Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Holger Mayer

Hi there,

I'm having the same bug as described in
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html
with my LyX 1.4.3 (21/09/2006).

Is there any workaround to this annoying bug?
Can't I tell LyX manually somehow to call pdflatex again after calling
bibtex? Isn't there a python-file where I can just add a line and
things work? After all, there are so many different export types, each
of which must be told what to do somehow.

I haven't found the bug in bugzilla, so is it already fixed?

Thanks for your help,
Holger


Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Paul A. Rubin

Holger Mayer wrote:

Hi there,

I'm having the same bug as described in
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html


That link seems to be broken, so I'm not entirely sure what the problem is.



with my LyX 1.4.3 (21/09/2006).

Is there any workaround to this annoying bug?
Can't I tell LyX manually somehow to call pdflatex again after calling
bibtex? Isn't there a python-file where I can just add a line and
things work? After all, there are so many different export types, each
of which must be told what to do somehow.

I haven't found the bug in bugzilla, so is it already fixed?

Thanks for your help,
Holger




Is this definitely a LyX problem?  Have you exported the document to a 
LaTeX file and successfully compiled it manually?  The reason I ask is 
that sometimes an incorrect entry in a BibTeX file causes missing 
references without giving any fatal compile errors.


/Paul



Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Georg Baum
Am Mittwoch, 24. Januar 2007 19:09 schrieb Paul A. Rubin:
 Holger Mayer wrote:
  Hi there,
  
  I'm having the same bug as described in
  http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html
 
 That link seems to be broken, so I'm not entirely sure what the problem 
is.

Try this one:

http://www.mail-archive.com/lyx-users%40lists.lyx.org/msg44439.html

The previous one does not work if you read this post via gmane, because 
gmane mangles the @. This link is identical, but the @ is replaced by %40 
(which is the @ encoded for urls).


Georg



Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Paul A. Rubin

Georg Baum wrote:


Try this one:

http://www.mail-archive.com/lyx-users%40lists.lyx.org/msg44439.html

The previous one does not work if you read this post via gmane, because 
gmane mangles the @. This link is identical, but the @ is replaced by %40 
(which is the @ encoded for urls).





Vielen Danke.  Turns out it's probably not the problem I thought it was 
(and it's not one I've ever encountered).  Maybe running LyX in debug 
mode would help identify whether the correct number of runs are being 
done and, if not, why not.


Does LyX skip the bibtex run if a .bbl file already exists and there 
have been no changes to the bibliography in the LyX doc?


/Paul



Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Holger Mayer

Hi there,

I'm having the same bug as described in
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html
with my LyX 1.4.3 (21/09/2006).

Is there any workaround to this annoying bug?
Can't I tell LyX manually somehow to call pdflatex again after calling
bibtex? Isn't there a python-file where I can just add a line and
things work? After all, there are so many different export types, each
of which must be told what to do somehow.

I haven't found the bug in bugzilla, so is it already fixed?

Thanks for your help,
Holger


Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Paul A. Rubin

Holger Mayer wrote:

Hi there,

I'm having the same bug as described in
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html


That link seems to be broken, so I'm not entirely sure what the problem is.



with my LyX 1.4.3 (21/09/2006).

Is there any workaround to this annoying bug?
Can't I tell LyX manually somehow to call pdflatex again after calling
bibtex? Isn't there a python-file where I can just add a line and
things work? After all, there are so many different export types, each
of which must be told what to do somehow.

I haven't found the bug in bugzilla, so is it already fixed?

Thanks for your help,
Holger




Is this definitely a LyX problem?  Have you exported the document to a 
LaTeX file and successfully compiled it manually?  The reason I ask is 
that sometimes an incorrect entry in a BibTeX file causes missing 
references without giving any fatal compile errors.


/Paul



Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Georg Baum
Am Mittwoch, 24. Januar 2007 19:09 schrieb Paul A. Rubin:
 Holger Mayer wrote:
  Hi there,
  
  I'm having the same bug as described in
  http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html
 
 That link seems to be broken, so I'm not entirely sure what the problem 
is.

Try this one:

http://www.mail-archive.com/lyx-users%40lists.lyx.org/msg44439.html

The previous one does not work if you read this post via gmane, because 
gmane mangles the @. This link is identical, but the @ is replaced by %40 
(which is the @ encoded for urls).


Georg



Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Paul A. Rubin

Georg Baum wrote:


Try this one:

http://www.mail-archive.com/lyx-users%40lists.lyx.org/msg44439.html

The previous one does not work if you read this post via gmane, because 
gmane mangles the @. This link is identical, but the @ is replaced by %40 
(which is the @ encoded for urls).





Vielen Danke.  Turns out it's probably not the problem I thought it was 
(and it's not one I've ever encountered).  Maybe running LyX in debug 
mode would help identify whether the correct number of runs are being 
done and, if not, why not.


Does LyX skip the bibtex run if a .bbl file already exists and there 
have been no changes to the bibliography in the LyX doc?


/Paul



Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Holger Mayer

Hi there,

I'm having the same bug as described in
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html
with my LyX 1.4.3 (21/09/2006).

Is there any workaround to this annoying bug?
Can't I tell LyX manually somehow to call pdflatex again after calling
bibtex? Isn't there a python-file where I can just add a line and
things work? After all, there are so many different export types, each
of which must be told what to do somehow.

I haven't found the bug in bugzilla, so is it already fixed?

Thanks for your help,
Holger


Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Paul A. Rubin

Holger Mayer wrote:

Hi there,

I'm having the same bug as described in
http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html


That link seems to be broken, so I'm not entirely sure what the problem is.



with my LyX 1.4.3 (21/09/2006).

Is there any workaround to this annoying bug?
Can't I tell LyX manually somehow to call pdflatex again after calling
bibtex? Isn't there a python-file where I can just add a line and
things work? After all, there are so many different export types, each
of which must be told what to do somehow.

I haven't found the bug in bugzilla, so is it already fixed?

Thanks for your help,
Holger




Is this definitely a LyX problem?  Have you exported the document to a 
LaTeX file and successfully compiled it manually?  The reason I ask is 
that sometimes an incorrect entry in a BibTeX file causes missing 
references without giving any fatal compile errors.


/Paul



Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Georg Baum
Am Mittwoch, 24. Januar 2007 19:09 schrieb Paul A. Rubin:
> Holger Mayer wrote:
> > Hi there,
> > 
> > I'm having the same bug as described in
> > http://www.mail-archive.com/lyx-users@lists.lyx.org/msg44439.html
> 
> That link seems to be broken, so I'm not entirely sure what the problem 
is.

Try this one:

http://www.mail-archive.com/lyx-users%40lists.lyx.org/msg44439.html

The previous one does not work if you read this post via gmane, because 
gmane mangles the @. This link is identical, but the @ is replaced by %40 
(which is the @ encoded for urls).


Georg



Re: Once more: Missing references bug: lyx not calling pdflatex again?

2007-01-24 Thread Paul A. Rubin

Georg Baum wrote:


Try this one:

http://www.mail-archive.com/lyx-users%40lists.lyx.org/msg44439.html

The previous one does not work if you read this post via gmane, because 
gmane mangles the @. This link is identical, but the @ is replaced by %40 
(which is the @ encoded for urls).





Vielen Danke.  Turns out it's probably not the problem I thought it was 
(and it's not one I've ever encountered).  Maybe running LyX in debug 
mode would help identify whether the correct number of runs are being 
done and, if not, why not.


Does LyX skip the bibtex run if a .bbl file already exists and there 
have been no changes to the bibliography in the LyX doc?


/Paul



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-08 Thread Georg Baum
Am Sonntag, 8. Januar 2006 03:22 schrieb Fernando Perez:
 This is a lyx bug, I'm pretty convinced.

I think so, too.

 I guess I should just take it up 
 on lyx-dev...

Please do, and enter it at http://bugzilla.lyx.org. It would be great if 
you could also attach an example document and create step-by-step 
instructions to reproduce the bug.


Georg



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-08 Thread Fernando Perez
Georg Baum wrote:

 Am Sonntag, 8. Januar 2006 03:22 schrieb Fernando Perez:
 This is a lyx bug, I'm pretty convinced.
 
 I think so, too.
 
 I guess I should just take it up
 on lyx-dev...
 
 Please do, and enter it at http://bugzilla.lyx.org. It would be great if
 you could also attach an example document and create step-by-step
 instructions to reproduce the bug.

OK, I will.  I'm not sure I'll be able to post a document, as it's very on
and off (the current one where I see it is too big and I can't make it
public).  I'll try though, and at least I'll explain it well.
 
Thanks.

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-08 Thread Georg Baum
Am Sonntag, 8. Januar 2006 03:22 schrieb Fernando Perez:
 This is a lyx bug, I'm pretty convinced.

I think so, too.

 I guess I should just take it up 
 on lyx-dev...

Please do, and enter it at http://bugzilla.lyx.org. It would be great if 
you could also attach an example document and create step-by-step 
instructions to reproduce the bug.


Georg



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-08 Thread Fernando Perez
Georg Baum wrote:

 Am Sonntag, 8. Januar 2006 03:22 schrieb Fernando Perez:
 This is a lyx bug, I'm pretty convinced.
 
 I think so, too.
 
 I guess I should just take it up
 on lyx-dev...
 
 Please do, and enter it at http://bugzilla.lyx.org. It would be great if
 you could also attach an example document and create step-by-step
 instructions to reproduce the bug.

OK, I will.  I'm not sure I'll be able to post a document, as it's very on
and off (the current one where I see it is too big and I can't make it
public).  I'll try though, and at least I'll explain it well.
 
Thanks.

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-08 Thread Georg Baum
Am Sonntag, 8. Januar 2006 03:22 schrieb Fernando Perez:
> This is a lyx bug, I'm pretty convinced.

I think so, too.

> I guess I should just take it up 
> on lyx-dev...

Please do, and enter it at http://bugzilla.lyx.org. It would be great if 
you could also attach an example document and create step-by-step 
instructions to reproduce the bug.


Georg



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-08 Thread Fernando Perez
Georg Baum wrote:

> Am Sonntag, 8. Januar 2006 03:22 schrieb Fernando Perez:
>> This is a lyx bug, I'm pretty convinced.
> 
> I think so, too.
> 
>> I guess I should just take it up
>> on lyx-dev...
> 
> Please do, and enter it at http://bugzilla.lyx.org. It would be great if
> you could also attach an example document and create step-by-step
> instructions to reproduce the bug.

OK, I will.  I'm not sure I'll be able to post a document, as it's very on
and off (the current one where I see it is too big and I can't make it
public).  I'll try though, and at least I'll explain it well.
 
Thanks.

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-07 Thread Fernando Perez
David L. Johnson wrote:

 On Fri, 06 Jan 2006 16:19:03 -0700
 Fernando Perez [EMAIL PROTECTED] wrote:
 
 I have a document with a bibtex-generated list of references, and when I
 try to export it to PDF or postscript (via the GUI or with 'lyx -e pdf2',
 for example), all the citations appear as [??] marks, though the
 references section is correctly generated.
 
 Typically with Latex the first run would generate missing references such
 as
 this.  If I am running Latex manually, I simply run it twice.  That way
 the appropriate temporary files are generated so that the second run can
 read them.
 
 I thought LyX would do the same thing.

It should, and sometimes it does, as I mention below.  But the problem is
that it misses many times, and requires a no-op fiddle with the bibtex box
to realize that it has to make an extra pass.

 The only workaround I've been able to find is to click on the 'bibtex
 references' box at the end, make some trivial change (choose a different
 style, or check the 'add to TOC' box), and rerun the PDF/PS generation. 
 THEN, the numbers appear, and I can revert my trivial change and
 continue.
 
 Needless to say, it is incredibly annoying to have to do this every time,
 and it breaks my makefile-based workflow (this is a document being
 developed in collaboration from many places, so I wrote a makefile to
 generate all the required PDFs without human intervention).
 
 Try adding a second Latex run into that makefile.

Well, it's not that simple: the makefile calls

lyx -e pdf2 master.lyx

to make 'master.pdf'.  This master file has many subdocuments, EPS figures,
and more.  To generate the final one manually, I'd have to write out the
raw latex, convert all figures from .eps format to .pdf (pdflatex doesn't
understand eps figures), etc.  That's _precisely_ all the magic and
convenience that lyx does for you when you say 'export PDF', but it's
borking out on bibtex management.

This is a lyx bug, I'm pretty convinced.  I guess I should just take it up
on lyx-dev...

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-07 Thread Fernando Perez
David L. Johnson wrote:

 On Fri, 06 Jan 2006 16:19:03 -0700
 Fernando Perez [EMAIL PROTECTED] wrote:
 
 I have a document with a bibtex-generated list of references, and when I
 try to export it to PDF or postscript (via the GUI or with 'lyx -e pdf2',
 for example), all the citations appear as [??] marks, though the
 references section is correctly generated.
 
 Typically with Latex the first run would generate missing references such
 as
 this.  If I am running Latex manually, I simply run it twice.  That way
 the appropriate temporary files are generated so that the second run can
 read them.
 
 I thought LyX would do the same thing.

It should, and sometimes it does, as I mention below.  But the problem is
that it misses many times, and requires a no-op fiddle with the bibtex box
to realize that it has to make an extra pass.

 The only workaround I've been able to find is to click on the 'bibtex
 references' box at the end, make some trivial change (choose a different
 style, or check the 'add to TOC' box), and rerun the PDF/PS generation. 
 THEN, the numbers appear, and I can revert my trivial change and
 continue.
 
 Needless to say, it is incredibly annoying to have to do this every time,
 and it breaks my makefile-based workflow (this is a document being
 developed in collaboration from many places, so I wrote a makefile to
 generate all the required PDFs without human intervention).
 
 Try adding a second Latex run into that makefile.

Well, it's not that simple: the makefile calls

lyx -e pdf2 master.lyx

to make 'master.pdf'.  This master file has many subdocuments, EPS figures,
and more.  To generate the final one manually, I'd have to write out the
raw latex, convert all figures from .eps format to .pdf (pdflatex doesn't
understand eps figures), etc.  That's _precisely_ all the magic and
convenience that lyx does for you when you say 'export PDF', but it's
borking out on bibtex management.

This is a lyx bug, I'm pretty convinced.  I guess I should just take it up
on lyx-dev...

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-07 Thread Fernando Perez
David L. Johnson wrote:

> On Fri, 06 Jan 2006 16:19:03 -0700
> Fernando Perez <[EMAIL PROTECTED]> wrote:
> 
>> I have a document with a bibtex-generated list of references, and when I
>> try to export it to PDF or postscript (via the GUI or with 'lyx -e pdf2',
>> for example), all the citations appear as [??] marks, though the
>> references section is correctly generated.
> 
> Typically with Latex the first run would generate missing references such
> as
> this.  If I am running Latex manually, I simply run it twice.  That way
> the appropriate temporary files are generated so that the second run can
> read them.
> 
> I thought LyX would do the same thing.

It should, and sometimes it does, as I mention below.  But the problem is
that it misses many times, and requires a no-op fiddle with the bibtex box
to realize that it has to make an extra pass.

>> The only workaround I've been able to find is to click on the 'bibtex
>> references' box at the end, make some trivial change (choose a different
>> style, or check the 'add to TOC' box), and rerun the PDF/PS generation. 
>> THEN, the numbers appear, and I can revert my trivial change and
>> continue.
>> 
>> Needless to say, it is incredibly annoying to have to do this every time,
>> and it breaks my makefile-based workflow (this is a document being
>> developed in collaboration from many places, so I wrote a makefile to
>> generate all the required PDFs without human intervention).
> 
> Try adding a second Latex run into that makefile.

Well, it's not that simple: the makefile calls

lyx -e pdf2 master.lyx

to make 'master.pdf'.  This master file has many subdocuments, EPS figures,
and more.  To generate the final one manually, I'd have to write out the
raw latex, convert all figures from .eps format to .pdf (pdflatex doesn't
understand eps figures), etc.  That's _precisely_ all the magic and
convenience that lyx does for you when you say 'export PDF', but it's
borking out on bibtex management.

This is a lyx bug, I'm pretty convinced.  I guess I should just take it up
on lyx-dev...

Cheers,

f



Missing references bug: lyx not calling pdflatex again?

2006-01-06 Thread Fernando Perez
Hi all,

I've searched both bugzilla and the lists for help on this problem, so far
without luck.  Any hints would be most welcome.

I have a document with a bibtex-generated list of references, and when I try to
export it to PDF or postscript (via the GUI or with 'lyx -e pdf2', for
example), all the citations appear as [??] marks, though the references
section is correctly generated.

The only workaround I've been able to find is to click on the 'bibtex
references' box at the end, make some trivial change (choose a different
style, or check the 'add to TOC' box), and rerun the PDF/PS generation.  THEN,
the numbers appear, and I can revert my trivial change and continue.

Needless to say, it is incredibly annoying to have to do this every time, and
it breaks my makefile-based workflow (this is a document being developed in
collaboration from many places, so I wrote a makefile to generate all the
required PDFs without human intervention).

I'd be very appreciative of any help or hints.

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-06 Thread David L. Johnson
On Fri, 06 Jan 2006 16:19:03 -0700
Fernando Perez [EMAIL PROTECTED] wrote:

 I have a document with a bibtex-generated list of references, and when I try 
 to
 export it to PDF or postscript (via the GUI or with 'lyx -e pdf2', for
 example), all the citations appear as [??] marks, though the references
 section is correctly generated.

Typically with Latex the first run would generate missing references such as
this.  If I am running Latex manually, I simply run it twice.  That way the
appropriate temporary files are generated so that the second run can read
them.  

I thought LyX would do the same thing.
 
 The only workaround I've been able to find is to click on the 'bibtex
 references' box at the end, make some trivial change (choose a different
 style, or check the 'add to TOC' box), and rerun the PDF/PS generation.  THEN,
 the numbers appear, and I can revert my trivial change and continue.
 
 Needless to say, it is incredibly annoying to have to do this every time, and
 it breaks my makefile-based workflow (this is a document being developed in
 collaboration from many places, so I wrote a makefile to generate all the
 required PDFs without human intervention).

Try adding a second Latex run into that makefile. 

-- 

David L. Johnson

   __o   | Business! cried the Ghost. Mankind was my business. The
 _`\(,_  | common welfare  was my business; charity, mercy, forbearance, 
(_)/ (_) | and benevolence, were, all,  my business. The dealings of my
   trade were but a drop of water in the comprehensive ocean of my 
business! --Dickens, A Christmas Carol  


Missing references bug: lyx not calling pdflatex again?

2006-01-06 Thread Fernando Perez
Hi all,

I've searched both bugzilla and the lists for help on this problem, so far
without luck.  Any hints would be most welcome.

I have a document with a bibtex-generated list of references, and when I try to
export it to PDF or postscript (via the GUI or with 'lyx -e pdf2', for
example), all the citations appear as [??] marks, though the references
section is correctly generated.

The only workaround I've been able to find is to click on the 'bibtex
references' box at the end, make some trivial change (choose a different
style, or check the 'add to TOC' box), and rerun the PDF/PS generation.  THEN,
the numbers appear, and I can revert my trivial change and continue.

Needless to say, it is incredibly annoying to have to do this every time, and
it breaks my makefile-based workflow (this is a document being developed in
collaboration from many places, so I wrote a makefile to generate all the
required PDFs without human intervention).

I'd be very appreciative of any help or hints.

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-06 Thread David L. Johnson
On Fri, 06 Jan 2006 16:19:03 -0700
Fernando Perez [EMAIL PROTECTED] wrote:

 I have a document with a bibtex-generated list of references, and when I try 
 to
 export it to PDF or postscript (via the GUI or with 'lyx -e pdf2', for
 example), all the citations appear as [??] marks, though the references
 section is correctly generated.

Typically with Latex the first run would generate missing references such as
this.  If I am running Latex manually, I simply run it twice.  That way the
appropriate temporary files are generated so that the second run can read
them.  

I thought LyX would do the same thing.
 
 The only workaround I've been able to find is to click on the 'bibtex
 references' box at the end, make some trivial change (choose a different
 style, or check the 'add to TOC' box), and rerun the PDF/PS generation.  THEN,
 the numbers appear, and I can revert my trivial change and continue.
 
 Needless to say, it is incredibly annoying to have to do this every time, and
 it breaks my makefile-based workflow (this is a document being developed in
 collaboration from many places, so I wrote a makefile to generate all the
 required PDFs without human intervention).

Try adding a second Latex run into that makefile. 

-- 

David L. Johnson

   __o   | Business! cried the Ghost. Mankind was my business. The
 _`\(,_  | common welfare  was my business; charity, mercy, forbearance, 
(_)/ (_) | and benevolence, were, all,  my business. The dealings of my
   trade were but a drop of water in the comprehensive ocean of my 
business! --Dickens, A Christmas Carol  


Missing references bug: lyx not calling pdflatex again?

2006-01-06 Thread Fernando Perez
Hi all,

I've searched both bugzilla and the lists for help on this problem, so far
without luck.  Any hints would be most welcome.

I have a document with a bibtex-generated list of references, and when I try to
export it to PDF or postscript (via the GUI or with 'lyx -e pdf2', for
example), all the citations appear as [??] marks, though the references
section is correctly generated.

The only workaround I've been able to find is to click on the 'bibtex
references' box at the end, make some trivial change (choose a different
style, or check the 'add to TOC' box), and rerun the PDF/PS generation.  THEN,
the numbers appear, and I can revert my trivial change and continue.

Needless to say, it is incredibly annoying to have to do this every time, and
it breaks my makefile-based workflow (this is a document being developed in
collaboration from many places, so I wrote a makefile to generate all the
required PDFs without human intervention).

I'd be very appreciative of any help or hints.

Cheers,

f



Re: Missing references bug: lyx not calling pdflatex again?

2006-01-06 Thread David L. Johnson
On Fri, 06 Jan 2006 16:19:03 -0700
Fernando Perez <[EMAIL PROTECTED]> wrote:

> I have a document with a bibtex-generated list of references, and when I try 
> to
> export it to PDF or postscript (via the GUI or with 'lyx -e pdf2', for
> example), all the citations appear as [??] marks, though the references
> section is correctly generated.

Typically with Latex the first run would generate missing references such as
this.  If I am running Latex manually, I simply run it twice.  That way the
appropriate temporary files are generated so that the second run can read
them.  

I thought LyX would do the same thing.
> 
> The only workaround I've been able to find is to click on the 'bibtex
> references' box at the end, make some trivial change (choose a different
> style, or check the 'add to TOC' box), and rerun the PDF/PS generation.  THEN,
> the numbers appear, and I can revert my trivial change and continue.
> 
> Needless to say, it is incredibly annoying to have to do this every time, and
> it breaks my makefile-based workflow (this is a document being developed in
> collaboration from many places, so I wrote a makefile to generate all the
> required PDFs without human intervention).

Try adding a second Latex run into that makefile. 

-- 

David L. Johnson

   __o   | "Business!" cried the Ghost. "Mankind was my business. The
 _`\(,_  | common welfare  was my business; charity, mercy, forbearance, 
(_)/ (_) | and benevolence, were, all,  my business. The dealings of my
   trade were but a drop of water in the comprehensive ocean of my 
business!" --Dickens, "A Christmas Carol"