refdb-devel — List for RefDB developers

Re: [Refdb-devel] latex bibliographies with multiple databases

[Damien J. D. <D.J...@cs...>]

Gidday gidday

As for entering unicode via jedit, there is a graphical plugin for it:
http://plugins.jedit.org/plugins/?CharacterMap
But I haven't been able to get it to work with unicode and it seems that 
the current implementation is a tad broken:
http://community.jedit.org/?q=node/view/1628&pollresults%5B1252%5D=1
We have to wait for a fix to be uploaded.

The good thing about using unicode as storage is that it's a blank slate 
and that means that if the community decides that some kind of markup is 
in fact useful the maintainer(s!) can choose to support it at a later 
point via whatever method they like and in theory they(he!) know(s) 
exactly what kind of data is in the database at any given time: i.e. 
more control over what is coming in and out. See I wouldn't be surprised 
if the required-capitalisation markup was asked for at some time in the 
future when a user wants to use latex+docbook but exploit the latex 
markup, but it can be done from a unicode starting point anyway. My 8.2 
cents worth

Incidentally, how do docbook users deal with this capitalisation issue? 
i.e. capitalisation of acronyms and proper nouns versus of subtitles and 
improper nouns. Anyone?

Peace
Damien

David Nebauer wrote:
> Damien Jade Duff wrote:
> 
>>>all-caps, and mixed case output.
>>>    
>>
>>The latter is fine except, as before, when your article title 
>>capitalises verbs and improper nouns. I'm happy to do it this way 
>>though, I'll just make sure no capitalised verbs and improper nouns get 
>>into my database and hope not to encounter citation styles that require 
>>them.
> 
> 
> This has been bothering me. If the default model for encoding is:
> 
> ...........XML......LaTeX
> ............|.........|
> ............|.........|
> INPUT.....unicode.unicode
> .............\......./
> ..............\...../
> ...............\.../
> ................\./
> .................v
> STORAGE.......unicode
> ................/.\
> .............../...\
> ............../.....\
> ............./.......\
> OUTPUT....convert.convert
> ............|.........|
> ............|.........|
> ............v.........v
> 
> There will undoubtedly be users like Damien who make the choice to 
> include markup in their bibliographic data. Although it effectively 
> traps them into one output format the trade-off is greater control over 
> how that data is eventually displayed.
> 
> Would not it be simple, given the above model, to have a command line 
> switch for runbib and refdbib that skips the conversion step? That seems 
> to me an easy way to accommodate the wishes of everybody.
> 
> Regards,
> David.
> 
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys -- and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Refdb-devel mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-devel

Re: [Refdb-devel] xnote links

[Damien J. D. <D.J...@cs...>]

Gidday gidday

Sorry if I'm a bit obscure. I'll try and clarify what I meant.

By non-directional links (at a user interface level) I meant only that 
if I link note A to note B then note B would automatically be linked to 
note A.
A directional link would be that if I link note A to note B then when I 
query note B I don't get back any reference to note A.

At an implemention level non-directionality means that rather than 
having note A "link to" note B and, conversely, having note B "linked 
from" note A, you would have note A "link to and linked from" note B. 
This would involve an extra table.

Now, you can have non-directional links at a user interface level but 
not at the implementation level. If this was the approach, you would 
need two distinct query processes, finding all those notes linking to 
your current note and finding all the notes linked from your current 
note, and then exclude any duplicates. Which is fine, if you're okay 
with a bit of potential duplication in your DB and/or manual constraint 
enforcement. I guess I'm just being a pedantic relational purist here 
(wherein the relational DB enforces this kind of constraint rather than 
the app).

It also depends on what behaviour we want - I really don't care which we 
get at the user level and it only seems that directional links are 
easier to implement without adding in, either extra database redundancy 
management code as discussed in the previous paragraph, or a new table.

Anyway, I shouldn't argue with you on the implementation details! I'm 
just happy that you're considering putting the feature in!

Peace
Damien

Markus Hoenicka wrote:
> Hi Damien,
> 
> probably I'm a bit dense here, but I think that links via the t_xnote
> table are bidirectional by nature. It is just a matter of the proper
> query. We've got the same issue with the t_refdb, t_author, and
> t_xauthor tables. I can start with a name and find all
> references in t_refdb that use that name as an author. I can also
> start with a reference ID and retrieve all authors of this
> reference. Speaking in terms of extended notes, "links to" and "is
> linked from" should be pretty much the same story. Or am I missing
> something here?
> 
> regards,
> Markus
> 
> Damien Jade Duff writes:
>  > I think I know what you mean - you'd allow presumably a NOTE string in 
>  > the xnote_type field of the t_xnote table. Though I think that would 
>  > only allow for unidirectional links unless you were happy to let your 
>  > backend try to keep two links updated (I believe this is sort of frowned 
>  > upon in the relational DB world) or to search two indices, note_id and 
>  > xref_id for a particular note_id (maybe okay but seems clumsy).
>  > 
>  > I could handle non-directional links outside of RefDB by automatically 
>  > generating dummy references to group notes with but it's kind of messy, 
>  > particularly as there's no real reason to group notes in groups bigger 
>  > than 2 (since you could then group notes by linking them all to another, 
>  > group note, anyway).
>  > 
>  > On the other hand, while non-directional links would be nice, 
>  > unidirectional links would be just fine as far as I'm concerned. It 
>  > would be up to the DB user to specify if he/she wanted a link going both 
>  > ways.
>  > 
>  > As far as a GUI tree view on the data is concerned, well it may recurse 
>  > sometimes, but that's just a consequence of choosing a tree to view a 
>  > potentially cyclic directed (or undirected) graph.
>  > 
>  > Feel free to talk me out of it!
>  > 
>  > Peace
>  > Damien
>  > 
>  > -------------------------------------------------------------------------
>  > Take Surveys. Earn Cash. Influence the Future of IT
>  > Join SourceForge.net's Techsay panel and you'll get the chance to share your
>  > opinions on IT & business topics through brief surveys -- and earn cash
>  > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>  > _______________________________________________
>  > Refdb-devel mailing list
>  > Ref...@li...
>  > https://lists.sourceforge.net/lists/listinfo/refdb-devel
>  > 
> 

Re: [Refdb-devel] Docs in split packages

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> I've separated the switches for building docs and man pages (actually
> I only now understand one of your original comments about this
> problem).

Building documentation fails on conversion of refdbmanualfig5.svg:
-----------------------------------------------------------------
convert ../doc/refdbmanualfig5.svg ../doc/refdbmanualfig5.png
convert: unbalanced graphic context push-pop `graphic-context'.
make[2]: *** [../doc/refdbmanualfig5.png] Error 1
-----------------------------------------------------------------

You will see the build uses 'convert' as batik-rasteriser is 
unavailable.  I see you made some changes to that file in the last 48 
hours which have presumably caused this error to occur.  Unfortunately, 
ViewCVS is currently unable to show the changes made in that revision so 
I can't look for myself.

Regards,
David.

Re: [Refdb-devel] Docs in split packages

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> I've separated the switches for building docs and man pages.
>   

More feedback, this time all on the server build:

1.  Missing manpage symlink targets.

The following symlinks occur in man1:
    refdb-init-pgsql.1 -> ../man8/refdb-init.8
    refdb.sh.1 -> ../man8/refdb.8
but there is no man8 directory at all.

2.  Missing refdb-init manpage altogether.

There is no refdb-init manpage symlink in man1 and/or no equivalent in 
man8 (since man8 is missing entirely.

3.  Missing interpreter

The script refdbctl has no interpreter in its first line.  I note it is 
the only one of the server-built scripts whose '.in' file uses the 
'<myshell>' placeholder.

>  > These directories and their contents build in both clients and server:
>  >     /usr/share/refdb/sql, and
>  >     /usr/share/refdb/examples.
>
> I've fixed #1 by using a conditional and #2 by including the examples
> only in the client package - actually none of the files is required
> for the server.

These two directories have been 'fixed'.

Regards,
David.

Re: [Refdb-devel] Docs in split packages

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

Hi David,

thanks for testing the stuff. As usual, version 1 is crap.

David Nebauer writes:
 > No man pages at all built for client or server.
 > 
 > 

I've separated the switches for building docs and man pages (actually
I only now understand one of your original comments about this
problem). Now you have to fiddle with these switches:

<no switches> builds everything
--disable-server --disable-docs    only clients and their man pages
--disable-clients --disable-docs   only server and its man pages
--disable-clients --disable-server only documentation
--disable-docs --disable-manpages  builds the binaries, no DocBook
                                   installation required


 > 2. Duplicate files
 > 
 > These directories and their contents build in both clients and server:
 >     /usr/share/refdb/sql, and
 >     /usr/share/refdb/examples.
 > Obviously this is not allowed in package building as the same files 
 > cannot be under the control of multiple packages.
 > 

I've fixed #1 by using a conditional and #2 by including the examples
only in the client package - actually none of the files is required
for the server.

I hope this version builds ok.

regards,
Markus

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

Re: [Refdb-devel] Docs in split packages

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> You should now be able to build three packages:
>
> --disable-clients --disable-docs (server package)
> --disable-server --disable-docs (client package)
> --disable-server --disable-clients (doc package)
>
> Both the client and the server builds should be accompanied by their
> respective man pages. Let me know if I got something wrong here.

Have built clients and server packages so far.  The doc package is still 
to come.

Results of first attempt to build split debian packages:


1. Man pages

No man pages at all built for client or server.


2. Duplicate files

These directories and their contents build in both clients and server:
    /usr/share/refdb/sql, and
    /usr/share/refdb/examples.
Obviously this is not allowed in package building as the same files 
cannot be under the control of multiple packages.

Regards,
David.

Re: [Refdb-devel] Docs in split packages

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

Hi David,

David Nebauer writes:
 > I've just built a version of refdb using 'disable-server' and 
 > 'disable-clients' to see if I could produce a document-only install that 
 > might form the basis of a debian package.  I note one major and one 
 > minor problem.  The minor first: the install includes the file 
 > 'refdb-manual.fo'.  It is over 3 MB in size and not needed as the pdf 
 > version installs also.
 > 

That's a bummer. I guess this was a backfiring attempt to force the
.fo file into the package to silence make. I've fixed that.

 > The major problem is the man pages build as part of the documentation 
 > and not alongside the client or server.  I quite understand why you 
 > designed it this way.  Unfortunately, it violates an inflexible Debian 
 > rule that any executable installing to one of the recognised bin 
 > directories MUST have an accompanying man page.  If you could alter the 
 > man page build such that their inclusion depends on the 
 > 'disable-[clients|server]' flags (and ditch 'refdb-manual.fo') it would 
 > be quite simple to build a 'refdb-doc' package alongside 'refdb-clients' 
 > and 'refdb-server'.
 > 

I tried to implement this suggestion. You should now be able to build
three packages:

--disable-clients --disable-docs (server package)
--disable-server --disable-docs (client package)
--disable-server --disable-clients (doc package)

Both the client and the server builds should be accompanied by their
respective man pages. Let me know if I got something wrong here.

regards,
Markus

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

Re: [Refdb-devel] Docs in split packages

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> Well, a third approach is to build the docs as a separate package and make both
> the client and the server package depend on it. This would require a few minor
> changes to configure.in.
>
> Could you please check whether the Debian policy has specific requirements for
> the docs?

There is no absolute requirement in Debian that general documentation be 
installed with the main application files.  In fact, it is not uncommon 
to have a 'widget' package and an accompanying, recommended but not 
dependent, package called 'widget-doc'.

I've just built a version of refdb using 'disable-server' and 
'disable-clients' to see if I could produce a document-only install that 
might form the basis of a debian package.  I note one major and one 
minor problem.  The minor first: the install includes the file 
'refdb-manual.fo'.  It is over 3 MB in size and not needed as the pdf 
version installs also.

The major problem is the man pages build as part of the documentation 
and not alongside the client or server.  I quite understand why you 
designed it this way.  Unfortunately, it violates an inflexible Debian 
rule that any executable installing to one of the recognised bin 
directories MUST have an accompanying man page.  If you could alter the 
man page build such that their inclusion depends on the 
'disable-[clients|server]' flags (and ditch 'refdb-manual.fo') it would 
be quite simple to build a 'refdb-doc' package alongside 'refdb-clients' 
and 'refdb-server'.

Regards,
David.

Re: [Refdb-devel] Docs in split packages

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

David Nebauer <dav...@sw...> was heard to say:

> Hi Markus,
>
> I've been thinking about Justus' suggestion to split the Debian package
> into server and client.  You clearly anticipate such an eventuality with
> the 'disable-[server|clients]' configure flags.  Most of the machinery,
> in fact, is already available to build separate packages.  I can see
> only one problem: the monolithic documentation.  It cannot be split
> during the build process.  At the moment the choice would be building
> full documentation in both, or only one, of the packages.  Both
> approaches are obviously less than perfect.
>
> Have you considered splitting refdb's documentation into two parts --
> able to be installed individually but, when installed together, making a
> cohesive whole?
>
> Or perhaps there is another approach?

Well, a third approach is to build the docs as a separate package and make both
the client and the server package depend on it. This would require a few minor
changes to configure.in.

Splitting the docs is a non-trivial task as I've put a lot of work into
cross-linking the contents. The only part of the docs which could be built
separately is the reference manual which is composed mostly of the man pages.
But then you'd end up with a client reference manual, a server reference
manual, and a maintenance/usage manual. The latter would contain large parts of
the installation and administration stuff that most users would probably expect
in the client or server manuals. I guess this makes the separate docs package
the more obvious choice.

Could you please check whether the Debian policy has specific requirements for
the docs? I mean, the proper man pages would be installed anyway with both the
server and the client package. If the Debian policy doesn't mind, you could
even make the docs package recommended instead of required, for those who want
to access the docs through the internet.

regards,
Markus


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

[Refdb-devel] Docs in split packages

[David N. <dav...@sw...>]

Hi Markus,

I've been thinking about Justus' suggestion to split the Debian package 
into server and client.  You clearly anticipate such an eventuality with 
the 'disable-[server|clients]' configure flags.  Most of the machinery, 
in fact, is already available to build separate packages.  I can see 
only one problem: the monolithic documentation.  It cannot be split 
during the build process.  At the moment the choice would be building 
full documentation in both, or only one, of the packages.  Both 
approaches are obviously less than perfect.

Have you considered splitting refdb's documentation into two parts -- 
able to be installed individually but, when installed together, making a 
cohesive whole?

Or perhaps there is another approach?

Regards,
David.

Re: [Refdb-devel] latex bibliographies with multiple databases

[David N. <dav...@sw...>]

David Nebauer wrote:
> If the default model for encoding is:
>
> XML LaTeX
> | |
> | |
> INPUT unicode unicode
> \ /
> \ /
> \ /
> \ /
> v
> STORAGE unicode
> / \
> / \
> / \
> / \
> OUTPUT convert convert
> | |
> | |
> v v
> XML LaTeX

Spaces were stripped.  That should look like:

...........XML......LaTeX
............|.........|
............|.........|
INPUT.....unicode.unicode
.............\......./
..............\...../
...............\.../
................\./
.................v
STORAGE.......unicode
................/.\
.............../...\
............../.....\
............./.......\
OUTPUT....convert.convert
............|.........|
............|.........|
............v.........v
...........XML......LaTeX

Regards,
David.

Re: [Refdb-devel] latex bibliographies with multiple databases

[David N. <dav...@sw...>]

Damien Jade Duff wrote:
>> all-caps, and mixed case output.
>>     
> The latter is fine except, as before, when your article title 
> capitalises verbs and improper nouns. I'm happy to do it this way 
> though, I'll just make sure no capitalised verbs and improper nouns get 
> into my database and hope not to encounter citation styles that require 
> them.

This has been bothering me. If the default model for encoding is:

XML LaTeX
| |
| |
INPUT unicode unicode
\ /
\ /
\ /
\ /
v
STORAGE unicode
/ \
/ \
/ \
/ \
OUTPUT convert convert
| |
| |
v v
XML LaTeX


There will undoubtedly be users like Damien who make the choice to 
include markup in their bibliographic data. Although it effectively 
traps them into one output format the trade-off is greater control over 
how that data is eventually displayed.

Would not it be simple, given the above model, to have a command line 
switch for runbib and refdbib that skips the conversion step? That seems 
to me an easy way to accommodate the wishes of everybody.

Regards,
David.

Re: [Refdb-devel] refdb-elisp problems

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> If I understand correctly, the two installation runs create
> installations for Emacs in general (undefined version) as well as for
> specifically installed versions. During the first run, loading
> 50refdb-elisp most likely fails because refdb-mode is not yet
> installed completely (the file contains a "require 'refdb-mode"
> call). It is sort of a bootstrapping problem which could only be
> avoided by manually specifying the order in which the files are
> installed. I don't know whether this is possible within a .deb
> package. In any case, after the second successful run everything works
> ok on my Debian box.

Thanks for your analysis, Marcus.  What I've found here is that after 
installation I have to run emacs twice before it loads the refdb modes 
automatically.  Previously I was assuming total failure on the first 
post-install run.

Regards,
David.

[Refdb-devel] refdb-elisp problems

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

Hi,

David Nebauer writes:
 > My problem is that, even though it appears to install correctly, it is 
 > not available in emacs.
 > 
 > Neither mode becomes active when I open an xml or ris file.  Neither is 
 > refdb-mode available to start manually as per the manual.
 > 

I can't reproduce this here. I've deleted a previously installed
package, then fetched the latest .deb (using apt-get mysteriously
failed - maybe I'm no enough of a Debian guy) and installed it using
dpkg. After doing that, both refdb-mode and ris-mode are
available. RefDB Mode is available as a menu entry in the Tools
menu. I've repeated the test after starting Emacs with the -q switch -
this bypasses my ~/.emacs to make sure I don't use any private
settings to magically load either of the modes. It still works ok.

 > While compiling refdb-set-default-database in file 
 > /home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
 >   ** assignment to free variable refdb-database-default
 >   ** reference to free variable refdb-database-default

These messages appear to be harmless. I also see them on my system,
and I see them if I build other Emacs extensions from the sources.

[...first run...]
 > Loading 50refdb-elisp (source)...
 > Error while loading 50refdb-elisp

[...second run...]
 > Loading 50refdb-elisp (source)...

[...]
 > There is clearly a problem loading refdb-elisp.  I see two files were 
 > written immediately after the load error, so here they are as well in 
 > case they provide a hint:
 > 

If I understand correctly, the two installation runs create
installations for Emacs in general (undefined version) as well as for
specifically installed versions. During the first run, loading
50refdb-elisp most likely fails because refdb-mode is not yet
installed completely (the file contains a "require 'refdb-mode"
call). It is sort of a bootstrapping problem which could only be
avoided by manually specifying the order in which the files are
installed. I don't know whether this is possible within a .deb
package. In any case, after the second successful run everything works
ok on my Debian box.

Could you or Justus try the following command in emacs:

Alt-x load-file RETURN /etc/refdb-mode-config.el RETURN

and see whether refdb-mode and ris-mode are available after that?

regards,
Markus

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

[Refdb-devel] refdb-elisp problems

[David N. <dav...@sw...>]

Hi Markus,

As Justus pointed out, there is a problem with the refdb-elisp debian 
package.  When I checked the package it didn't contain either of the 
'.el' files.  I have no idea how that came to be.  I've just rebuilt it 
again and the new package contains the missing files.  I've uploaded it 
to sf.

My problem is that, even though it appears to install correctly, it is 
not available in emacs.

Neither mode becomes active when I open an xml or ris file.  Neither is 
refdb-mode available to start manually as per the manual.

You can examine the debian package yourself -- midnight commander (mc) 
will open the deb archive and let you poke around inside.

Here are some of the files installed as part of the debian package install:

---------------------------------------------------------------------------------------
$ ls /usr/share/emacs/site-lisp/refdb-elisp/
total 384
-rw-r--r-- 1 root root 207298 2006-07-29 17:32 refdb-mode.el
-rw-r--r-- 1 root root 151572 2006-07-29 17:32 refdb-mode.elc
-rw-r--r-- 1 root root   9363 2006-07-29 17:32 ris.el
-rw-r--r-- 1 root root   6796 2006-07-29 17:32 ris.elc

$ ls /usr/share/emacs21/site-lisp/refdb-elisp/
total 160
-rw-r--r-- 1 root root 151509 2006-07-29 20:19 refdb-mode.elc
-rw-r--r-- 1 root root   6733 2006-07-29 20:19 ris.elc

$ ls /etc/emacs/site-start.d/50refdb-elisp*
lrwxrwxrwx 1 root root   25 2006-07-29 20:19 
/etc/emacs/site-start.d/50refdb-elisp -> /etc/refdb-mode-config.el
-rw-r--r-- 1 root root 1755 2006-07-29 17:32 
/etc/emacs/site-start.d/50refdb-elisp.el

$ ls /etc/refdb-mode-config.el
-rw-r--r-- 1 root root 1755 2006-07-29 17:32 /etc/refdb-mode-config.el
$
---------------------------------------------------------------------------------------

Here is the build process occurring during the debian package build.  Do 
those compilation messages indicate errors or are they normal?  As you 
can see, I know nothing about emacs.

---------------------------------------------------------------------------------------
CFLAGS="-Wall -g -O2" ./configure \
           --host=i486-linux-gnu \
           --build=i486-linux-gnu \
           --prefix=/usr \
           --mandir=\${prefix}/share/man \
           --infodir=\${prefix}/share/info \
           --with-lispdir=\${datadir}/emacs/site-lisp/\${PACKAGE} \
           --sysconfdir=/etc
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for emacs... emacs
checking where .elc files should go... ${datadir}/emacs/site-lisp/${PACKAGE}
checking for refdbd... /usr/bin/refdbd
checking for refdbctl... /usr/bin/refdbctl
checking for refdbc... /usr/bin/refdbc
checking for refdba... /usr/bin/refdba
checking for refdbnd... /usr/bin/refdbnd
checking for sudo... /usr/bin/sudo
checking for gmake... no
checking for make... /usr/bin/make
checking for xpdf... /usr/bin/xpdf
checking for gv... /usr/bin/gv
checking for ted... /usr/bin/ted
checking for sh... /bin/sh
checking for docbook2texi... no
checking for docbook2x-texi... /usr/bin/docbook2x-texi
configure: creating ./config.status
config.status: creating Makefile
dh_testdir
# Add here commands to compile the package.
/usr/bin/make
make[1]: Entering directory 
`/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3'
./striptable.pl < refdb-mode-manual.xml > refdb-mode-manual-stripped.xml
/usr/bin/docbook2x-texi --to-stdout refdb-mode-manual-stripped.xml > 
refdb-mode.texi
/book/chapter[@id='chapter-commands']/sect1[1]/sect2[@id='submenu-get-references-on-region']/sect3[@id='command-get-references-author-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[1]/sect2[@id='submenu-get-references-on-region']/sect3[@id='command-get-references-title-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[1]/sect2[@id='submenu-get-references-on-region']/sect3[@id='command-get-references-keyword-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[1]/sect2[@id='submenu-get-references-on-region']/sect3[@id='command-get-references-periodical-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[1]/sect2[@id='submenu-get-references-on-region']/sect3[@id='command-get-references-id-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes']/sect3[@id='command-get-notes-title']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes']/sect3[@id='command-get-notes-title-regexp']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes']/sect3[@id='command-get-notes-keyword']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes']/sect3[@id='command-get-notes-keyword-regexp']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes']/sect3[@id='command-get-notes-citationkey']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-title-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-keyword-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-authorlink-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-keywordlink-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-periodicallink-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-idlink-region']: 
Node name collision
/book/chapter[@id='chapter-commands']/sect1[2]/sect2[@id='submenu-get-notes-on-region']/sect3[@id='command-get-notes-citekeylink-region']: 
Node name collision
restore=: && \
    backupdir=".am$$" && \
    am__cwd=`pwd` && cd . && \
    rm -rf $backupdir && mkdir $backupdir && \
    for f in refdb-mode.info refdb-mode.info-[0-9] 
refdb-mode.info-[0-9][0-9] refdb-mode.i[0-9] refdb-mode.i[0-9][0-9]; do \
      if test -f $f; then \
        mv $f $backupdir; \
        restore=mv; \
      fi; \
    done; \
    cd "$am__cwd"; \
    if /bin/sh 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/missing 
--run makeinfo   -I . \
     -o refdb-mode.info refdb-mode.texi; \
    then \
      rc=0; \
      cd .; \
    else \
      rc=$?; \
      cd . && \
      $restore $backupdir/* `echo "./refdb-mode.info" | sed 's|[^/]*$||'`; \
    fi; \
    rm -rf $backupdir; \
    exit $rc
WARNING: Warnings can be ignored. :-)
if test "emacs" != no; then \
      set x; \
      list='refdb-mode.el ris.el'; for p in $list; do \
        if test -f "$p"; then d=; else d="./"; fi; \
        set x "$@" "$d$p"; shift; \
      done; \
      shift; \
      EMACS="emacs" /bin/sh ./elisp-comp "$@" || exit 1; \
    else : ; fi
Loading 00debian-vars...
Loading 50a2ps (source)...
Loading a2ps-print...
Loading 50autoconf (source)...
Loading 50cscope (source)...
Loading 50devhelp (source)...
Loading 50dictionaries-common (source)...
Loading debian-ispell...
Loading /var/cache/dictionaries-common/emacsen-ispell-default.el (source)...
Loading /var/cache/dictionaries-common/emacsen-ispell-dicts.el (source)...
Loading 50emacs-goodies-el (source)...
Package emacs-goodies-el removed but not purged.  Skipping setup.
Loading 50festival (source)...
Loading 50gettext (source)...
Loading 50psgml-init (source)...
Loading 50psvn (source)...
Loading 50refdb-elisp (source)...
While compiling refdb-set-default-database in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-database-default
  ** reference to free variable refdb-database-default
While compiling refdb-scan-database-list in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-selectdb-submenu-contents
  ** assignment to free variable refdb-current-database-list
While compiling refdb-update-database-menu in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-selectdb-submenu-contents
While compiling refdb-scan-admin-database-list in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-current-admin-database-list
While compiling refdb-scan-keywords-list in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-current-keywords-list
While compiling refdb-scan-authors-list in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-current-authors-list
While compiling refdb-list-periodicals in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-periodical-regexp
While compiling refdb-scan-periodicals-list in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-current-periodicals-list
While compiling refdb-scan-styles-list in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-current-styles-list
While compiling refdb-find-dbengine in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-regexp-query-string
  ** assignment to free variable refdb-periodical-regexp
  ** assignment to free variable refdb-regexp-prompt
While compiling refdb-select-data-output-type in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-data-output-type
While compiling refdb-select-data-output-format in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-data-output-format
  ** assignment to free variable refdb-data-output-formatstring
While compiling refdb-select-notesdata-output-type in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-notesdata-output-type
While compiling refdb-select-citation-type in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-citation-type
While compiling refdb-select-citation-format in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-citation-format
While compiling refdb-determine-input-type in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-input-type-risx
While compiling refdb-deleteref-on-region in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-display-messages-flag
While compiling refdb-deleteref in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getref-by-field in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-data-output-format
  ** reference to free variable refdb-data-output-type
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getref-by-field-regexp in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-data-output-format
  ** reference to free variable refdb-data-output-type
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getref-by-field-on-region in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-regexp-query-string
While compiling refdb-output-buffer-choose-mode in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-data-output-type
While compiling refdb-getref-by-advanced-search in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-data-output-format
  ** reference to free variable refdb-data-output-type
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-pickref in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-dumpref in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-notes-output-buffer-choose-mode in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-notesdata-output-type
While compiling refdb-deletenote-on-region in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-display-messages-flag
While compiling refdb-deletenote in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getnote-by-field in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-data-output-format
  ** reference to free variable refdb-notesdata-output-type
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getnote-by-field-regexp in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-data-output-format
  ** reference to free variable refdb-notesdata-output-type
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getnote-by-field-on-region in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-regexp-query-string
While compiling refdb-getnote-by-advanced-search in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-data-output-format
  ** reference to free variable refdb-notesdata-output-type
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-addlink in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-deletelink in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-whichdb in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-create-document in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-current-styles-list
While compiling refdb-get-ris-idstring-from-region in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-citation-type
  ** reference to free variable refdb-citation-format
While compiling refdb-get-risx-idstring-from-region in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-citation-type
  ** reference to free variable refdb-citation-format
While compiling refdb-get-ris-id-from-point in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-citation-type
  ** reference to free variable refdb-citation-format
While compiling refdb-get-risx-id-from-point in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-citation-type
  ** reference to free variable refdb-citation-format
While compiling refdb-adduser in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-current-admin-database-list
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-addword in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-createdb in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-deletedb in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-deletestyle in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-deleteuser in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-current-admin-database-list
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-deleteword in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-getstyle in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-scankw in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-current-admin-database-list
While compiling refdb-list-item in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-listuser in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-current-admin-database-list
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-backup-database in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable refdb-current-admin-database-list
While compiling refdb-restore-database in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** reference to free variable main-database
While compiling refdb-import-refdata in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-export-refdata in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable resize-mini-windows-default
  ** reference to free variable refdb-display-messages-flag
  ** reference to free variable resize-mini-windows-default
While compiling refdb-make-selectdb-menu in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-selectdb-submenu-items
  ** reference to free variable refdb-current-database-list
  ** assignment to free variable my-database-list
  ** reference to free variable my-database-list
  ** assignment to free variable current-database
  ** reference to free variable refdb-selectdb-submenu-items
  ** reference to free variable current-database
  ** assignment to free variable refdb-selectdb-submenu-contents
While compiling refdb-initialize-all-menus in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** assignment to free variable refdb-data-output-submenu-contents
  ** assignment to free variable refdb-data-output-submenu-definition
  ** assignment to free variable refdb-getref-submenu-contents
  ** assignment to free variable refdb-getref-submenu-definition
  ** assignment to free variable refdb-getref-on-region-submenu-contents
  ** assignment to free variable refdb-getref-on-region-submenu-definition
  ** assignment to free variable refdb-getnote-submenu-contents
  ** assignment to free variable refdb-getnote-submenu-definition
  ** assignment to free variable refdb-getnote-on-region-submenu-contents
  ** assignment to free variable refdb-getnote-on-region-submenu-definition
  ** assignment to free variable refdb-customize-submenu-contents
  ** assignment to free variable refdb-customize-submenu-definition
  ** assignment to free variable refdb-insert-submenu-contents
  ** assignment to free variable refdb-insert-submenu-definition
  ** assignment to free variable refdb-administration-submenu-contents
  ** assignment to free variable refdb-administration-submenu-definition
  ** assignment to free variable refdb-convert-submenu-contents
  ** assignment to free variable refdb-convert-submenu-definition
  ** assignment to free variable refdb-cite-references-submenu-contents
  ** assignment to free variable refdb-cite-references-submenu-definition
  ** assignment to free variable refdb-create-document-submenu-contents
  ** assignment to free variable refdb-create-document-submenu-definition
  ** assignment to free variable refdb-transform-submenu-contents
  ** assignment to free variable refdb-transform-submenu-definition
  ** assignment to free variable refdb-view-output-submenu-contents
  ** assignment to free variable refdb-view-output-submenu-definition
  ** assignment to free variable refdb-menu-contents
  ** assignment to free variable refdb-menu-definition
While compiling the end of the data in file 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.el:
  ** The following functions are not known to be defined: nxml-mode,
    xml-mode, refdb-output-buffer-mode, rng-compute-mode-line-string
Wrote 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/refdb-mode.elc
Wrote 
/home/david/data/computing/projects/refdb/packages/elisp/pkg/debianise/source/refdb-elisp-1.3/elc.20477/ris.elc
Done
---------------------------------------------------------------------------------------

During the package install this feedback was generated:

---------------------------------------------------------------------------------------
Setting up refdb-elisp (1.3-4) ...
emacsen-common: Handling install of emacsen flavor emacs
emacsen-common: Handling install of emacsen flavor emacs21
emacsen-common: byte-compiling for emacs21
Loading 00debian-vars (source)...
Loading 50a2ps (source)...
Loading a2ps-print...
Loading 50autoconf (source)...
Loading 50cscope (source)...
Loading 50devhelp (source)...
Loading 50dictionaries-common (source)...
Loading debian-ispell...
Loading /var/cache/dictionaries-common/emacsen-ispell-default.el (source)...
Loading /var/cache/dictionaries-common/emacsen-ispell-dicts.el (source)...
Loading 50emacs-goodies-el (source)...
Package emacs-goodies-el removed but not purged.  Skipping setup.
Loading 50festival (source)...
Loading 50gettext (source)...
Loading 50psgml-init (source)...
Loading 50psvn (source)...
Loading 50refdb-elisp (source)...
Error while loading 50refdb-elisp
Wrote /etc/emacs21/site-start.d/00debian-vars.elc
Wrote /usr/share/emacs21/site-lisp/debian-startup.elc
Done
install/refdb-elisp: Handling install for emacsen flavor emacs21
Loading 00debian-vars...
Loading 50a2ps (source)...
Loading a2ps-print...
Loading 50autoconf (source)...
Loading 50cscope (source)...
Loading 50devhelp (source)...
Loading 50dictionaries-common (source)...
Loading debian-ispell...
Loading /var/cache/dictionaries-common/emacsen-ispell-default.el (source)...
Loading /var/cache/dictionaries-common/emacsen-ispell-dicts.el (source)...
Loading 50emacs-goodies-el (source)...
Package emacs-goodies-el removed but not purged.  Skipping setup.
Loading 50festival (source)...
Loading 50gettext (source)...
Loading 50psgml-init (source)...
Loading 50psvn (source)...
Loading 50refdb-elisp (source)...
Wrote /usr/share/emacs21/site-lisp/refdb-elisp/refdb-mode.elc
Wrote /usr/share/emacs21/site-lisp/refdb-elisp/ris.elc
Done
---------------------------------------------------------------------------------------

There is clearly a problem loading refdb-elisp.  I see two files were 
written immediately after the load error, so here they are as well in 
case they provide a hint:

---------------------------------------------------------------------------------------
;; 00debian-vars.el
;;
;; Initialize some emacs variables from debian policy files.
;;
;; Copyright (C) 1997, Frederic Lepied <Fre...@su...>
;;
;; original Author: Frederic Lepied <Fre...@su...>
;; enhanced and documented by: Mark Eichin <ei...@ki...>

;;=============================================================================
;; Autoloaded section.
;;=============================================================================


;;;###

;;;***


;;=============================================================================
;; Configuration section.
;;=============================================================================
(defun debian-file->string (name &optional func)
  "Convert a file into a string"
  (interactive "fFile name : ")
  (let ((filename (expand-file-name name)))
    (if (not (file-readable-p filename))
    nil
      (let ((buf (create-file-buffer filename))
        ret)
    (save-excursion
      (set-buffer buf)
      (insert-file-contents filename)
      (if func (funcall func))
      (setq ret (buffer-string)))
    (kill-buffer buf)
    ret))))

(defun debian-clean-mailname ()
  (while (search-forward "\n" nil t)
    (replace-match "" nil t)))

;; Particular variables, and their justification:
;; policy/ch4.html, 4.3 Mail processing on Debian systems, /etc/mailname
;; policy/ch-binarypkg.html, 3.5 Maintainer scripts, /etc/news/server

(let ((mailname
       (debian-file->string "/etc/mailname" (function 
debian-clean-mailname))))
  (if (not mailname)
      (message "No /etc/mailname. Reverting to default...")
    (setq mail-host-address mailname)))

;; Don't need to check NNTPSERVER for override, gnus does that for us.
(if (file-readable-p "/etc/news/server")
    (defvar gnus-nntpserver-file "/etc/news/server"))

;;; 00debian-vars.el ends here
---------------------------------------------------------------------------------------

and

---------------------------------------------------------------------------------------
;ELC

-;;; Compiled by root@hezmana on Sat Jul 29 20:19:20 2006
;;; from file /usr/share/emacs21/site-lisp/debian-startup.el
;;; in Emacs version 21.4.1
;;; with bytecomp version 2.85.4.1
;;; with all optimizations.

;;; This file uses dynamic docstrings, first added in Emacs 19.29.
(if (and (boundp 'emacs-version)
     (< (aref emacs-version (1- (length emacs-version))) ?A)
     (or (and (boundp 'epoch::version) epoch::version)
         (string-lessp emacs-version "19.29")))
    (error "`debian-startup.el' was compiled for Emacs 19.29 or later"))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;


#@233 Takes a path item (a string) and adds it to load path in the
correct position for an add-on package, before the emacs system
directories, but after the /usr/local/ directories.  After modifying
load-path, returns the new load-path.
(defalias 'debian-pkg-add-load-path-item #[(item) "\306\307    \203#
--------------------------------------------------------------------------------------

Something strange is going on here and I have no idea what.  I hope you 
can give me some clue.

Regards,
David.

Re: [Refdb-devel] latex bibliographies with multiple databases

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
>> Many unicode characters (and certainly all the commonly used ones) are
>> entered by means of digraphs (using two or more keystrokes to specify
>> one character).  The mnemonics for these are fairly intuitive, like 'a:'
>> for a-umlaut.  Any unicode character can be entered with 'Ctrl-v uxxxx'
>> where 'xxxx' is the character code.
>>     
>
> Is there a link to some doc that explains this, by any chance? I thought about
> adding something like a tip box to the docs that briefly explains how to deal
> with Unicode characters for the most popular editors. I'd like to add URLs for
> further information.

Vim documentation is the ultimate triumph of substance over style.  In 
aggregate it contains every fact you could or would ever want to know 
about Vim.  The problem is it's almost impossible to find the 
information you want.  On the rare occasion you do it is so dry and 
technical as to be a foreign language altogether.

There actually appear to be three general methods of entering unicode 
characters:

1. Digraphs

I mentioned these in my previous post.  This is the easiest method to 
learn and remember.  Documentation is here: 
<http://vimdoc.sourceforge.net/htmldoc/digraph.html>.  Same 
documentation is available within Vim by typing ':h digraphs'.  Type 
':digraphs' for a list of digraphs.

2. Keymaps

Frankly, I've skimmed this topic a few times and can't make head nor 
tail of it.  It claims unicode characters can be entered as combinations 
of other characters (sounds somewhat like digraphs but apparently is 
different).  Documentation is here: 
<http://vimdoc.sourceforge.net/htmldoc/mbyte.html>.  Same documentation 
is available within Vim by typing ':h multibyte'.

3. Direct entry

This is done by 'Ctrl-v u xxxx' where 'xxxx' is the hex number of a 
unicode character.  Documentation is included in multi-byte help at 
<http://vimdoc.sourceforge.net/htmldoc/mbyte.html#utf-8-typing> or 
within Vim by typing ':h utf-8-typing'.

Regards,
David.

Re: [Refdb-devel] latex bibliographies with multiple databases

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

David Nebauer <dav...@sw...> was heard to say:

> > 4) SGML/XML output (bibliographies, db31/tei/html backends)
> > "<>&" are replaced with their corresponding entities. In addition, the
> > current code contains replacements for &mdash; &lsquo; and &rsquo;. I
> > know that I was asked to add these, but I can't remember the
> > context. I wonder whether it would make more sense to keep these
> > characters as Unicode.
> >
>
> I fear I may have partly the cause.  I was using refdb purely for
> docbook and since I didn't use UTF-8 encoding for my references the only
> way to preserve characters like em dash was to protect them as entities
> throughout the reference's life cycle.  They were not only protected
> during output, as you mention above, but were protected at input also.
> In moving to a more sensible unicode-based system, however, it no longer
> makes any sense to replace those characters with entities.

I see. Then I'll remove these entities again.

> > 5) LaTeX output
> > There are currently no attempts to escape LaTeX command
> > characters. I'm about to add this code.
> >
>
> I see this code arrived today.

Yes. I didn't get round to announce it, but please give it a real-world test to
see whether it works ok.

> Many unicode characters (and certainly all the commonly used ones) are
> entered by means of digraphs (using two or more keystrokes to specify
> one character).  The mnemonics for these are fairly intuitive, like 'a:'
> for a-umlaut.  Any unicode character can be entered with 'Ctrl-v uxxxx'
> where 'xxxx' is the character code.

Is there a link to some doc that explains this, by any chance? I thought about
adding something like a tip box to the docs that briefly explains how to deal
with Unicode characters for the most popular editors. I'd like to add URLs for
further information.

regards,
Markus

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

Re: [Refdb-devel] latex bibliographies with multiple databases

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

David Nebauer <dav...@sw...> was heard to say:

> Hi Markus,
>
> Markus Hoenicka wrote:
> > Actually we can still use ISO-8859-1 or whatever as the RIS input
> > format as refdbd internally converts it to UTF-8 if the database uses
> > this encoding. Forcing UTF-8 for RIS data actually makes only sense if
> > people use both bibtex and RIS data.
>
> The advantage of making UTF-8 the default encoding at each step in the
> life cycle is you don't have to remember when to specify UTF-8 encoding
> and when not to.  Still, the most important thing is making sure to
> document clearly what the default encoding is at each step so the user
> knows what is happening.
>

This is approximately what I intended to say, but I guess I was too tired to be
as clear as I should. I plan to set all defaults to UTF-8, but users are still
free to configure their systems differently if they have a good reason.

regards,
Markus


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

Re: [Refdb-devel] latex bibliographies with multiple databases

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> Actually we can still use ISO-8859-1 or whatever as the RIS input
> format as refdbd internally converts it to UTF-8 if the database uses
> this encoding. Forcing UTF-8 for RIS data actually makes only sense if
> people use both bibtex and RIS data.

The advantage of making UTF-8 the default encoding at each step in the 
life cycle is you don't have to remember when to specify UTF-8 encoding 
and when not to.  Still, the most important thing is making sure to 
document clearly what the default encoding is at each step so the user 
knows what is happening.

Regards,
David.

Re: [Refdb-devel] latex bibliographies with multiple databases

[David N. <dav...@sw...>]

Hi Markus,

Markus Hoenicka wrote:
> 1) BibTeX input
> [W]e can import bibtex data as plain Unicode.
>
> 2) RIS input
> All it takes is to set the default input
> encoding of refdbd for RIS data to UTF-8.
>
> 3) risx input
> [N]o extra conversion step is required to get rid of
> entities and to store plain Unicode.

All looks too easy so far.
> 4) SGML/XML output (bibliographies, db31/tei/html backends)
> "<>&" are replaced with their corresponding entities. In addition, the
> current code contains replacements for &mdash; &lsquo; and &rsquo;. I
> know that I was asked to add these, but I can't remember the
> context. I wonder whether it would make more sense to keep these
> characters as Unicode.
>   

I fear I may have partly the cause.  I was using refdb purely for 
docbook and since I didn't use UTF-8 encoding for my references the only 
way to preserve characters like em dash was to protect them as entities 
throughout the reference's life cycle.  They were not only protected 
during output, as you mention above, but were protected at input also.  
In moving to a more sensible unicode-based system, however, it no longer 
makes any sense to replace those characters with entities.
> 5) LaTeX output
> There are currently no attempts to escape LaTeX command
> characters. I'm about to add this code.
>   

I see this code arrived today.
> 6) other output (RIS, screen)
> No replacements. If you retrieve data as UTF-8, you'll get what you want.
>
>
> One thing that should be discussed is how easy it is for RefDB users
> to author UTF-8 data, be it RIS, bibtex, or XML. Is there [Unicode input] support
> available for other editors (vim, jedit) which should be mentioned in
> the manual?
>   

Many unicode characters (and certainly all the commonly used ones) are 
entered by means of digraphs (using two or more keystrokes to specify 
one character).  The mnemonics for these are fairly intuitive, like 'a:' 
for a-umlaut.  Any unicode character can be entered with 'Ctrl-v uxxxx' 
where 'xxxx' is the character code.
Regards,
David.

Re: [Refdb-devel] xnote links

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

Hi Damien,

probably I'm a bit dense here, but I think that links via the t_xnote
table are bidirectional by nature. It is just a matter of the proper
query. We've got the same issue with the t_refdb, t_author, and
t_xauthor tables. I can start with a name and find all
references in t_refdb that use that name as an author. I can also
start with a reference ID and retrieve all authors of this
reference. Speaking in terms of extended notes, "links to" and "is
linked from" should be pretty much the same story. Or am I missing
something here?

regards,
Markus

Damien Jade Duff writes:
 > I think I know what you mean - you'd allow presumably a NOTE string in 
 > the xnote_type field of the t_xnote table. Though I think that would 
 > only allow for unidirectional links unless you were happy to let your 
 > backend try to keep two links updated (I believe this is sort of frowned 
 > upon in the relational DB world) or to search two indices, note_id and 
 > xref_id for a particular note_id (maybe okay but seems clumsy).
 > 
 > I could handle non-directional links outside of RefDB by automatically 
 > generating dummy references to group notes with but it's kind of messy, 
 > particularly as there's no real reason to group notes in groups bigger 
 > than 2 (since you could then group notes by linking them all to another, 
 > group note, anyway).
 > 
 > On the other hand, while non-directional links would be nice, 
 > unidirectional links would be just fine as far as I'm concerned. It 
 > would be up to the DB user to specify if he/she wanted a link going both 
 > ways.
 > 
 > As far as a GUI tree view on the data is concerned, well it may recurse 
 > sometimes, but that's just a consequence of choosing a tree to view a 
 > potentially cyclic directed (or undirected) graph.
 > 
 > Feel free to talk me out of it!
 > 
 > Peace
 > Damien
 > 
 > -------------------------------------------------------------------------
 > Take Surveys. Earn Cash. Influence the Future of IT
 > Join SourceForge.net's Techsay panel and you'll get the chance to share your
 > opinions on IT & business topics through brief surveys -- and earn cash
 > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
 > _______________________________________________
 > Refdb-devel mailing list
 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-devel
 > 

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

Re: [Refdb-devel] xnote links

[Damien J. D. <D.J...@cs...>]

Hello hello

Markus Hoenicka wrote:

> The current svn version appears to
> work ok with the data and the procedure that you described.

Thanks Markus, cool - I can't get svn to work across my network and I'm 
a bit lazy so I'll wait for the next pre-release. No rush.

> 
>  > Incidentally, what are the chances of getting note-note links working so 
> 
> (afait it boils down to allowing an additional type string in one of
> the fields).

I think I know what you mean - you'd allow presumably a NOTE string in 
the xnote_type field of the t_xnote table. Though I think that would 
only allow for unidirectional links unless you were happy to let your 
backend try to keep two links updated (I believe this is sort of frowned 
upon in the relational DB world) or to search two indices, note_id and 
xref_id for a particular note_id (maybe okay but seems clumsy).

I could handle non-directional links outside of RefDB by automatically 
generating dummy references to group notes with but it's kind of messy, 
particularly as there's no real reason to group notes in groups bigger 
than 2 (since you could then group notes by linking them all to another, 
group note, anyway).

On the other hand, while non-directional links would be nice, 
unidirectional links would be just fine as far as I'm concerned. It 
would be up to the DB user to specify if he/she wanted a link going both 
ways.

As far as a GUI tree view on the data is concerned, well it may recurse 
sometimes, but that's just a consequence of choosing a tree to view a 
potentially cyclic directed (or undirected) graph.

Feel free to talk me out of it!

Peace
Damien

Re: [Refdb-devel] latex bibliographies with multiple databases

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

Markus Hoenicka writes:
 > 2) RIS input
 > We'd have to educate users to author their RIS datasets in UTF-8, and
 > to run RIS data from web sources (like Pubmed) through iconv before
 > adding them to RefDB. All it takes is to set the default input
 > encoding of refdbd for RIS data to UTF-8 (see above). Currently there
 > are no provisions to translate entities or LaTeX commands, but if used
 > correctly there should be no need to use such hacks. The result is, as
 > above, plain Unicode.
 > 

Actually we can still use ISO-8859-1 or whatever as the RIS input
format as refdbd internally converts it to UTF-8 if the database uses
this encoding. Forcing UTF-8 for RIS data actually makes only sense if
people use both bibtex and RIS data.

regards,
Markus

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

Re: [Refdb-devel] latex bibliographies with multiple databases

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

Hi David,

David Nebauer writes:
 > Yes, in my view the storage format is Unicode without markup:
 > 
 > 
 > BibTeX -------               ---------> DocBook
 >              |               |
 >              |               |
 > RIS ---------+--> STORAGE ----
 >              |   (Unicode)   |
 >              |               |
 > RISX ---------               ---------> LaTeX
 > 
 > 
 > 

I've done a little source code reading and testing in order to find
out how RefDB mangles these kinds of input and output data. My results
are as follows:

1) BibTeX input
bib2ris appears to work ok with UTF-8 encoded bibtex data. You can
import the resulting RIS data as long as the input encoding is set to
UTF-8 (the current default is ISO-8859-1, but it certainly makes sense
to change that). If your bibtex data is plain ASCII with foreign and
special characters encoded as LaTeX commands, the bib2ris output
should be sent through the new refdb_latex2utf8txt script. I don't
know whether it really has 100% coverage of the character-related
LaTeX command, but it is easy to extend if need arises. With this in
mind we can import bibtex data as plain Unicode.

2) RIS input
We'd have to educate users to author their RIS datasets in UTF-8, and
to run RIS data from web sources (like Pubmed) through iconv before
adding them to RefDB. All it takes is to set the default input
encoding of refdbd for RIS data to UTF-8 (see above). Currently there
are no provisions to translate entities or LaTeX commands, but if used
correctly there should be no need to use such hacks. The result is, as
above, plain Unicode.

3) risx input
I've rediscovered a nice feature of expat (which refdbd
uses to parse all incoming XML data). The output data of expat are
always UTF-8, with all entities expanded to their Unicode
equivalents. Thus no extra conversion step is required to get rid of
entities and to store plain Unicode.

4) SGML/XML output (bibliographies, db31/tei/html backends)
"<>&" are replaced with their corresponding entities. In addition, the
current code contains replacements for &mdash; &lsquo; and &rsquo;. I
know that I was asked to add these, but I can't remember the
context. I wonder whether it would make more sense to keep these
characters as Unicode.

5) LaTeX output
There are currently no attempts to escape LaTeX command
characters. I'm about to add this code.

6) other output (RIS, screen)
No replacements. If you retrieve data as UTF-8, you'll get what you
want.


As always, I might have missed some bordercases. If you experience a
different behaviour, please let me know.

One thing that should be discussed is how easy it is for RefDB users
to author UTF-8 data, be it RIS, bibtex, or XML. You can always insert
the numeric form into XML data (e.g. &#0x00B1) but I'm afraid this
won't work for the other data formats. As an Emacs user I've got Norm
Walsh's xmlunicode.el (http://nwalsh.com/emacs/xmlchars/) which allows
to select characters from a pop-up list or from the minibuffer with
entity-name completion, and which also defines an input mode which
offers on-the-fly replacement of entities. Is there similar support
available for other editors (vim, jedit) which should be mentioned in
the manual?

regards,
Markus

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

Re: [Refdb-devel] latex bibliographies with multiple databases

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

Hi David,

David Nebauer writes:
 >     latex2utf8txt  converts LaTeX files to UTF-8 text, removes line 
 > breaks from paragraphs

I used parts of this script to hack a tex2mail replacement. It isn't
more than a collection of regular expression substitutions which is to
be used as a post-processing filter of bib2ris output. I've added it
to the subversion repository, but it is not yet included into the
build system. Please test it against your data and modify it as
needed or let me know what else should be covered.

Either update your svn sources, or visit the svn web interface:

http://svn.sourceforge.net/viewcvs.cgi/refdb/refdb/trunk/scripts/refdb_latex2utf8txt?view=log

The script does the following:

- replace foreign characters encoded as {\..} constructs with their
  UTF-8 counterparts

- remove {\xy ...} commands, leaving only the enclosed text

- remove non-escaped curly brackets

- unescape escaped command characters: # $ % & ~ _ ^ \ { }

- convert the LaTeX dashes '--' and '---' to '-'

regards,
Markus

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