From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Kitchin Subject: Re: Error exporting org-ref.org to LaTeX (was: Re: Warnings while installing org-ref) Date: Sat, 27 May 2017 21:41:56 +0000 Message-ID: References: <20170527205147.GM14793@lamasti.net> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="94eb2c073dee666c3c0550885374" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:58498) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1dEjTR-0004Pi-Js for emacs-orgmode@gnu.org; Sat, 27 May 2017 17:42:15 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1dEjTO-0004P3-DP for emacs-orgmode@gnu.org; Sat, 27 May 2017 17:42:13 -0400 Received: from mail-wm0-f42.google.com ([74.125.82.42]:38143) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1dEjTO-0004OW-25 for emacs-orgmode@gnu.org; Sat, 27 May 2017 17:42:10 -0400 Received: by mail-wm0-f42.google.com with SMTP id e127so19153853wmg.1 for ; Sat, 27 May 2017 14:42:09 -0700 (PDT) In-Reply-To: <20170527205147.GM14793@lamasti.net> 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.org@gnu.org Sender: "Emacs-orgmode" To: =?UTF-8?Q?Lars_Bj=C3=B8rndal?= , "emacs-orgmode@gnu.org" --94eb2c073dee666c3c0550885374 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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. On Sat, May 27, 2017 at 4:52 PM Lars Bj=C3=B8rndal 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 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 Bj=C3=B8rndal 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 kno= wn > > > 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 `en= d' > > > 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 variabl= e > > > `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 variabl= e > > > `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 variabl= e > > > `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 t= o > > > 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 > > 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 http://kitchingroup.cheme.cmu.edu --94eb2c073dee666c3c0550885374 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
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.



On Sat, May 27, 2017 = at 4:52 PM Lars Bj=C3=B8rndal <lars@= lamasti.net> 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 ar= e
> 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 org-ref.org
to LaTeX. The .tex file is produced, but I get the following error
message:

=C2=A0 user-error: Unable to resolve link: "id:212B487E-CC38-4BDF-9F0E= -6993845AF49B"

What does that mean?

Thanks and regards, Lars

> Lars Bj=C3=B8rndal writes:
>
> > I installed org-ref from Elpa, and I got some warnings. Emacs ver= sion:
> >
> > 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-20160227.4= 38/'
> >
> > In key-chord-input-method:
> > key-chord.el:341:16:Warning: sit-for called with 3 arguments, but=
> > accepts only
> >=C2=A0 =C2=A0 =C2=A01-2
> > i May 26 14:59:45 2017
> > Entering directory `/home/tstl/.emacs.d/elpa/helm-core-20170526.3= 6/'
> >
> > 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\
> > :
> >=C2=A0 =C2=A0 =C2=A0helm-interpret-value, helm-get-current-source<= br> > >
> > 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:
> >=C2=A0 =C2=A0 =C2=A0reftex-what-macro, org-find-property,
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0reftex-locate-bibliography-files=
> >
> > Entering directory `/home/tstl/.emacs.d/elpa/org-ref-20170523.182= 1/'
> >
> > In end of data:
> > doi-utils.el:1361:1:Warning: the following functions are not know= n to be
> > define\
> > d:
> >=C2=A0 =C2=A0 =C2=A0org-ref-find-bibliography, reftex-get-bib-fiel= d,
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-bib-citation
> >
> > Compiling file
> > /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-bibtex.el\=
> >=C2=A0 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
> >=C2=A0 =C2=A0 =C2=A0`org-ref-pdf-directory'
> >
> > In orhc-bibtex-field-formatter:
> > org-ref-bibtex.el:1092:27:Warning: reference to free variable
> >=C2=A0 =C2=A0 =C2=A0`org-ref-pdf-directory'
> >=C2=A0 =C2=A0 =C2=A0org-ref-bibtex.el:1098:27:Warning: reference t= o free variable
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0`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:
> >=C2=A0 =C2=A0 =C2=A0reftex-get-bib-field, org-ref-find-bibliograph= y
> >
> > 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
> >=C2=A0 =C2=A0 =C2=A0`org-ref-get-bibtex-key-and-file' is not k= nown 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 fo= r
> > interactive use
> >=C2=A0 =C2=A0 =C2=A0only; use `delete-char' instead.
> >=C2=A0 =C2=A0 =C2=A0org-ref-core.el:3260:12:Warning: `delete-backw= ard-char' is for
> >=C2=A0 =C2=A0 =C2=A0interactive use
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0only; use `delete-char' inst= ead.
> >
> > In end of data:
> > org-ref-core.el:3498:1:Warning: the following functions are not k= nown to
> > be def\
> > ined:
> >=C2=A0 =C2=A0 =C2=A0org-ref-match-next-cite-link, org-ref-match-ne= xt-label-link,
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-match-next-ref-link,
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-make-org-l= ink-cite-key-visible,
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-in-commented-h= eading-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 variabl= e `end'
> > org-ref-helm-bibtex.el:313:37:Warning: assignment to free variabl= e
> > `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,
> >=C2=A0 =C2=A0 =C2=A0but requires 2-3
> >=C2=A0 =C2=A0 =C2=A0org-ref-helm-bibtex.el:313:18:Warning: referen= ce to free variable
> >=C2=A0 =C2=A0 =C2=A0`path'
> >
> > In org-ref-helm-load-completions-async:
> > org-ref-helm-bibtex.el:367:22:Warning: assignment to free variabl= e
> >=C2=A0 =C2=A0 =C2=A0`bibtex-completion-cached-candidates'
> >=C2=A0 =C2=A0 =C2=A0org-ref-helm-bibtex.el:371:20:Warning: assignm= ent to free variable
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0`bibtex-completion-bibliography-= hash'
> >
> > In org-ref-browser:
> > org-ref-helm-bibtex.el:681:20:Warning: `show-all' is an obsol= ete
> > function (as
> >=C2=A0 =C2=A0 =C2=A0of 25.1); use `outline-show-all' instead.<= br> > >=C2=A0 =C2=A0 =C2=A0org-ref-helm-bibtex.el:712:61:Warning: assignm= ent to free variable
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0`count-key-pos'
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-helm-bibtex.el:715:68:Wa= rning: reference to free
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0variable
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0`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 lex= ical var
> > `matches';
> >=C2=A0 =C2=A0 =C2=A0use `push' or `cl-pushnew'
> >=C2=A0 =C2=A0 =C2=A0org-ref-helm.el:317:54:Error: `add-to-list'= ; can't use lexical var
> >=C2=A0 =C2=A0 =C2=A0`matches';
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0use `push' or `cl-pushnew= 9;
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-helm.el:306:39:Error: `a= dd-to-list' can't use lexical
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0var `matches';
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0use `push' or = `cl-pushnew'
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0org-ref-helm.el:38= 0:47:Warning: reference to free variable
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0`org-latex-prefer-= user-labels'
> >
> > Compiling file
> > /home/tstl/.emacs.d/elpa/org-ref-20170523.1821/org-ref-pdf.el at\=
> >=C2=A0 Fri May 26 14:59:59 2017
> >
> > In end of data:
> > org-ref-pdf.el:248:1:Warning: the following functions are not kno= wn to
> > be defin\
> > ed:
> >=C2=A0 =C2=A0 =C2=A0pdf-view-assert-active-region, pdf-view-active= -region-text,
> >=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0pdf-view-deactivate-region
> >
> > Lars
>
>
> --
> 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
>

--
John

---= --------------------------------
Professor John Kitchin=C2=A0
Doherty= Hall A207F
Department of Chemical Engineering
Carnegie Mellon Univer= sity
Pittsburgh, PA 15213
412-268-7803
--94eb2c073dee666c3c0550885374--