Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 13:26:44 -0400, u...@debian.org (Aaron M. Ucko) wrote: I haven't tried either myself, but you may have better luck with nbibtex or pybtex (as found in the eponymous packages); I'd be particularly surprised if the latter had any such limit. There may also be some configuration parameter you can tune. Hey, Aaron. Thanks for the suggestions. I had noticed those, but packages but hadn't realized that they were actually (supposedly) drop in replacements for bibtex. Unfortunately they're not really, and both of them fail to compile bibliographies that compile fine with bibtex (see pastes below). Time to file some bugs! Anyone able to get either of these to work? Or have any other suggestions? jamie. 0 $ bibtex thesis This is BibTeX, Version 0.99c (TeX Live 2009/Debian) The top-level auxiliary file: thesis.aux A level-1 auxiliary file: chapters/intro.aux A level-1 auxiliary file: chapters/gr.aux A level-1 auxiliary file: chapters/mm.aux A level-1 auxiliary file: chapters/llts.aux A level-1 auxiliary file: chapters/results.aux A level-1 auxiliary file: chapters/conclusion.aux A level-1 auxiliary file: appendices/infrastructure.aux A level-1 auxiliary file: bibliography/aas_macros.aux The style file: plain.bst Database file #1: /home/jrollins/documents/ads/thesis.bib Database file #2: bibliography/books.bib Database file #3: bibliography/theses.bib Warning--I didn't find a database entry for ? Warning--I didn't find a database entry for 2008PhRvL.101u1102A Warning--I didn't find a database entry for 2009PhRvD..80j2001A Warning--I didn't find a database entry for 2010PhRvD..81j2001A (There were 4 warnings) 0 $ pybtex thesis Traceback (most recent call last): File /usr/bin/pybtex, line 21, in module main() File /usr/lib/pymodules/python2.6/pybtex/cmdline.py, line 42, in __call__ self.main() File /usr/lib/pymodules/python2.6/pybtex/cmdline.py, line 84, in main self.run(options, args) File /usr/lib/pymodules/python2.6/pybtex/__main__.py, line 145, in run engine.make_bibliography(filename, **kwargs) File /usr/lib/pymodules/python2.6/pybtex/bibtex/__init__.py, line 47, in make_bibliography interpreter.run(bst_script, aux_data.citations, bib_filenames, bbl_file, min_crossrefs=min_crossrefs) File /usr/lib/pymodules/python2.6/pybtex/bibtex/interpreter.py, line 226, in run getattr(self, commandname)() File /usr/lib/pymodules/python2.6/pybtex/bibtex/interpreter.py, line 290, in command_read self.bib_data = p.parse_files(self.bib_files) File /usr/lib/pymodules/python2.6/pybtex/database/input/__init__.py, line 40, in parse_files self.parse_file(filename, fileext) File /usr/lib/pymodules/python2.6/pybtex/database/input/__init__.py, line 35, in parse_file self.parse_stream(f) File /usr/lib/pymodules/python2.6/pybtex/database/input/bibtex.py, line 135, in parse_stream s = pybtex.io.reader(stream, self.encoding).read() File /usr/lib/python2.6/codecs.py, line 477, in read newchars, decodedbytes = self.decode(data, self.errors) UnicodeDecodeError: 'utf8' codec can't decode byte 0xd7 in position 118533: invalid continuation byte 1 $ nbibtex thesis Call failed: /usr/share/nbibtex/bibtex.lua:1460: module 'nbib-plain' not found: no field package.preload['nbib-plain'] no file './nbib-plain.lua' no file '/usr/local/share/lua/5.1/nbib-plain.lua' no file '/usr/local/share/lua/5.1/nbib-plain/init.lua' no file '/usr/local/lib/lua/5.1/nbib-plain.lua' no file '/usr/local/lib/lua/5.1/nbib-plain/init.lua' no file '/usr/share/lua/5.1/nbib-plain.lua' no file '/usr/share/lua/5.1/nbib-plain/init.lua' no file './nbib-plain.so' no file '/usr/local/lib/lua/5.1/nbib-plain.so' no file '/usr/lib/lua/5.1/nbib-plain.so' no file '/usr/local/lib/lua/5.1/loadall.so' 2 $ pgpyJ8NILIc84.pgp Description: PGP signature
Re: how to deal with bibtex with long fields
Jameson Rollins jroll...@finestructure.net writes: Hey, Aaron. Thanks for the suggestions. No problem. UnicodeDecodeError: 'utf8' codec can't decode byte 0xd7 in position 118533: invalid continuation byte That looks like an encoding issue; I would suggest either converting your .bib file to UTF-8 or running pybtex -e ISO-8859-1. 1 $ nbibtex thesis Call failed: /usr/share/nbibtex/bibtex.lua:1460: module 'nbib-plain' not found: no field package.preload['nbib-plain'] That looks more like a packaging bug. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?...@monk.mit.edu -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/udl7hj660dc@dr-wily.mit.edu
Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 15:35:59 -0400, u...@debian.org (Aaron M. Ucko) wrote: UnicodeDecodeError: 'utf8' codec can't decode byte 0xd7 in position 118533: invalid continuation byte That looks like an encoding issue; I would suggest either converting your .bib file to UTF-8 or running pybtex -e ISO-8859-1. Thanks again, Aaron. I could tell encoding was the issue there, but I wasn't sure what the solution was. Still certainly not a drop in replacement. In any event, using ISO-8859-1 didn't work either: 0 $ pybtex -e ISO-8859-1 thesis Traceback (most recent call last): File /usr/bin/pybtex, line 21, in module main() File /usr/lib/pymodules/python2.6/pybtex/cmdline.py, line 42, in __call__ self.main() File /usr/lib/pymodules/python2.6/pybtex/cmdline.py, line 84, in main self.run(options, args) File /usr/lib/pymodules/python2.6/pybtex/__main__.py, line 145, in run engine.make_bibliography(filename, **kwargs) File /usr/lib/pymodules/python2.6/pybtex/bibtex/__init__.py, line 47, in make_bibliography interpreter.run(bst_script, aux_data.citations, bib_filenames, bbl_file, min_crossrefs=min_crossrefs) File /usr/lib/pymodules/python2.6/pybtex/bibtex/interpreter.py, line 226, in run getattr(self, commandname)() File /usr/lib/pymodules/python2.6/pybtex/bibtex/interpreter.py, line 259, in command_iterate self._iterate(self.citations) File /usr/lib/pymodules/python2.6/pybtex/bibtex/interpreter.py, line 265, in _iterate self.current_entry = self.bib_data.entries[key] KeyError: u'?' 1 $ Nor did just plane 'ASCII'. Not sure what else to try. Suggestions? It would be nice if it could figure out the file encoding for itself. Maybe after I defend... 1 $ nbibtex thesis Call failed: /usr/share/nbibtex/bibtex.lua:1460: module 'nbib-plain' not found: no field package.preload['nbib-plain'] That looks more like a packaging bug. Yeah, I filed a bug (595069). jamie. pgp3uxzj0URm8.pgp Description: PGP signature
Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 15:08:53 -0500 (CDT), Jim Crumley crum...@fields.space.umn.edu wrote: Have you seen the BibTex FAQ? See question 37 in the FAQ http://www.google.com/url?sa=tsource=webcd=4ved=0CCUQFjADurl=ftp%3A%2F%2Fftp.tex.ac.uk%2Ftex-archive%2Fbiblio%2Fbibtex%2Fcontrib%2Fdoc%2FbtxFAQ.pdfrct=jq=bibtex%20field%20too%20longei=AFp9TPrDF8mmnAel4N2dCwusg=AFQjCNEKPH3GMSeHXI5ewvX-SqbT6S1MMQcad=rja It sounds like you might be able to solve the problem by changing a parameter or two in the source and recompiling BibTeX. Hey, Jim. Yeah, I did see that but yikes! I should have put that on my list of unacceptable solutions! Someone else suggested this might be the only solution, but they thought it might also require rebuilding all of tex as well. Not something I have any intention of doing. Hopefully a better solution will present itself. Still holding out hope for pybtex at the moment... jamie. pgpqGu44ar6HB.pgp Description: PGP signature
Re: how to deal with bibtex with long fields
Jameson Rollins jroll...@finestructure.net writes: Hey, Jim. Yeah, I did see that but yikes! I should have put that on my list of unacceptable solutions! Someone else suggested this might be the only solution, but they thought it might also require rebuilding all of tex as well. Not something I have any intention of doing. Take a closer look; the the FAQ also mentions the possibility of running bibtex8, which Debian ships (right in texlive-binaries). It appears to be only optionally encoding-aware, so you may be able to dodge that issue while still requesting capacity increases with -B, -H, -W, or individual --m* flags. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?...@monk.mit.edu -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/udlpqwy4iug@dr-wily.mit.edu
Re: how to deal with bibtex with long fields
Jameson Rollins jroll...@finestructure.net writes: replacement. In any event, using ISO-8859-1 didn't work either: Bleh; so much for that idea. Maybe after I defend... Priorities, priorities. ;-) -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?...@monk.mit.edu -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/udlzkw24j0u@dr-wily.mit.edu
Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 16:39:51 -0400, u...@debian.org (Aaron M. Ucko) wrote: Jameson Rollins jroll...@finestructure.net writes: Hey, Jim. Yeah, I did see that but yikes! I should have put that on my list of unacceptable solutions! Someone else suggested this might be the only solution, but they thought it might also require rebuilding all of tex as well. Not something I have any intention of doing. Take a closer look; the the FAQ also mentions the possibility of running bibtex8, which Debian ships (right in texlive-binaries). It appears to be only optionally encoding-aware, so you may be able to dodge that issue while still requesting capacity increases with -B, -H, -W, or individual --m* flags. I tried bibtex8, with all the various HUGE settings and -m* ## lengths maxed out but with no luck. I did manage to figure out why pybtex was failing, though. It turns out that it fails if it can't find a citation in the bibtex. This is another failure that breaks drop in compatibility. However, after fixing all my citations pybtex *still* fails to compile. This time it just gets stuck and never returns, while consuming most of my cpu. sigh. Why are these bibtex tools so flaky? Am I really the only one that's had to deal with long author lists? That's really hard for me to believe in this day and age. jamie. pgp4yQM3s37o1.pgp Description: PGP signature
Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 17:16:47 -0400, Denis Laxalde dlaxa...@gmail.com wrote:
Jameson Rollins a écrit :
Any suggestions? There must be some next-gen version of bibtex out
there that doesn't have limits from the 80's, right?
Have you tried bibtex8 (in texlive-extra-utils Debian package)? It has
some options (--big, --huge, ...) which are supposed to overcome
limitations from the original bibtex.
Hi, Denis. I just sent replied to another note about this saying yes, I
have. As far as I can tell those overcome limitations of the bibtex
file size, but not the field size. At least none of them fix the
problem. I still get a field size error:
2 $ bibtex8 --8bit --wolfgang thesis
The top-level auxiliary file: thesis.aux
A level-1 auxilliary file: chapters/intro.aux
A level-1 auxilliary file: chapters/gr.aux
A level-1 auxilliary file: chapters/mm.aux
A level-1 auxilliary file: chapters/llts.aux
A level-1 auxilliary file: chapters/results.aux
A level-1 auxilliary file: chapters/conclusion.aux
A level-1 auxilliary file: appendices/infrastructure.aux
A level-1 auxilliary file: bibliography/aas_macros.aux
The style file: plain.bst
Database file #1: /home/jrollins/documents/ads/thesis.bib
Database file #2: /home/jrollins/documents/ads/LIGO.bib
Your field is more than 1 characters---line 144 of file
/home/jrollins/documents/ads/LIGO.bib
: {Scott}, J. and {S
:cott}, S.~M. and {Searle}, A.~C. and {Seifert}, F. and
I'm skipping whatever remains of this entry
Database file #3: bibliography/books.bib
Database file #4: bibliography/theses.bib
Warning--to sort, need author or key in 2010PhRvD..81j2001A
Warning--empty author in 2010PhRvD..81j2001A
Warning--empty title in 2010PhRvD..81j2001A
Warning--empty journal in 2010PhRvD..81j2001A
Warning--empty year in 2010PhRvD..81j2001A
Warning--you've exceeded 1000%ld, the global-string-size, for entry
2008PhRvL.101u1102A
while executing--line 1090 of file plain.bst
*Please notify the bibstyle designer*
Warning--you've exceeded 1000%ld, the global-string-size, for entry
2009PhRvD..80j2001A
while executing--line 1090 of file plain.bst
*Please notify the bibstyle designer*
(There was 1 error message)
2 $
jamie.
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Re: how to deal with bibtex with long fields
Jameson Rollins a écrit : I did manage to figure out why pybtex was failing, though. It turns out that it fails if it can't find a citation in the bibtex. This is another failure that breaks drop in compatibility. Indeed, see: http://sourceforge.net/tracker/?func=detailaid=3039667group_id=151578atid=781406 Cheers, Denis. -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100831214522.gb13...@schloss.campus.mcgill.ca
Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 17:45:23 -0400, Denis Laxalde dlaxa...@gmail.com wrote: Jameson Rollins a écrit : I did manage to figure out why pybtex was failing, though. It turns out that it fails if it can't find a citation in the bibtex. This is another failure that breaks drop in compatibility. Indeed, see: http://sourceforge.net/tracker/?func=detailaid=3039667group_id=151578atid=781406 http://bugs.debian.org/595079 jamie. pgpbHuFy9s3n4.pgp Description: PGP signature
Re: how to deal with bibtex with long fields
On Tue, 31 Aug 2010 17:26:44 -0400, Jameson Rollins jroll...@finestructure.net wrote: However, after fixing all my citations pybtex *still* fails to compile. This time it just gets stuck and never returns, while consuming most of my cpu. http://bugs.debian.org/595082 talk about frustrating! jamie. pgpMCTOUjHADL.pgp Description: PGP signature
