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Markus Hoenicka | 5 Aug 2007 16:55
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Re: make problem on Darwin

Hi Chris,

besides the fact that I don't know of another bibliographic software
that specifically targets markup languages, I don't intend to let go
so easily :-)

Would you care to send me your config.log file? I'd like to check that
file for obvious problems. Could you please also include the output of
the commands

find / -name "libreadline*"
find / -name "readline*"

As mentioned previously on the refdb-users list, RefDB basically works
on OS X. If it doesn't work on your box, there may be minor
configuration problems that RefDB doesn't take into account yet. I
understand that you'd prefer to just go ahead with something that
works out of the box. But if we manage to get RefDB going on your box,
we can probably fix a problem that also affects others.

regards,
Markus

Chris Ferrall writes:
 > 
 > Thanks for your reply from a couple weeks ago.  Following up on another 
 > suggestion I installed Fink and did as suggested in the RefDB 
 > instructions.  
 > 
 > But I still get the exact same error.  The readline library files and
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Markus Hoenicka | 5 Aug 2007 17:18
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ANN: refdb-0.9.9-pre3 available for testing

Hi all,

I've uploaded another prerelease for the upcoming version 0.9.9 of
RefDB. As always, the tarball is available here:

http://refdb.sourceforge.net/pre/refdb-latest.tar.gz

The focus of this prerelease is a cleanup of the internal data
representation which was moved away from the RIS mess towards a more
sane part/publication/series approach. While at it, I've also improved
the handling of the M1-M3 fields which contain a lot of reference
type-specific information like conference location, sender and
recipient of an email message, running time of movies and so on. These
fields are internally represented according to what they stand
for. This both simplifies the data export to non-RIS/risx formats, and
it also makes the contents of these fields available for the citation
styles. The citestylex.dtd was changed accordingly. Due to the changes
in the internal representation of authors and titles, you may have to
apply some minor fixes to any styles that you have written yourself.
The details are described in the file UPGRADING. A full list of the
changes is appended below.

As both the main database schema and the reference database schema
were changed, it is recommended to re-create both from scratch instead
of trying to upgrade them. Export your reference data and citation
styles with your existing RefDB setup, then upgrade, and add your
data again.

There's only a few more things on my todo list, so this prerelease
contains most functionality of what you can expect in 0.9.9. I'd
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Markus Hoenicka | 5 Aug 2007 17:21
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Re: Producing modified bibtex output.

Picking up an old thread...

The new prerelease (0.9.9-pre3, see the separate announcement on this
list) now supports the export of the contents of the U1-U5 and M1-M3
fields into aptly named bibtex fields.

regards,
Markus

Markus Hoenicka writes:
 > Markus Hoenicka writes:
 >  > The mapping of RIS fields to bibtex fields during data export is  
 >  > currently hard-wired. UR and L1-L4 are being exported as "URL = {}"  
 >  > entries. Some fields, most notably M1-M3 and U1-U5 are currently  
 >  > ignored (which is not a good thing).
 >  > 
 > 

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

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Jeremy Malcolm | 6 Aug 2007 07:46
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Re: ANN: refdb-0.9.9-pre3 available for testing

Markus Hoenicka wrote:
> There's only a few more things on my todo list, so this prerelease
> contains most functionality of what you can expect in 0.9.9. I'd
> appreciate if you could spend some time testing this prerelease.

Something is askew again on Mac OS X.  Like with 0.9.8,[0] I just get 
"error" from runbib after a long pause. Previously with this problem, I 
would at least get a log from the back end to trawl through.  But now I 
don't even get that.  "refdbd -s -e 0 -l 7" produces no output after 
"server waiting n_max_fd=5".  So I guess the lack of debugging is the 
biggest problem here.  The underlying problem may be more simple.

Also, I have a feature request: although the includearg variable can be 
set in the runbib script, it would be better if it could be set in a 
configuration file.  That way, it doesn't get lost whenever the user 
upgrades refdb.  (I need it set in order to raise jade's maximum error 
count since I have many references and the normal "reference to 
non-existent ID" bootstrapping errors come up for each of them.)

Thanks.

[0] See http://sourceforge.net/mailarchive/forum.php? \
     thread_name=452E036A.7020000%40Malcolm.id.au&forum_name=refdb-users

--

-- 
Jeremy Malcolm LLB (Hons) B Com
Internet and Open Source lawyer, IT consultant, actor
host -t NAPTR 1.0.8.0.3.1.2.9.8.1.6.e164.org|awk -F! '{print $3}'

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Markus Hoenicka | 6 Aug 2007 09:53
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Re: ANN: refdb-0.9.9-pre3 available for testing

Quoting Jeremy Malcolm <Jeremy <at> Malcolm.id.au>:

> Something is askew again on Mac OS X.  Like with 0.9.8,[0] I just get
> "error" from runbib after a long pause. Previously with this problem, I
> would at least get a log from the back end to trawl through.  But now I
> don't even get that.  "refdbd -s -e 0 -l 7" produces no output after
> "server waiting n_max_fd=5".  So I guess the lack of debugging is the
> biggest problem here.  The underlying problem may be more simple.
>

If you don't mind, I'll follow up on this off-list and try to collect  
some debug information from your box.

> Also, I have a feature request: although the includearg variable can be
> set in the runbib script, it would be better if it could be set in a
> configuration file.  That way, it doesn't get lost whenever the user
> upgrades refdb.  (I need it set in order to raise jade's maximum error
> count since I have many references and the normal "reference to
> non-existent ID" bootstrapping errors come up for each of them.)
>

I've added a feature request to the SF tracker.

regards,
Markus

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
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Markus Hoenicka | 14 Aug 2007 21:48
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Re: ANN: refdb-0.9.9-pre3 available for testing

Hi all,

this is to summarize the OS X related problems that I've been working
on lately with the kind help of Jeremy.

Jeremy Malcolm writes:
 > Something is askew again on Mac OS X.  Like with 0.9.8,[0] I just get 
 > "error" from runbib after a long pause. Previously with this problem, I 
 > would at least get a log from the back end to trawl through.  But now I 
 > don't even get that.  "refdbd -s -e 0 -l 7" produces no output after 
 > "server waiting n_max_fd=5".  So I guess the lack of debugging is the 
 > biggest problem here.  The underlying problem may be more simple.
 > 

While I wasn't able to reproduce the lack of a log file, it was pretty
apparent that the bibliography processing time exceeded the
client-side timeout (default: 600s) by a couple of minutes, resulting
in the "error" message. I have to add to my defense that these OS X
tests ran on fairly old hardware. A similar setup on my FreeBSD box
created the same 800+ reference bibliography in less than three
minutes, not anywhere close to a timeout.

Anyway, there were two reasons why the processing time increased
substantially from 0.9.9-pre2 to pre3. First, the database schemas of
both refdb and the reference database now have a bunch of new columns
to retrieve, which slows down the operation a bit. Second, the
bibliography style migration instructions were incomplete and, in
part, just plain wrong. Jeremy's attempt to migrate his custom style
caused most in-text citations to use the author "Anonymous", which in
turn led to the problem that all these references had to be
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Markus Hoenicka | 15 Aug 2007 04:17
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ANN: refdb-0.9.9-pre4 available for testing

Hi again,

this is to announce another prerelease which is available right here:

http://refdb.sourceforge.net/pre/refdb-latest.tar.gz

This prerelease cleans up a couple of problems in pre3 and adds some
new features. See below for a full list of changes. In order to
test-drive the new standalone SRU server, you also need an updated
Perl RefDB-SRU package:

http://refdb.sourceforge.net/pre/RefDB-SRU-0.7.tar.gz

As usual, please send any comments, suggestions, and bug reports to
this list.

regards,
Markus

Bugfixes:

- fixed the style export on OS X (PPC)

- fixed the publication year output in RIS export if the otherinfo
  field is empty

Improvements:

- added config files for runbib and refdbjade to pass additional
  options to (open)jade, especially to increase or disable the error
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Markus Hoenicka | 15 Aug 2007 12:47
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Re: ANN: refdb-0.9.9-pre4 available for testing

Quoting Markus Hoenicka <markus.hoenicka <at> mhoenicka.de>:

> Hi again,
>
> this is to announce another prerelease which is available right here:
>

Well, 'twas 4am, so I forgot to mention the upgrading information. Here goes.

If you run 0.9.8, refdbd -a should be able to upgrade the main  
database for you. See the manual or the man page for further details.  
If you run one of the 0.9.9 prereleases, please drop the existing main  
database (refdb) and have refdbd -a create a new one (or create it  
manually as per the manual). Make sure to export any custom styles  
before upgrading, unless you have the XML sources handy anyway.

If you run 0.9.8, 0.9.9-pre1, or 0.9.9-pre2, you need to export your  
reference data, drop the reference database, upgrade, create a new  
reference database, and add your data again. If you already had  
0.9.9-pre3 running, existing reference databases are supposed to be ok.

regards,
Markus

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de
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