refdb-users — List for RefDB users

[Refdb-users] ANN: refdb-0.9.9-pre4 available for testing

[Markus H. <mar...@mh...>]

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
  limit

- added a standalone SRU server for personal use or for testing purposes

- bibliography styles now have elements to record the style author, a
  description, and an URL that points to the source of the
  bibliographic rules.

- added a new legal bibliography style contributed by Jeremy Malcolm

- DocBook and TEI XML output is now indented and can optionally be namespaced

- DocBook XML V5.0 support


Backwards-incompatible changes:

- the -i option of refdbjade was changed to I (capital i) to make it
  the same as in runbib (which uses -i for a different
  purpose). runbib in turn now uses -s instead of -I to skip the ID
  extraction step, and -I instead of -m to set include options

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] ANN: refdb-0.9.9-pre3 available for testing

[Markus H. <mar...@mh...>]

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
distinguished by a year suffix as in (Anonymous, 2002ah). The unique
suffix is selected by a recursive function which uses one SQL query
per iteration. As you may guess, having 50-odd references by
"Anonymous" in the same year increases processing times quite a bit.

As a consequence, the style migration instructions in the file
"UPGRADING" were corrected and enhanced, and there is also some more
information in the documentation which ships with each source
tarball. If you use custom styles, please do read these instructions
to avoid major hassles.

While working on an OS X box I came across another PPC specific
bug. The style export was entirely broken. This has also been fixed in
the subversion sources.

 > 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 addressed this problem by adding configuration files for runbib
and for refdbjade. Among other tweaks you can now increase or disable
jade's maximum error limit.

All these changes will be available in the upcoming 0.9.9-pre4 which I
hope to announce shortly.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] ANN: refdb-0.9.9-pre3 available for testing

[Markus H. <mar...@mh...>]

Quoting Jeremy Malcolm <Je...@Ma...>:

> 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=3D5".  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 =20
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

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] ANN: refdb-0.9.9-pre3 available for testing

[Jeremy M. <Je...@Ma...>]

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}'

[Refdb-users] ANN: refdb-0.9.9-pre3 available for testing

[Markus H. <mar...@mh...>]

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
appreciate if you could spend some time testing this prerelease.

regards,
Markus

Bugfixes:

- crash during bibliography creation on OS X was fixed

- unknown reference data types are now changed to "GEN" when importing
  risx data as well

- abbreviated journal names which use periods without spaces are now
  imported properly

- config.rpath was added to the tarball to avoid configure errors on
  particular OSes

- upgrading the main database no longer creates duplicate entries in
  t_meta when using PostgreSQL as the database engine

- fixed missing permissions after upgrading the main PostgreSQL database

- the preconfigured locations of log and pid files now honor the
  prefix (usually /usr or /usr/local)


Improvements:

- the internal representation of authors and titles is now based on
  the three-level library system (part, publication, series) instead of
  on the once-and-for-all-screwed RIS definition. This makes both the
  programmer's life and the style author's life quite a bit easier

- the internal representation of the M1-M3 fields was improved to
  simplify data access. The contents of these RIS fields is now stored
  in separate fields which reflect the purpose in context of the
  respective reference type

- citation styles now support both authors and editors in monographic data

- citation styles now support the replacements of the M1-M3 fields,
  i.e. stuff like conference location, sender and recipient email
  addresses, class codes, running time and so on

- the output of adduser/deleteuser was cleaned up if no hostname is
  available

- the format specifier NX of the getref command no longer retrieves
  all extended notes associated with a particular reference, as these
  would always include the users reference lists. If you positively want
  those lists, use ALL or NXNL instead.

- the citestylex.dtd now supports different formatting options for
  authors (TEXT) and editors (TEXTED). The styles shipped with RefDB
  were updated accordingly.

- all backends were updated and now export the contents of the RIS
  fields M1-M3 as far as possible

- two new citation styles were added (Tissue_Eng. and Biomaterials)

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Producing modified bibtex output.

[Markus H. <mar...@mh...>]

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
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] make problem on Darwin

[Markus H. <mar...@mh...>]

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 
 > header files exist and ./configure for RefDB passes the readline tests. 
 > 
 > I've tried about 10 different ways to resolve this and now I'm stumped.  
 > It appears I have to give up on RefDB and try something else because 
 > this project has to go forward.  Do you have suggestions for other packages?
 > 

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] make problem on Darwin

[Jeremy M. <Je...@Ma...>]

On Thu, Jul 19, 2007 at 11:47:45PM +0200, Markus Hoenicka wrote:
> BTW I've cc'ed the RefDB mailing list as other OS X user might be able
> to help you better than me.

I use Fink (http://fink.sourceforge.net/), so I can't comment on whether
RefDB compiles on OS X without Fink.  With Fink, as the RefDB
documentation says, you need to:

export CFLAGS="-I/sw/include"
export LDFLAGS="-L/sw/lib" 

It then compiles fine for me...  Note you also need libdbi installed and
the version in Fink is too low, so you need to compile your own (or I
can probably find you a backported Fink package that I made).

--
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}'

[Refdb-users] make problem on Darwin

[Markus H. <mar...@mh...>]

Hi Chris,

I don't think that using gmake would solve this problem. If your
regular make can't handle the autotools-created Makefiles, you'd get
error messages about the Makefile syntax, not linker errors like the
one you saw.

As far as I can tell the linker error tries to tell you that a
readline function is not available. However, in this case ./configure
should have exited with an error. Did that work ok for you? If not,
you might have to install the readline library (including the
development files, that is the .a libraries and the headers). Also,
make check is not implemented in RefDB, and the results of running it
nevertheless are unpredictable. It is probably best to first check
whether make generates any errors and then run make install. If you
see errors here, please post the output so we can work it out.

BTW I've cc'ed the RefDB mailing list as other OS X user might be able
to help you better than me.

regards,
Markus

Chris Ferrall writes:
 > 
 > Hello,
 > 
 > I've run into the error below when installing RefDB on Darwin (this 
 > occurs at make check).  I went ahead and did "make install" and the 
 > refdb binary failed to be created. Your documentation suggests using 
 > gmake, which I haven't installed.  If you think this will solve the 
 > problem or have other suggestions please let me know.
 > 
 > Thank you
 > --Chris Ferrall
 > 
 > /usr/bin/ld: Undefined symbols:
 > _rl_completion_matches
 > collect2: ld returned 1 exit status
 > make[2]: *** [refdbc] Error 1
 > make[1]: *** [check] Error 2
 > make: *** [check-recursive] Error 1
 > 
 > 
 > 

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Producing modified bibtex output.

[Markus H. <mar...@mh...>]

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).
 > 

The bibtex backend now exports the U1-U5 fields as USER1 = {} and so
on entries. This is available as of revision 417.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Producing modified bibtex output.

[Markus H. <mar...@mh...>]

Quoting Markus Hoenicka <mar...@mh...>:
> Would you mind to reinstall 0.9.8 and send in
> the refdbd log with the log level set to 7?

Just to make sure: use 0.9.8-1 instead of 0.9.8 as the latter  
contained a few bugs.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Producing modified bibtex output.

[Markus H. <mar...@mh...>]

Quoting Josef Karthauser <jo...@ta...>:

>
> What's the first version which exports the URL tags?  I'm using 0.9.6
> currently, as when I upgraded to 0.9.8 I couldn't get the refdbc to work
> - it complained about not being able to connect to the database, despite
> the refdbd running without startup errors.
>

I believe 0.9.7 did export the URL tags. I can see the code in the =20
first subversion revision after we migrated from CVS to subversion. =20
This was a month or two before 0.9.7.

However, instead of looking for older versions I'd recommend to fix =20
the 0.9.8 installation problems. I'm pretty sure this is a setup =20
problem caused by the migration of 0.9.6 to 0.9.8, and you might bump =20
into the very same problem when attempting to upgrade to 0.9.7. =20
Usually these problems can be fixed as long as the debug logs of =20
refdbd are available. Would you mind to reinstall 0.9.8 and send in =20
the refdbd log with the log level set to 7?

regards,
Markus



--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Producing modified bibtex output.

[Josef K. <jo...@ta...>]

On Fri, Jul 13, 2007 at 09:08:36AM +0200, Markus Hoenicka wrote:
> Hi Joe,
>=20
> Quoting Josef Karthauser <jo...@ta...>:
>=20
> > I want to add an extra field to each bibtex record, called 'EPRINT'
> > which would carry the value of one of the refdb tags (although I'm not
> > sure which one yet), perhap the UR.
> >
> > How do I go about doing this?  Is it a modification to the style xml
> > file, or do I need to hack code?
> >
>=20
> The mapping of RIS fields to bibtex fields during data export is =20
> currently hard-wired. UR and L1-L4 are being exported as "URL =3D {}" =20
> entries. Some fields, most notably M1-M3 and U1-U5 are currently =20
> ignored (which is not a good thing).
>=20

What's the first version which exports the URL tags?  I'm using 0.9.6
currently, as when I upgraded to 0.9.8 I couldn't get the refdbc to work
- it complained about not being able to connect to the database, despite
the refdbd running without startup errors.

Joe

Re: [Refdb-users] Producing modified bibtex output.

[Markus H. <mar...@mh...>]

Hi Joe,

Quoting Josef Karthauser <jo...@ta...>:

> I want to add an extra field to each bibtex record, called 'EPRINT'
> which would carry the value of one of the refdb tags (although I'm not
> sure which one yet), perhap the UR.
>
> How do I go about doing this?  Is it a modification to the style xml
> file, or do I need to hack code?
>

The mapping of RIS fields to bibtex fields during data export is =20
currently hard-wired. UR and L1-L4 are being exported as "URL =3D {}" =20
entries. Some fields, most notably M1-M3 and U1-U5 are currently =20
ignored (which is not a good thing).

I believe the mapping of RIS fields to bibtex tags should remain =20
hard-wired on the server side, as RefDB is designed as a multi-user =20
system. The tag names could then be fixed on the client side using sed =20
as every user sees fit.

Support for U1-U5 could be added in no time if it is ok to export them =20
to the pseudo-bibtex fields U1-U5 (which you could then change on the =20
client side to something meaningful). I've been reluctant to export =20
M1-M3 because their contents depend on the reference type. I'm =20
currently in the process of disentangling these along the lines of the =20
proposed rbib data format (see =20
http://refdb.sourceforge.net/rbib.html). I'm not going to switch to an =20
internal rbib representation in 0.9.9 yet, but some features are =20
likely to get implemented anyway. This holds true for the M1-M3 fields =20
which will be split into several fields according to their true =20
meaning. Once that is implemented, it will be a snap to export them =20
properly to bibtex.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] Producing modified bibtex output.

[Josef K. <jo...@ta...>]

Having trouble understanding how to create a custom bibtex file using
refdb.

At the moment I'm running:

    runbib -d joe -S bibtex-abbrev -t bibtex out

which creates out.bib:

    @ARTICLE{ Burd1988,
      YEAR = {1988},
      AUTHOR = {Burd, A. B. and Barrow, J. D.},
      TITLE = {Inflationary Models with Exponential Potentials},
      JOURNAL = {Nucl.Phys.B.},
      VOLUME = {308},
      NUMBER = {4},
      PAGES = {929-945}
    }

and so on.

I want to add an extra field to each bibtex record, called 'EPRINT'
which would carry the value of one of the refdb tags (although I'm not
sure which one yet), perhap the UR.

How do I go about doing this?  Is it a modification to the style xml
file, or do I need to hack code?

Joe

[Refdb-users] ANN: refdb-elisp-1.4 available

[Markus H. <mar...@mh...>]

Hi all,

I've just uploaded a new version of refdb-mode, the Emacs frontend for
RefDB. Version 1.4 adds support for Muse documents. You can now insert
citations and look up references from citations in Muse documents just
as you can in DocBook, TEI, and LaTeX documents.

The latest release is available here:

http://sourceforge.net/project/showfiles.php?group_id=26091

Muse (http://mwolson.org/projects/EmacsMuse.html) is an authoring
system for Emacs which uses a simple, Wiki-like syntax to author all
sorts of documents. It can optionally use CamelCase support to create
Wikis (this is used e.g. in Planner). You can transform Muse documents
to all sorts of output formats, including DocBook XML. Citation
support is not available in the latest official release, but it is
part of the shared arch repository.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] autoconf and install issues with 0.9.9-pre4

[Markus H. <mar...@mh...>]

Vincent Carey 525-2265 writes:
 > %vjc> ls scripts
 > Makefile.am             migrate_mysql_0.9.5     refdb.in
 > bib2ris-utf8.in         refdb-backup            refdb_dos2unix.in
 > db2ris.in               refdb-bug.in            refdb_latex2utf8txt
 > dtdparseweave           refdb-init.in           refdbctl.in
 > empty.2.dump.mysql41.in refdb-ms                refdbjade.in
 > empty.2.dump.pgsql.in   refdb-restore           refdbnd.in
 > empty.2.dump.sqlite3.in refdb-upgrade.sql       refdbsru.in
 > en2ris.in               refdb.2.dump.mysql.in   refdbxml.in
 > libgen.pl               refdb.2.dump.mysql41.in runbib.in
 > marc2ris.in             refdb.2.dump.pgsql.in   statgen.pl
 > med2ris.in              refdb.2.dump.sqlite.in  vargen.pl

Weird. After running make I see the files empty.2.dump.mysql41,
empty.2.dump.pgsql, and empty.2.dump.sqlite3 in addition to those
listed above. Is your error a consequence of the other missing files,
by any chance? I've added those to the svn repository so you can try
again after updating your sources.

regards
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] autoconf and install issues with 0.9.9-pre4

[Markus H. <mar...@mh...>]

Markus Hoenicka writes:
 > > /usr/bin/install: cannot stat `refdb.3.dump.mysql': No such file or directory
 > > /usr/bin/install: cannot stat `refdb.3.dump.mysql41': No such file   
 > > or directory
 > > /usr/bin/install: cannot stat `refdb.3.dump.pgsql': No such file or directory
 > > /usr/bin/install: cannot stat `refdb.3.dump.sqlite': No such file or  
 > >  directory
 > 
 > These failures are my fault. I've forgotten to add the refdb.3.dump.xx  
 > files to the repository. I'll do so asap.
 > 

Done in revision 395.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] autoconf and install issues with 0.9.9-pre4

[Vincent C. 525-2. <st...@ch...>]

>
> > /usr/bin/install: cannot stat `refdb.3.dump.mysql': No such file or directory
> > /usr/bin/install: cannot stat `refdb.3.dump.mysql41': No such file
> > or directory
> > /usr/bin/install: cannot stat `refdb.3.dump.pgsql': No such file or directory
> > /usr/bin/install: cannot stat `refdb.3.dump.sqlite': No such file or
> >  directory
>
> These failures are my fault. I've forgotten to add the refdb.3.dump.xx
> files to the repository. I'll do so asap.

OK

>
> > /usr/bin/install: cannot stat `empty.2.dump.mysql41': No such file
> > or directory
> > /usr/bin/install: cannot stat `empty.2.dump.pgsql': No such file or directory
> > /usr/bin/install: cannot stat `empty.2.dump.sqlite3': No such file
> > or directory
>
> I cannot explain these failures though. I've just checked out the svn
> version on my Windoze/Cygwin box at work. I cannot reproduce this
> problem here. What does "ls scripts/" say?

%vjc> ls scripts
Makefile.am             migrate_mysql_0.9.5     refdb.in
bib2ris-utf8.in         refdb-backup            refdb_dos2unix.in
db2ris.in               refdb-bug.in            refdb_latex2utf8txt
dtdparseweave           refdb-init.in           refdbctl.in
empty.2.dump.mysql41.in refdb-ms                refdbjade.in
empty.2.dump.pgsql.in   refdb-restore           refdbnd.in
empty.2.dump.sqlite3.in refdb-upgrade.sql       refdbsru.in
en2ris.in               refdb.2.dump.mysql.in   refdbxml.in
libgen.pl               refdb.2.dump.mysql41.in runbib.in
marc2ris.in             refdb.2.dump.pgsql.in   statgen.pl
med2ris.in              refdb.2.dump.sqlite.in  vargen.pl
%vjc> head scripts/.svn/entries
<?xml version="1.0" encoding="utf-8"?>
<wc-entries
   xmlns="svn:">
<entry
   committed-rev="391"
   name=""
   committed-date="2007-06-21T23:10:21.628367Z"
   url="https://svn.sourceforge.net/svnroot/refdb/refdb/trunk/scripts"
   last-author="mhoenicka"
   kind="dir"


I will look into the iconv issues.

Re: [Refdb-users] autoconf and install issues with 0.9.9-pre4

[Markus H. <mar...@mh...>]

Quoting Jeremy Malcolm <Je...@Ma...>:

> Did I miss something?  There is no 0.9.9-pre4, or for that matter
> 0.9.9-pre3, on the FTP site...?
>
> --

I don't think so. The test build that I just pulled from svn reports as

refdbd 0.9.9-pre3 built from svn revision 394

pre3 has not been released yet, but I've bumped up the version tag  
with a recent change in configure.in. I've planned to run some  
thorough tests on the current revision and release pre3 as soon as the  
problems are fixed.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] autoconf and install issues with 0.9.9-pre4

[Jeremy M. <Je...@Ma...>]

Did I miss something?  There is no 0.9.9-pre4, or for that matter 
0.9.9-pre3, on the FTP site...?

-- 
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}'

Re: [Refdb-users] autoconf and install issues with 0.9.9-pre4

[Markus H. <mar...@mh...>]

Hi Vince,

Quoting Vincent Carey 525-2265 <st...@ch...>:

> %stvjc2> sh autogen.sh
> aclocal:configure.in:270: warning: macro `AM_ICONV_LINK' not found in libr=
ary
>

Could you please check your iconv installation? If iconv is installed, =20
could it be there are separate packages like iconv and iconv-dev? The =20
message says the support macros provided by iconv are not installed, =20
or in the wrong place.

> a configure script is built none the less and runs
>

Could you please check the configure output for the results of the =20
iconv tests? There should be two tests like:

checking for iconv
checking how to link with libiconv

If these lines are missing, or if they give weird results, I'd reckon =20
refdbd won't work properly.

> /usr/bin/install: cannot stat `refdb.3.dump.mysql': No such file or direct=
ory
> /usr/bin/install: cannot stat `refdb.3.dump.mysql41': No such file  =20
> or directory
> /usr/bin/install: cannot stat `refdb.3.dump.pgsql': No such file or direct=
ory
> /usr/bin/install: cannot stat `refdb.3.dump.sqlite': No such file or =20
>  directory

These failures are my fault. I've forgotten to add the refdb.3.dump.xx =20
files to the repository. I'll do so asap.

> /usr/bin/install: cannot stat `empty.2.dump.mysql41': No such file  =20
> or directory
> /usr/bin/install: cannot stat `empty.2.dump.pgsql': No such file or direct=
ory
> /usr/bin/install: cannot stat `empty.2.dump.sqlite3': No such file  =20
> or directory

I cannot explain these failures though. I've just checked out the svn =20
version on my Windoze/Cygwin box at work. I cannot reproduce this =20
problem here. What does "ls scripts/" say?

regards,
Markus


--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] autoconf and install issues with 0.9.9-pre4

[Vincent C. 525-2. <st...@ch...>]

Thanks for prompt confrontation of issues I mentioned previously.

I have begun to experiment with the 0.9.9-pre4 release available
through svn.   my OS is

Linux stvjc2.bwh.harvard.edu 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux

and i build from source because i need to port to mac and elsewhere; no
interest in RPMs.  i have a package that builds each of

btparse-0.34    libdbi-0.8.2
sqlite-3.4.0 	expat-2.0.1          libdbi-drivers-0.8.2-1
refdb-0.9.9-pre4

in one place to ensure compatible infrastructure

first issue:
%stvjc2> autoconf -V
autoconf (GNU Autoconf) 2.59
Written by David J. MacKenzie and Akim Demaille.

%stvjc2> sh autogen.sh
aclocal:configure.in:270: warning: macro `AM_ICONV_LINK' not found in library

a configure script is built none the less and runs

cd refdb-0.9.9-pre4; CFLAGS=-I/home/stvjc/Work/ExternalSoft/REFDB-BUILD/include ./configure --prefix=/home/stvjc/Work/ExternalSoft/REFDB-BUILD --with-libdbi-inc=/home/stvjc/Work/ExternalSoft/REFDB-BUILD/include --with-libdbi-lib=/home/stvjc/Work/ExternalSoft/REFDB-BUILD/lib --with-expat-lib=/home/stvjc/Work/ExternalSoft/REFDB-BUILD/lib --with-btparse-lib=/home/stvjc/Work/ExternalSoft/REFDB-BUILD/lib; \

make seems to do OK; in the install phase

 /usr/bin/install -c 'refdb_latex2utf8txt' '/home/stvjc/Work/ExternalSoft/REFDB-BUILD/bin/refdb_latex2utf8txt'
 /usr/bin/install -c 'bib2ris-utf8' '/home/stvjc/Work/ExternalSoft/REFDB-BUILD/bin/bib2ris-utf8'
/bin/sh .././conf/mkinstalldirs /home/stvjc/Work/ExternalSoft/REFDB-BUILD/share/refdb/sql
/usr/bin/install: cannot stat `refdb.3.dump.mysql': No such file or directory
/usr/bin/install: cannot stat `refdb.3.dump.mysql41': No such file or directory
/usr/bin/install: cannot stat `refdb.3.dump.pgsql': No such file or directory
/usr/bin/install: cannot stat `refdb.3.dump.sqlite': No such file or directory
/usr/bin/install: cannot stat `empty.2.dump.mysql41': No such file or directory
/usr/bin/install: cannot stat `empty.2.dump.pgsql': No such file or directory
/usr/bin/install: cannot stat `empty.2.dump.sqlite3': No such file or directory
make[3]: *** [install-data-local] Error 1
make[3]: Leaving directory `/home/stvjc/stvjc/ExternalSoft/REFDB-SRC/refdb-0.9.9-pre4/scripts'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/stvjc/stvjc/ExternalSoft/REFDB-SRC/refdb-0.9.9-pre4/scripts'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/home/stvjc/stvjc/ExternalSoft/REFDB-SRC/refdb-0.9.9-pre4'
make: *** [/home/stvjc/Work/ExternalSoft/REFDB-BUILD/bin/refdbd] Error 2




---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
st...@ch...

On Wed, 4 Jul 2007, Markus Hoenicka wrote:

> Markus Hoenicka writes:
>  > > note the *dump.sqlite* has a .2.
>  > >
>  > > in line 190  of refdb-init.in in the same folder we have
>  > >     checkFile "<pkgdatadir>/sql/refdb.dump.sqlite" "read" \
>  > >
>  > > and the lack of the .2. is a problem for refdb-init
>  > >
>  >
>  > That's me being careless... however, the 0.9.9 prereleases use a
>  > different mechanism to create or update the main database. refdbd now
>  > has a maintenance mode that takes care of this stuff. Therefore the
>  > line above no longer exists in refdb-init. To the best of my knowledge
>  > the new mechanism does not show this problem, but I'll check again to
>  > make sure. I'll probably make a fixed version of the old refdb-init
>  > available on the web page for those who still use 0.9.8-1.
>  >
>
> I should have checked the facts before drawing my
> conclusions. Actually, the maintenance mode of refdbd was already
> implemented in 0.9.8, and the lines that cause the problem in
> refdb-init (only if you use sqlite3 btw) are simply leftovers from
> previous versions. The proper fix is to delete lines 190 through 193
> and re-run make in the scripts subdirectory. The bug had been fixed
> with other changes in refdb-init.in about three months ago, so the
> 0.9.9 prereleases are not affected by this problem. I'll also add a
> news item to the RefDB homepage that mentions this problem.
>
> regards,
> Markus
>
> --
> Markus Hoenicka
> mar...@ca...
> (Spam-protected email: replace the quadrupeds with "mhoenicka")
> http://www.mhoenicka.de
>
>

Re: [Refdb-users] slight problem with refdb 0.9.8-1 distribution

[Markus H. <mar...@mh...>]

Markus Hoenicka writes:
 > > note the *dump.sqlite* has a .2.
 > >
 > > in line 190  of refdb-init.in in the same folder we have
 > >     checkFile "<pkgdatadir>/sql/refdb.dump.sqlite" "read" \
 > >
 > > and the lack of the .2. is a problem for refdb-init
 > >
 > 
 > That's me being careless... however, the 0.9.9 prereleases use a  
 > different mechanism to create or update the main database. refdbd now  
 > has a maintenance mode that takes care of this stuff. Therefore the  
 > line above no longer exists in refdb-init. To the best of my knowledge  
 > the new mechanism does not show this problem, but I'll check again to  
 > make sure. I'll probably make a fixed version of the old refdb-init  
 > available on the web page for those who still use 0.9.8-1.
 > 

I should have checked the facts before drawing my
conclusions. Actually, the maintenance mode of refdbd was already
implemented in 0.9.8, and the lines that cause the problem in
refdb-init (only if you use sqlite3 btw) are simply leftovers from
previous versions. The proper fix is to delete lines 190 through 193
and re-run make in the scripts subdirectory. The bug had been fixed
with other changes in refdb-init.in about three months ago, so the
0.9.9 prereleases are not affected by this problem. I'll also add a
news item to the RefDB homepage that mentions this problem.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] slight problem with refdb 0.9.8-1 distribution

[Markus H. <mar...@mh...>]

Markus Hoenicka writes:
 > The log destinations, log files, and pid files are configurable in the  
 > init files (<prefix>/etc/refdb/refdbXrc) and via the command line (see  
 > the -e, -L, and -P switches). I agree that the default locations  
 > should include the prefix, although I think that on most systems both  
 > /var/log and /usr/local/var/log are root controlled. I'll add the  
 > prefix asap.
 > 

I've checked in a fixed configure.in. The config files will now use
$localstatedir/log and $localstatedir/run for log and pid files,
respectively, unless you manually specify different folders.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de