customising org-latex-to-pdf-process for bibtex

customising org-latex-to-pdf-process for bibtex

[suvayu ali]

Hi everyone,

I am trying to use bibtex with pdf export for my thesis. So I tried
customising =org-latex-to-pdf-process= so that bibtex is run before
pdflatex. So from the customise buffer I set it to something like this:

pdflatex -interaction nonstopmode -output-directory %o %f
bibtex %b
pdflatex -interaction nonstopmode -output-directory %o %f
pdflatex -interaction nonstopmode -output-directory %o %f

I also tried these,

pdflatex -interaction nonstopmode -output-directory %o %b
bibtex %b
pdflatex -interaction nonstopmode -output-directory %o %b
pdflatex -interaction nonstopmode -output-directory %o %b

But none of these run bibtex properly. For now I am exporting to latex
everytime I change the bibliography and run bibtex from the terminal.
For subsequent pdf exports the default values then give me a proper pdf
with all the citations displayed correctly.

Any thoughts on what I am doing wrong?

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

suvayu ali <fatkasuvayu+linux@gmail.com> writes:

> Hi everyone,
>
> I am trying to use bibtex with pdf export for my thesis. So I tried
> customising =org-latex-to-pdf-process= so that bibtex is run before
> pdflatex. So from the customise buffer I set it to something like
> this:

I have 

#+begin_src emacs-lisp
(setq org-latex-to-pdf-process 
  '("pdflatex %f" "bibtex %b" "pdflatex %f" "pdflatex %f"))
#+end_src

which seems to work just fine for me.  You may wish (for security) to
add the fully qualified paths for these executables, of course.
-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.532.g7b21.dirty)

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hi Eric,

On Sat, 26 Feb 2011 00:23:15 +0000
Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> suvayu ali <fatkasuvayu+linux@gmail.com> writes:
> 
> > Hi everyone,
> >
> > I am trying to use bibtex with pdf export for my thesis. So I tried
> > customising =org-latex-to-pdf-process= so that bibtex is run before
> > pdflatex. So from the customise buffer I set it to something like
> > this:
> 
> I have 
> 
> #+begin_src emacs-lisp
> (setq org-latex-to-pdf-process 
>   '("pdflatex %f" "bibtex %b" "pdflatex %f" "pdflatex %f"))
> #+end_src
> 

I tried that, no luck. It gets stuck at some line and fails. I think
there is some problem with one of the packages I am using for
equations. Putting back "-interactionmode nonstop" makes the pdflatex
process continue to the end and produce the pdf.

> which seems to work just fine for me.  You may wish (for security) to
> add the fully qualified paths for these executables, of course.

Its my private desktop and laptop, and I can be quite paranoid about
security usually so that part is somewhat covered. :) Maybe I'll
consider it later.

If you are otherwise worried about whether I'm picking up the correct
version of pdflatex, I see the following version information in the
"*Org PDF LaTeX output*" buffer:

> This is pdfTeX, Version 3.1415926-1.40.11 (TeX Live 2010)

So its as expected.

Thank you for your thoughts about my issue, appreciate it. 

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:

> Hi Eric,
>
> On Sat, 26 Feb 2011 00:23:15 +0000
> Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>
>> suvayu ali <fatkasuvayu+linux@gmail.com> writes:
>> 
>> > Hi everyone,
>> >
>> > I am trying to use bibtex with pdf export for my thesis. So I tried
>> > customising =org-latex-to-pdf-process= so that bibtex is run before
>> > pdflatex. So from the customise buffer I set it to something like
>> > this:
>> 
>> I have 
>> 
>> #+begin_src emacs-lisp
>> (setq org-latex-to-pdf-process 
>>   '("pdflatex %f" "bibtex %b" "pdflatex %f" "pdflatex %f"))
>> #+end_src
>> 
>
> I tried that, no luck. It gets stuck at some line and fails. I think
> there is some problem with one of the packages I am using for
> equations. Putting back "-interactionmode nonstop" makes the pdflatex
> process continue to the end and produce the pdf.

I think you should try to sort this out first.  What happens if you
export to latex and then invoke pdflatex directly yourself?  Which
package is causing the error?

In any case, once you have the latex, you can try the individual steps
directly.  I would recommend using auctex mode within Emacs.  You should
be able to mimic the behaviour of org's pdf export by repeated use of
C-c C-c in auctex mode.

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.529.gb23d.dirty)

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hey Thomas,

Thanks for your response. I have outlined what I tried and found below.

On Fri, 25 Feb 2011 14:08:31 -1000
"Thomas S. Dye" <tsd@tsdye.com> wrote:

> Aloha Suvayu,
> 
> I had what sounds like a similar problem.  You don't say why bibtex  
> fails, but in my case it wasn't able to find the .aux file.  When I
> do this:
> 
>    (setq org-export-pdf-remove-logfiles nil)
> 
> then I'm able to run bibtex without problems.
> 

I tried that after your post, didn't seem to make a difference. I don't
know how to find how bibtex fails. All I see are these lines in the
"*Org PDF LaTeX Output*" buffer:

> No file msthesis.bbl.
> [5] (/home/jallad/org/masters-thesis//msthesis.aux)
> 
> LaTeX Warning: There were undefined references.

Does that say anything to you? How do I capture the output from bibtex?
I presumed it is being overwritten by subsequent pdflatex runs. So I
removed the later pdflatex runs from the variable and that gives me
this output in the "*Org PDF LaTeX Output*" buffer.

> bibtex: Not writing to /home/user/org/masters-thesis/msthesis.blg
> (openout_any = p). I couldn't open file name
> `/home/user/org/masters-thesis/msthesis.blg'

However with the same tex file, after I run "bibtex msthesis" from the
terminal everything is fine! I even tried specifying the %b.aux in the
org-latex-to-pdf-process variable with no luck.

> I haven't tested your org-latex-to-pdf-process setups, so can't say  
> whether or not there is a problem with them.

I use the TeXLive distributed by CTAN in isos. I setup my path so it
finds the right binaries whenever I'm working with latex. I am sure my
setup is fine as things are as expected when run from the teminal.

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hi Tom,

On Fri, 25 Feb 2011 16:39:35 -1000
"Thomas S. Dye" <tsd@tsdye.com> wrote:

> Aloha Suvayu,
> 
> it sounds like you have a different problem than the one I  
> experienced.  Your error message seems to indicate the the .aux file  
> is present, but that it points to a missing .bbl file.
> 

I am not very familiar with pdflatex/bibtex. I don't know when bibtex
looks for that particular file.

> I noticed that the output you sent has different
> paths: /home/jallad/ vs. /home/user/
> Not sure if that is an issue or not, but it might explain why
> the .aux file would point to an absent file.
> 

Sorry that was a typo on my part. They are the same. Is there anything
else I could try to better understand what is going wrong?

> All the best,
> Tom

Thanks a lot.

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

[-- Attachment #1: Type: text/plain, Size: 674 bytes --]

Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:

[...]

>
> Does that say anything to you? How do I capture the output from bibtex?
> I presumed it is being overwritten by subsequent pdflatex runs. So I
> removed the later pdflatex runs from the variable and that gives me
> this output in the "*Org PDF LaTeX Output*" buffer.

[...]

You could try creating a shell script (such as attached) which invokes
both pdflatex and bibtex and tell org to use that command for exporting
to pdf instead.  Then all the output should come out to the screen.

I've tried this and all the output (3 pdflatex and 1 bibtex invocations)
comes out into the =*Org PDF Latex Output*= buffer.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: org 2 pdf shell scripts --]
[-- Type: text/x-sh, Size: 331 bytes --]

#!/bin/sh -f
# first argument should be base latex file name
F=$1
echo 'Using ' $F
echo '--------------------------------- running pdflatex first'
pdflatex $F
echo '--------------------------------- running bibtex next'
bibtex  $F
echo '--------------------------------- running pdflatex again (and again)'
pdflatex $F
pdflatex $F

[-- Attachment #3: Type: text/plain, Size: 126 bytes --]


-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.529.gb23d.dirty)

[-- Attachment #4: Type: text/plain, Size: 201 bytes --]

_______________________________________________
Emacs-orgmode mailing list
Please use `Reply All' to send replies to the list.
Emacs-orgmode@gnu.org
http://lists.gnu.org/mailman/listinfo/emacs-orgmode

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hi Eric,

On Mon, 28 Feb 2011 16:06:06 +0000
Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> You could try creating a shell script (such as attached) which invokes
> both pdflatex and bibtex and tell org to use that command for
> exporting to pdf instead.  Then all the output should come out to the
> screen.
> 
> I've tried this and all the output (3 pdflatex and 1 bibtex
> invocations) comes out into the =*Org PDF Latex Output*= buffer.
> 

Thank you for this nice idea. I tried it, but every time I (without the
-interaction nonstopmode option) the pdflatex process stops at this:

> ! LaTeX Error: Command \iint already defined.
>                Or name \end... illegal, see p.192 of the manual.
> 
> See the LaTeX manual or LaTeX Companion for explanation.
> Type  H <return>  for immediate help.
>  ...                                              
>                                                   
> l.506 ...d{\iint}{\DOTSI\protect\MultiIntegral{2}}
>                                                   
> ? 
> ! Emergency stop.
>  ...                                              
>                                                   
> l.506 ...d{\iint}{\DOTSI\protect\MultiIntegral{2}}
>                                                   
> !  ==> Fatal error occurred, no output PDF file produced!
> Transcript written on msthesis.log.

The amsmath package is loaded before this.

In my preamble in the org file I have the following LaTeX options:

> #+LaTeX_HEADER: \usepackage{cancel}
> #+LaTeX_HEADER: \usepackage{amsmath}
> #+LaTeX_HEADER: \usepackage{mathtools}
> #+LaTeX_HEADER: \numberwithin{equation}{section}
> #+LaTeX_CLASS_OPTIONS: [colorlinks]
> # #+LaTeX_HEADER: \definecolor{myblue}{rgb}{0.235,0.263,0.867}
> # #+LaTeX_HEADER: \definecolor{mygreen}{rgb}{0.012,0.467,0.059}

In the tex file this exports to:

> % Created 2011-02-28 Mon 12:34
> \documentclass[colorlinks]{article}
> \usepackage[utf8]{inputenc}
> \usepackage[T1]{fontenc}
> \usepackage{fixltx2e}
> \usepackage{graphicx}
> \usepackage{longtable}
> \usepackage{float}
> \usepackage{wrapfig}
> \usepackage{soul}
> \usepackage{textcomp}
> \usepackage{marvosym}
> \usepackage{wasysym}
> \usepackage{latexsym}
> \usepackage{amssymb}
> \usepackage{hyperref}
> \tolerance=1000
> \usepackage{cancel}
> \usepackage{amsmath}
> \usepackage{mathtools}
> \numberwithin{equation}{section}
> \providecommand{\alert}[1]{\textbf{#1}}

At first I thought its a problem with the mathtools package, but
removing it doesn't help either.

Is this a problem with my Latex installation? I tried both my
distribution provided texlive-2007 and texlive-2010 from the CTAN
archives with the same result. If its a problem with my texlive
installation, do you have any ideas where I can seek help? I'm rather
pressed for time.

Thanks a lot for being so patient. :)

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

On Mon, 28 Feb 2011 12:45:36 -0800
Suvayu Ali <fatkasuvayu+linux@gmail.com> wrote:

> Thank you for this nice idea. I tried it, but every time I (without
> the -interaction nonstopmode option) the pdflatex process stops at
> this:

Strangely, with "-interaction nonstopmode" using the shell script trick
gives me perfect results! I guess I can keep using this until the real
issue is resolved.

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:

> On Mon, 28 Feb 2011 12:45:36 -0800
> Suvayu Ali <fatkasuvayu+linux@gmail.com> wrote:
>
>> Thank you for this nice idea. I tried it, but every time I (without
>> the -interaction nonstopmode option) the pdflatex process stops at
>> this:
>
> Strangely, with "-interaction nonstopmode" using the shell script trick
> gives me perfect results! I guess I can keep using this until the real
> issue is resolved.

Well, not so strange:  if the error (iint redefined) is not one that
actually affects your latex code, then telling latex to not stop on
errors allows it to create your pdf file.  more importantly, it is able
to generate the information that bibtex subsequently needs to generate
the bibliography.

Anyway, I'm glad I could help!  See my other email on how to solve the
original problem.

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.555.gfcf66)

Re: customising org-latex-to-pdf-process for bibtex

[Thomas S. Dye]

Aloha Suvayu,

I haven't looked into this in depth, but I think your problem might  
come from loading amssymb and amsmath.  LaTeX is complaining that  
something is already defined; the AMS packages are a prime suspect  
here.  Perhaps you could inhibit amssymb?

All the best,
Tom

On Feb 28, 2011, at 10:45 AM, Suvayu Ali wrote:

> Hi Eric,
>
> On Mon, 28 Feb 2011 16:06:06 +0000
> Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>
>> You could try creating a shell script (such as attached) which  
>> invokes
>> both pdflatex and bibtex and tell org to use that command for
>> exporting to pdf instead.  Then all the output should come out to the
>> screen.
>>
>> I've tried this and all the output (3 pdflatex and 1 bibtex
>> invocations) comes out into the =*Org PDF Latex Output*= buffer.
>>
>
> Thank you for this nice idea. I tried it, but every time I (without  
> the
> -interaction nonstopmode option) the pdflatex process stops at this:
>
>> ! LaTeX Error: Command \iint already defined.
>>               Or name \end... illegal, see p.192 of the manual.
>>
>> See the LaTeX manual or LaTeX Companion for explanation.
>> Type  H <return>  for immediate help.
>> ...
>>
>> l.506 ...d{\iint}{\DOTSI\protect\MultiIntegral{2}}
>>
>> ?
>> ! Emergency stop.
>> ...
>>
>> l.506 ...d{\iint}{\DOTSI\protect\MultiIntegral{2}}
>>
>> !  ==> Fatal error occurred, no output PDF file produced!
>> Transcript written on msthesis.log.
>
> The amsmath package is loaded before this.
>
> In my preamble in the org file I have the following LaTeX options:
>
>> #+LaTeX_HEADER: \usepackage{cancel}
>> #+LaTeX_HEADER: \usepackage{amsmath}
>> #+LaTeX_HEADER: \usepackage{mathtools}
>> #+LaTeX_HEADER: \numberwithin{equation}{section}
>> #+LaTeX_CLASS_OPTIONS: [colorlinks]
>> # #+LaTeX_HEADER: \definecolor{myblue}{rgb}{0.235,0.263,0.867}
>> # #+LaTeX_HEADER: \definecolor{mygreen}{rgb}{0.012,0.467,0.059}
>
> In the tex file this exports to:
>
>> % Created 2011-02-28 Mon 12:34
>> \documentclass[colorlinks]{article}
>> \usepackage[utf8]{inputenc}
>> \usepackage[T1]{fontenc}
>> \usepackage{fixltx2e}
>> \usepackage{graphicx}
>> \usepackage{longtable}
>> \usepackage{float}
>> \usepackage{wrapfig}
>> \usepackage{soul}
>> \usepackage{textcomp}
>> \usepackage{marvosym}
>> \usepackage{wasysym}
>> \usepackage{latexsym}
>> \usepackage{amssymb}
>> \usepackage{hyperref}
>> \tolerance=1000
>> \usepackage{cancel}
>> \usepackage{amsmath}
>> \usepackage{mathtools}
>> \numberwithin{equation}{section}
>> \providecommand{\alert}[1]{\textbf{#1}}
>
> At first I thought its a problem with the mathtools package, but
> removing it doesn't help either.
>
> Is this a problem with my Latex installation? I tried both my
> distribution provided texlive-2007 and texlive-2010 from the CTAN
> archives with the same result. If its a problem with my texlive
> installation, do you have any ideas where I can seek help? I'm rather
> pressed for time.
>
> Thanks a lot for being so patient. :)
>
> -- 
> Suvayu
>
> Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

"Thomas S. Dye" <tsd@tsdye.com> writes:

> Aloha Suvayu,
>
> I haven't looked into this in depth, but I think your problem might
> come from loading amssymb and amsmath.  LaTeX is complaining that
> something is already defined; the AMS packages are a prime suspect
> here.  Perhaps you could inhibit amssymb?
>
> All the best,
> Tom

Suvayu,

I think this is indeed the problem.  I had this problem a month or so
ago (search the mailing list!).  My solution is to add this to my
.emacs:

--8<---------------cut here---------------start------------->8---
;; to fix problems with amsmath conflicting with wasysym:
;;
;; From: Lawrence Mitchell <wence@gmx.li>
;; Subject: [Orgmode] Re: [bug] latex export ignores org-export-latex-default-packages-alist?
;; To: emacs-orgmode@gnu.org
;; Date: Wed, 26 Jan 2011 16:01:52 +0000
(add-to-list 'org-export-latex-packages-alist '("" "amsmath" t))
(setcar (rassoc '("wasysym" t) org-export-latex-default-packages-alist)	"integrals")
--8<---------------cut here---------------end--------------->8---

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.555.gfcf66)

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hi Tom and Eric,

On Tue, 01 Mar 2011 08:52:44 +0000
Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> "Thomas S. Dye" <tsd@tsdye.com> writes:
> 
> > Aloha Suvayu,
> >
> > I haven't looked into this in depth, but I think your problem might
> > come from loading amssymb and amsmath.  LaTeX is complaining that
> > something is already defined; the AMS packages are a prime suspect
> > here.  Perhaps you could inhibit amssymb?
> >
> > All the best,
> > Tom
> 
> Suvayu,
> 
> I think this is indeed the problem.  I had this problem a month or so
> ago (search the mailing list!).  My solution is to add this to my
> .emacs:
> 
> --8<---------------cut here---------------start------------->8---
> (add-to-list 'org-export-latex-packages-alist '("" "amsmath" t))
> (setcar (rassoc '("wasysym" t)
> org-export-latex-default-packages-alist)	"integrals")
> --8<---------------cut here---------------end--------------->8---
> 

Thanks a lot, that worked like a charm. :)

Although I get perfect results using the Fedora 13 provided texlive
(2007), I noticed I get that old error again (quoted below) when I use
the texlive 2010 install from CTAN. Maybe some problem in my setup. I
will use my distribution provided texlive for now.

Thanks again for being so patient and helping with my issues. :)

> bibtex: Not writing to /home/jallad/org/masters-thesis/msthesis.blg (openout_any = p).
> I couldn't open file name `/home/jallad/org/masters-thesis/msthesis.blg'

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:

[...]

> Although I get perfect results using the Fedora 13 provided texlive
> (2007), I noticed I get that old error again (quoted below) when I use
> the texlive 2010 install from CTAN. Maybe some problem in my setup. I
> will use my distribution provided texlive for now.
>
> Thanks again for being so patient and helping with my issues. :)
>
>> bibtex: Not writing to /home/jallad/org/masters-thesis/msthesis.blg (openout_any = p).
>> I couldn't open file name `/home/jallad/org/masters-thesis/msthesis.blg'

Sorry; this I cannot help with much as I'm not sure what is happening
here and I've never run into this before.

Are there any problems with that file (e.g. read only mode)?  Is the
file there?  If so, what happens if you remove it?  It should be created
automatically by bibtex.

Have you tried searching the web with that error message (e.g. google
bibtex openout_any)?

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.562.gc895)

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hi Eric and others,

On Tue, 01 Mar 2011 12:51:22 +0000
Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:
> 
> [...]
> 
> > Although I get perfect results using the Fedora 13 provided texlive
> > (2007), I noticed I get that old error again (quoted below) when I
> > use the texlive 2010 install from CTAN. Maybe some problem in my
> > setup. I will use my distribution provided texlive for now.
> >
> > Thanks again for being so patient and helping with my issues. :)
> >
> >> bibtex: Not writing
> >> to /home/jallad/org/masters-thesis/msthesis.blg (openout_any = p).
> >> I couldn't open file name
> >> `/home/jallad/org/masters-thesis/msthesis.blg'
> 
> Sorry; this I cannot help with much as I'm not sure what is happening
> here and I've never run into this before.
> 
> Are there any problems with that file (e.g. read only mode)?  Is the
> file there?  If so, what happens if you remove it?  It should be
> created automatically by bibtex.
> 

This happens with a clean working directory.

> Have you tried searching the web with that error message (e.g. google
> bibtex openout_any)?
> 

I found a recent (Jan 2010) discussion about this. There was a change in
behaviour for bibtex in the latest texlive build which leads to this
behaviour. You can follow the discussion in this thread[1]. The TeX
developers expect external tools like org and other editor plugins to
adapt to this change. I think this is why I was having problems in the
first place, not sure how this can be resolved though. If we find a
solution it would be worth a mention on Worg.

[1] http://web.archiveorange.com/archive/v/VBuN9l7WNXs4SXOn6Kxh

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:

[...]

>> Have you tried searching the web with that error message (e.g. google
>> bibtex openout_any)?
>> 
>
> I found a recent (Jan 2010) discussion about this. There was a change in
> behaviour for bibtex in the latest texlive build which leads to this
> behaviour. You can follow the discussion in this thread[1]. The TeX
> developers expect external tools like org and other editor plugins to
> adapt to this change. I think this is why I was having problems in the
> first place, not sure how this can be resolved though. If we find a
> solution it would be worth a mention on Worg.
>
> [1] http://web.archiveorange.com/archive/v/VBuN9l7WNXs4SXOn6Kxh

Ah, very interesting.  What I don't understand is why this is affecting
you.  I can see it affecting you if the aux file cannot be found but not
if the first pdflatex step worked okay.  Do you still have the problem
if the first step worked?

If so, and if you still have the sh file I sent to the list yesterday,
can you add the following line to the top:

echo 'Invoked in dir ' $PWD

and post the output (the first few lines only) of the export to PDF when
you get the error with bibtex?

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.576.g99675.dirty)

Re: customising org-latex-to-pdf-process for bibtex

[Suvayu Ali]

Hi Eric,

On Tue, 01 Mar 2011 20:41:20 +0000
Eric S Fraga <e.fraga@ucl.ac.uk> wrote:

> Ah, very interesting.  What I don't understand is why this is
> affecting you.  I can see it affecting you if the aux file cannot be
> found but not if the first pdflatex step worked okay.  Do you still
> have the problem if the first step worked?
> 

Before the first pdflatex run the working directory seems correct:

> Invoked in dir  /home/jallad/org/masters-thesis

In the output for this run I see some lines like these:

> [6]
> No file msthesis.bbl.
> [7] (./msthesis.aux)

I guess that means the .aux files are created?

> If so, and if you still have the sh file I sent to the list yesterday,
> can you add the following line to the top:
> 
> echo 'Invoked in dir ' $PWD
> 
> and post the output (the first few lines only) of the export to PDF
> when you get the error with bibtex?

Despite the above, for bibtex I get the following:

> --------------------------------- running bibtex next
> 
> Invoked in dir  /home/jallad/org/masters-thesis
> 
> bibtex: Not writing to /home/jallad/org/masters-thesis/msthesis.blg
> (openout_any = p). I couldn't open file name
> `/home/jallad/org/masters-thesis/msthesis.blg'


Explicitly calling the texlive 2007 bibtex resolves the problem.

As per one of Tom's suggestions earlier in the thread, if I set

(setq org-export-pdf-remove-logfiles nil)

I can see the .aux files present after the final pdflatex run. Not
sure why bibtex overlooks that since the working directory seems
correct.

-- 
Suvayu

Open source is the future. It sets us free.

Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

Suvayu Ali <fatkasuvayu+linux@gmail.com> writes:

> Hi Eric,
>
> On Tue, 01 Mar 2011 20:41:20 +0000
> Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>
>> Ah, very interesting.  What I don't understand is why this is
>> affecting you.  I can see it affecting you if the aux file cannot be
>> found but not if the first pdflatex step worked okay.  Do you still
>> have the problem if the first step worked?
>> 
>
> Before the first pdflatex run the working directory seems correct:
>
>> Invoked in dir  /home/jallad/org/masters-thesis
>
> In the output for this run I see some lines like these:
>
>> [6]
>> No file msthesis.bbl.
>> [7] (./msthesis.aux)
>
> I guess that means the .aux files are created?

Well, actually, this indicates that the aux file is being read by
pdflatex.  But obviously it must exist therefore...

>> If so, and if you still have the sh file I sent to the list yesterday,
>> can you add the following line to the top:
>> 
>> echo 'Invoked in dir ' $PWD
>> 
>> and post the output (the first few lines only) of the export to PDF
>> when you get the error with bibtex?
>
> Despite the above, for bibtex I get the following:
>
>> --------------------------------- running bibtex next
>> 
>> Invoked in dir  /home/jallad/org/masters-thesis
>> 
>> bibtex: Not writing to /home/jallad/org/masters-thesis/msthesis.blg
>> (openout_any = p). I couldn't open file name
>> `/home/jallad/org/masters-thesis/msthesis.blg'

Oh well, there goes that theory.  The web link you gave yesterday would
seem to indicate that the problem is present if you invoke the bibtex
command from another directory and this does not appear to be the case
here.  Very strange.

> Explicitly calling the texlive 2007 bibtex resolves the problem.

Well, at least you can get this working for now but obviously there is a
problem we are going to have to sort out as more users move to 2010.  I
am using texlive 2009 on Debian and that version doesn't have this
problem.  Texlive 2010 isn't available (yet) for Debian even in unstable
so I cannot easily test this out unfortunately.  I'll have a look to see
if it's in Debian's experimental distribution when I get a chance.

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.576.g99675)

Re: Re: customising org-latex-to-pdf-process for bibtex

[Carsten Dominik]

Hi Eric,  Thomas,

is there a problem in the default setup of LaTeX export that needs to be addressed?

- Carsten

On Mar 1, 2011, at 9:52 AM, Eric S Fraga wrote:

> "Thomas S. Dye" <tsd@tsdye.com> writes:
> 
>> Aloha Suvayu,
>> 
>> I haven't looked into this in depth, but I think your problem might
>> come from loading amssymb and amsmath.  LaTeX is complaining that
>> something is already defined; the AMS packages are a prime suspect
>> here.  Perhaps you could inhibit amssymb?
>> 
>> All the best,
>> Tom
> 
> Suvayu,
> 
> I think this is indeed the problem.  I had this problem a month or so
> ago (search the mailing list!).  My solution is to add this to my
> .emacs:
> 
> --8<---------------cut here---------------start------------->8---
> ;; to fix problems with amsmath conflicting with wasysym:
> ;;
> ;; From: Lawrence Mitchell <wence@gmx.li>
> ;; Subject: [Orgmode] Re: [bug] latex export ignores org-export-latex-default-packages-alist?
> ;; To: emacs-orgmode@gnu.org
> ;; Date: Wed, 26 Jan 2011 16:01:52 +0000
> (add-to-list 'org-export-latex-packages-alist '("" "amsmath" t))
> (setcar (rassoc '("wasysym" t) org-export-latex-default-packages-alist)	"integrals")
> --8<---------------cut here---------------end--------------->8---
> 
> -- 
> : Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
> : using Org-mode version 7.4 (release_7.4.555.gfcf66)
> 
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode

- Carsten

Re: Re: customising org-latex-to-pdf-process for bibtex

[Eric S Fraga]

Carsten Dominik <carsten.dominik@gmail.com> writes:

> Hi Eric,  Thomas,
>
> is there a problem in the default setup of LaTeX export that needs to be addressed?
>
> - Carsten

Not as such in the default.  

The issue arises when one wants to extend the defaults to include the
amsmath package.  This conflicts with the wasysym package included by
default by org.  Both packages define the =\iint= symbol and latex
doesn't allow for such clashes nicely.

The suggested fix is to use this magic (to me) code suggested by
Lawrence Mitchell earlier this year:

--8<---------------cut here---------------start------------->8---
;; to fix problems with amsmath conflicting with wasysym:
;;
;; From: Lawrence Mitchell <wence@gmx.li>
;; Subject: [Orgmode] Re: [bug] latex export ignores org-export-latex-default-packages-alist?
;; To: emacs-orgmode@gnu.org
;; Date: Wed, 26 Jan 2011 16:01:52 +0000
(add-to-list 'org-export-latex-packages-alist '("" "amsmath" t))
(setcar (rassoc '("wasysym" t) org-export-latex-default-packages-alist)	"integrals")
--8<---------------cut here---------------end--------------->8---

modifying, I guess, what is actually loaded from wasysym.  I've not
delved more into this but Lawrence may be able to help here?

Thanks,
eric
-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.50.1
: using Org-mode version 7.4 (release_7.4.562.gc895)