Re: [O] Error exporting org-ref.org to LaTeX (was: Re: Warnings while installing org-ref)

[John Kitchin]

I updated the documentation on the build requirements.

Lars Bjørndal writes:

> Thank you. You wrote:
>
>> You might have to require org-id and a few other org-ref libs for wos,
>> Scopus and arxiv links. See the notes near the end of that document. I
>> am traveling sans emacs right now so I don't have the exact place to
>> look, but it is in a section on alternate builds I think.
>
> Yes, I got it.
>
> Please note that `org-id' is not mentioned in the org-ref.org file.
>
> The .tex file is now prduced without errors/warnings. The pdf is
> produced as well, but with warnings. Some of them are:
>
> Package glossaries Warning: No \printglossary or \printglossaries
> found.
> (Remove \makeglossaries if you don't want any glossaries.)
> This document will not have a glossary.
>
> LaTeX Warning: There were undefined references.
>
> Thanks and regards, Lars
>
>
>> On Sat, May 27, 2017 at 4:52 PM Lars Bjørndal <address@hidden>
>> wrote:
>>
>>   On Fri, May 26, 2017 at 04:06:52PM -0400, John Kitchin wrote:
>>   > I pushed a bunch of commits today to clean up a lot of these.
>>   There are
>>   > still a few that I don't know how to get rid of, but it should be
>>   a lot
>>   > cleaner now.
>>   Thanks a lot.
>>   To learn Org, Org-ref and exports, I tried to export the
>>   [2]org-ref.org
>>   to LaTeX. The .tex file is produced, but I get the following error
>>   message:
>>     user-error: Unable to resolve link:
>>   "id:212B487E-CC38-4BDF-9F0E-6993845AF49B"
>>   What does that mean?
>>   Thanks and regards, Lars
>>   > Lars Bjørndal writes:
>>   >
>>   > > I installed org-ref from Elpa, and I got some warnings. Emacs
>>   version:
>>   > >
>>   > > GNU Emacs 25.2.1 (x86_64-redhat-linux-gnu, GTK+ Version 3.20.10)
>>   of 2017-05-02
>>   > >
>>   > > I'm not sure how critical these error messages are.
>>   > >
>>   > > Fri May 26 14:59:37 2017
>>   > > Entering directory
>>   `/home/tstl/.emacs.d/elpa/key-chord-20160227.438/'
>>   > >
>>   > > In key-chord-input-method:
>>   > > key-chord.el:341:16:Warning: sit-for called with 3 arguments,
>>   but
>>   > > accepts only
>>   > >     1-2
>>   > > i May 26 14:59:45 2017
>>   > > Entering directory
>>   `/home/tstl/.emacs.d/elpa/helm-core-20170526.36/'
>>   > >
>>   > > In helm-position:
>>   > > helm-lib.el:388:14:Warning: macro `helm-position' defined too
>>   late
>>   > >
>>   > > In end of data:
>>   > > helm-lib.el:1006:1:Warning: the following functions are not
>>   known to be
>>   > > defined\
>>   > > :
>>   > >     helm-interpret-value, helm-get-current-source
>>   > >
>>   > > Compiling file
>>   > >
>>   /home/tstl/.emacs.d/elpa/helm-bibtex-20170321.1306/bibtex-comple\
>>   > > tion.el at Fri May 26 14:59:54 2017
>>   > > Entering directory
>>   `/home/tstl/.emacs.d/elpa/helm-bibtex-20170321.1306/'
>>   > >
>>   > > In end of data:
>>   > > bibtex-completion.el:1210:1:Warning: the following functions are
>>   not
>>   > > known to b\
>>   > > e defined:
>>   > >     reftex-what-macro, org-find-property,
>>   > >         reftex-locate-bibliography-files
>>   > >
>>   > > Entering directory
>>   `/home/tstl/.emacs.d/elpa/org-ref-20170523.1821/'
>>   > >
>>   > > In end of data:
>>   > > doi-utils.el:1361:1:Warning: the following functions are not
>>   known to be
>>   > > define\
>>   > > d:
>>   > >     org-ref-find-bibliography, reftex-get-bib-field,
>>   > >         org-ref-bib-citation
>>   > >
>>   > > Compiling file
>>   > >
>>   /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-bibtex.el\
>>   > >  at Fri May 26 14:59:57 2017
>>   > >
>>   > > In org-ref-bibtex-assoc-pdf-with-entry:
>>   > > org-ref-bibtex.el:728:25:Warning: reference to free variable
>>   > >     `org-ref-pdf-directory'
>>   > >
>>   > > In orhc-bibtex-field-formatter:
>>   > > org-ref-bibtex.el:1092:27:Warning: reference to free variable
>>   > >     `org-ref-pdf-directory'
>>   > >     org-ref-bibtex.el:1098:27:Warning: reference to free
>>   variable
>>   > >         `org-ref-notes-directory'
>>   > >
>>   > > In end of data:
>>   > > org-ref-bibtex.el:1324:1:Warning: the following functions are
>>   not known
>>   > > to be d\
>>   > > efined:
>>   > >     reftex-get-bib-field, org-ref-find-bibliography
>>   > >
>>   > > Compiling file
>>   > >
>>   /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-citeproc.\
>>   > > el at Fri May 26 14:59:57 2017
>>   > >
>>   > > In end of data:
>>   > > org-ref-citeproc.el:919:1:Warning: the function
>>   > >     `org-ref-get-bibtex-key-and-file' is not known to be
>>   defined.
>>   > >
>>   > > Compiling file
>>   > > /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-core.el
>>   a\
>>   > > t Fri May 26 14:59:57 2017
>>   > >
>>   > > In org-ref-update-pre-post-text:
>>   > > org-ref-core.el:3259:16:Warning: `delete-backward-char' is for
>>   > > interactive use
>>   > >     only; use `delete-char' instead.
>>   > >     org-ref-core.el:3260:12:Warning: `delete-backward-char' is
>>   for
>>   > >     interactive use
>>   > >         only; use `delete-char' instead.
>>   > >
>>   > > In end of data:
>>   > > org-ref-core.el:3498:1:Warning: the following functions are not
>>   known to
>>   > > be def\
>>   > > ined:
>>   > >     org-ref-match-next-cite-link, org-ref-match-next-label-link,
>>   > >         org-ref-match-next-ref-link,
>>   > >             org-ref-make-org-link-cite-key-visible,
>>   > >             org-in-commented-heading-p
>>   > >
>>   > > Compiling file
>>   > >
>>   /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-helm-bibt\
>>   > > ex.el at Fri May 26 14:59:58 2017
>>   > >
>>   > > In org-ref-format-citation:
>>   > > org-ref-helm-bibtex.el:308:22:Warning: assignment to free
>>   variable `end'
>>   > > org-ref-helm-bibtex.el:313:37:Warning: assignment to free
>>   variable
>>   > > `path'
>>   > > org-ref-helm-bibtex.el:313:37:Warning: reference to free
>>   variable `end'
>>   > > org-ref-helm-bibtex.el:311:16:Warning: looking-back called with
>>   1
>>   > > argument,
>>   > >     but requires 2-3
>>   > >     org-ref-helm-bibtex.el:313:18:Warning: reference to free
>>   variable
>>   > >     `path'
>>   > >
>>   > > In org-ref-helm-load-completions-async:
>>   > > org-ref-helm-bibtex.el:367:22:Warning: assignment to free
>>   variable
>>   > >     `bibtex-completion-cached-candidates'
>>   > >     org-ref-helm-bibtex.el:371:20:Warning: assignment to free
>>   variable
>>   > >         `bibtex-completion-bibliography-hash'
>>   > >
>>   > > In org-ref-browser:
>>   > > org-ref-helm-bibtex.el:681:20:Warning: `show-all' is an obsolete
>>   > > function (as
>>   > >     of 25.1); use `outline-show-all' instead.
>>   > >     org-ref-helm-bibtex.el:712:61:Warning: assignment to free
>>   variable
>>   > >         `count-key-pos'
>>   > >         org-ref-helm-bibtex.el:715:68:Warning: reference to free
>>   > >         variable
>>   > >             `count-key-pos'
>>   > >
>>   > > Compiling file
>>   > > /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-helm.el
>>   a\
>>   > > t Fri May 26 14:59:58 2017
>>   > >
>>   > > In org-ref:
>>   > > org-ref-helm.el:289:78:Error: `add-to-list' can't use lexical
>>   var
>>   > > `matches';
>>   > >     use `push' or `cl-pushnew'
>>   > >     org-ref-helm.el:317:54:Error: `add-to-list' can't use
>>   lexical var
>>   > >     `matches';
>>   > >         use `push' or `cl-pushnew'
>>   > >         org-ref-helm.el:306:39:Error: `add-to-list' can't use
>>   lexical
>>   > >         var `matches';
>>   > >             use `push' or `cl-pushnew'
>>   > >             org-ref-helm.el:380:47:Warning: reference to free
>>   variable
>>   > >             `org-latex-prefer-user-labels'
>>   > >
>>   > > Compiling file
>>   > > /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-pdf.el
>>   at\
>>   > >  Fri May 26 14:59:59 2017
>>   > >
>>   > > In end of data:
>>   > > org-ref-pdf.el:248:1:Warning: the following functions are not
>>   known to
>>   > > be defin\
>>   > > ed:
>>   > >     pdf-view-assert-active-region, pdf-view-active-region-text,
>>   > >         pdf-view-deactivate-region
>>   > >
>>   > > Lars
>>   >
>>   >
>>   > --
>>   > Professor John Kitchin
>>   > Doherty Hall A207F
>>   > Department of Chemical Engineering
>>   > Carnegie Mellon University
>>   > Pittsburgh, PA 15213
>>   > 412-268-7803
>>   > @johnkitchin
>>   > [3]http://kitchingroup.cheme.cmu.edu
>>   >
>>
>> --
>>
>> John
>> -----------------------------------
>> Professor John Kitchin
>> Doherty Hall A207F
>> Department of Chemical Engineering
>> Carnegie Mellon University
>> Pittsburgh, PA 15213
>> 412-268-7803
>> @johnkitchin
>> [4]http://kitchingroup.cheme.cmu.edu
>>
>> References
>>
>> 1. mailto:address@hidden
>> 2. http://org-ref.org/
>> 3. http://kitchingroup.cheme.cmu.edu/
>> 4. http://kitchingroup.cheme.cmu.edu/


--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu