
		     (org-ref-match-next-bibliography-link (0 (quote org-link) t))
		     (org-ref-match-next-bibliographystyle-link (0 (quote org-link) t)))
		    t]
		   4]
		 #[0 "\300\301\302\303#\207"
		   [font-lock-add-keywords nil ((or-next-acronym-link (0 (quote org-ref-acronym-face) t))) t]
		   4]
		 #[0 "\300\301\302\303#\207"
		   [font-lock-add-keywords nil ((or-next-glossary-link (0 (quote org-ref-glossary-face) t))) t]
		   4]
		 #[nil "\300\301\302\303\304$\207"
		   [org-add-hook change-major-mode-hook org-show-block-all append local] 5]
		 #[nil "\300\301\302\303\304$\207"
		   [org-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-eldoc-load)
 org-ref-insert-link-function 'org-ref-helm-insert-cite-link
 org-ref-insert-ref-function 'org-ref-helm-insert-ref-link
 org-time-stamp-custom-formats '("«%d-%m-%Y %a»" . "«%d-%m-%Y %a %H:%M»")
 org-ascii-format-drawer-function '(lambda (name contents width) contents)
 org-format-latex-header "\\documentclass{article}\n\\usepackage[usenames]{color}\n[PACKAGES]\n[DEFAULT-PACKAGES]\n\\pagestyle{empty}             % do not remove\n% The settings below are copied from fullpage.sty\n\\setlength{\\textwidth}{\\paperwidth}\n\\addtolength{\\textwidth}{-3cm}\n\\setlength{\\oddsidemargin}{1.5cm}\n\\addtolength{\\oddsidemargin}{-2.54cm}\n\\setlength{\\evensidemargin}{\\oddsidemargin}\n\\setlength{\\textheight}{\\paperheight}\n\\addtolength{\\textheight}{-\\headheight}\n\\addtolength{\\textheight}{-\\headsep}\n\\addtolength{\\textheight}{-\\footskip}\n\\addtolength{\\textheight}{-3cm}\n\\setlength{\\topmargin}{1.5cm}\n\\newtheorem{thm}{Theorem}\n\\newtheorem{defn}{Definition}\n\\newtheorem{lem}{Lemma}\n\\newtheorem{cor}{Corollary}\n\\newtheorem{rem}{Remark}\n\\newtheorem{bei}{}\n\\newtheorem{prop}{Preposition}\n\\newcommand{\\setR}{{\\mathord{\\mathbb R}}}\n\\addtolength{\\topmargin}{-2.54cm} "
 org-ref-default-bibliography '("/home/oub/tex/bib/bibgraf.bib")
 org-odt-format-drawer-function '(lambda (name contents) contents)
 org-gnus-prefer-web-links t
 org-display-custom-times t
 org-from-is-user-regexp "\\<oub\\>"
 org-ref-bibliography-notes '("/home/oub/tex/bib/notes.org")
 org-html-format-drawer-function '(lambda (name contents) contents)
 org-export-before-processing-hook '(f-ox-filter-table-column-del)
 org-odt-format-headline-function 'org-odt-format-headline-default-function
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-ref-clean-bibtex-key-function '(lambda (key) (replace-regexp-in-string ":" "" key))
 org-odt-format-inlinetask-function 'org-odt-format-inlinetask-default-function
 org-ref-get-pdf-filename-function 'org-ref-get-pdf-filename
 org-babel-load-languages '((emacs-lisp . t) (R . t))
 org-ref-insert-cite-key "C-c c"
 org-latex-format-inlinetask-function 'org-latex-format-inlinetask-default-function
 org-confirm-shell-link-function 'yes-or-no-p
 )

Re: Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

[Nicolas Goaziou]

Hello,

Uwe Brauer <oub@mat.ucm.es> writes:

> Please look at the following example
>
> \documentclass[addpoints,12pt]{exam}
> \begin{document}
> % [[file:~/ALLES/tex/vorlesungen/HGBioQuim/Examen+geogebra/Examen2/README.org::*Overview][Overview]]
> \begin{questions}  
> % [[file:~/ALLES/tex/vorlesungen/HGBioQuim/Examen+geogebra/Examen2/README.org::*Overview][Overview]]
>
> \end{questions}
>
> `org-open-at-point' opens the first link, but not the one in the
> environment questions.

`org-open-at-point' in an Org function, which is meant to be called in
an Org buffer. IIUC, you are calling it from a LaTeX buffer.

`org-open-at-point-global' provides sloppy Org link (and time-stamp)
following in any buffer. You should use it in this case.

Note that however `org-open-at-point-global' was bugged, so I just fixed
it in master. Thank you for the report.


Regards,

-- 
Nicolas Goaziou

Re: Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

[Uwe Brauer]

    > Hello,
    > Uwe Brauer <oub@mat.ucm.es> writes:


    > `org-open-at-point' in an Org function, which is meant to be called in
    > an Org buffer. IIUC, you are calling it from a LaTeX buffer.

Ok, but one link worked with this function.


    > `org-open-at-point-global' provides sloppy Org link (and time-stamp)
    > following in any buffer. You should use it in this case.


Ok, thanks


    > Note that however `org-open-at-point-global' was bugged, so I just fixed
    > it in master. Thank you for the report.

Thank you for fixing it. I presume it will be on Monday  in ELPA?

regards

Uwe Brauer 

Re: Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

[Nicolas Goaziou]

Hello,

Uwe Brauer <oub@mat.ucm.es> writes:

> Ok, but one link worked with this function.

Sheer luck. `org-open-at-point' behaviour is undefined in non-Org
buffers. Note that, however, `org-open-at-point' wouldn't open the
second link even in an Org buffer because it is located within a LaTeX
environment. Org doesn't look for links into them.

> Thank you for fixing it. I presume it will be on Monday  in ELPA?

Unfortunately, no. I fixed it in master, which is development branch.
ELPA is a release from maint branch. I could cherry-pick it there, but
I need to be sure it doesn't break anything first.

Regards,

-- 
Nicolas Goaziou

Re: Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

[Uwe Brauer]

>>> "Nicolas" == Nicolas Goaziou <mail@nicolasgoaziou.fr> writes:

    > Hello,
    > Uwe Brauer <oub@mat.ucm.es> writes:

    >> Ok, but one link worked with this function.

    > Sheer luck. `org-open-at-point' behaviour is undefined in non-Org
    > buffers. Note that, however, `org-open-at-point' wouldn't open the
    > second link even in an Org buffer because it is located within a LaTeX
    > environment. Org doesn't look for links into them.

    >> Thank you for fixing it. I presume it will be on Monday  in ELPA?

    > Unfortunately, no. I fixed it in master, which is development branch.
    > ELPA is a release from maint branch. I could cherry-pick it there, but
    > I need to be sure it doesn't break anything first.

Ok, I could clone the git rep of org and then try to merge your
modification into ELPA, it is just that function you changed?

BTW I see that org is also in the trunk of Emacs master (25.1.5) which I
use, is org master the same as that version? I would then need to re
compile emacs...

regards


    > Regards,

Re: Bug: org links do not work in some latex files [8.3.4 (8.3.4-34-gacfd41-elpaplus @ /home/oub/.emacs.d/elpa/org-plus-contrib-20160411/)]

[Nicolas Goaziou]

Hello,

Uwe Brauer <oub@mat.ucm.es> writes:

> Ok, I could clone the git rep of org and then try to merge your
> modification into ELPA, it is just that function you changed?

That one and `org-open-at-point'.

> BTW I see that org is also in the trunk of Emacs master (25.1.5) which I
> use, is org master the same as that version? I would then need to re
> compile emacs...

Org in Emacs trunk is an outdated version no longer supported.

Regards,

-- 
Nicolas Goaziou