refdb-users — List for RefDB users

Re: [Refdb-users] Cannot create database in MySQL

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

Torsten Bronger writes:
 > Secondly, the name "references" is bad for the database because it
 > seems to be a reserved word or something like that (unfortunately,
 > at the same time it's a good name for a references DB ;-).  With
 > "biblio", it worked.

According to the MySQL manual "references" is a clause in the
"alter table" syntax, so it is indeed a reserved word. I'll add this
to the documentation as it is all too easy to get trapped here.

 > 
 > However, I run into trouble here and there because "deb
 > http://refdb.sourceforge.net/debian/svn testing main" gives me an
 > outdated version (from March 2007 or so).  Is it feasible to update
 > this?  If not, I'm highly probably able to install the SVN version.
 > :)
 > 

Unfortunately RefDB has to make do without a Debian maintainer. We
can't update the .debs unless someone "in the know"
volunteers. However, the svn version or the latest prerelease should
work fine. RefDB does not install stuff in weird places, and a "make
uninstall" should remove most traces of it from your system if you
ever want to get rid of it.

regards,
Markus

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

Re: [Refdb-users] Cannot create database in MySQL

[Torsten B. <br...@ph...>]

Hallöchen!

Markus Hoenicka writes:

> Torsten Bronger writes:
>
>>     CREATE DATABASE references CHARACTER SET 'utf8'
>> 1064: You have an error in your SQL syntax; check the manual that
>> corresponds to your MySQL server version for the right syntax to use near
>> references CHARACTER SET 'utf8'' at line 1
>
> Which mysql version are you using? I'd like to check why mysql
> complains about the syntax (which apparently works ok in versions
> 4.1 through 5.0).

I must correct myself.  First, I mixed up the MySQL version on two
of my machines.  The server runs with 5.0.51a.

Secondly, the name "references" is bad for the database because it
seems to be a reserved word or something like that (unfortunately,
at the same time it's a good name for a references DB ;-).  With
"biblio", it worked.

However, I run into trouble here and there because "deb
http://refdb.sourceforge.net/debian/svn testing main" gives me an
outdated version (from March 2007 or so).  Is it feasible to update
this?  If not, I'm highly probably able to install the SVN version.
:)

Tschö,
Torsten.

-- 
Torsten Bronger, aquisgrana, europa vetus
                   Jabber ID: tor...@ja...

Re: [Refdb-users] Cannot create database in MySQL

[Torsten B. <br...@ph...>]

Hallöchen!

Markus Hoenicka writes:

> Torsten Bronger writes:
>
>>     CREATE DATABASE references CHARACTER SET 'utf8'
>> 1064: You have an error in your SQL syntax; check the manual that
>> corresponds to your MySQL server version for the right syntax to
>> use near references CHARACTER SET 'utf8'' at line 1
>
> Which mysql version are you using?

I use MySQL 5.0.67.  What I changed from the default configuration
is:

default-storage_engine = innodb
character-set-server=utf8
collation-server=utf8_unicode_ci
init_connect='set collation_connection = utf8_unicode_ci;'

Tschö,
Torsten.

-- 
Torsten Bronger, aquisgrana, europa vetus
                   Jabber ID: tor...@ja...

[Refdb-users] Cannot create database in MySQL

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

Torsten Bronger writes:
 >     CREATE DATABASE references CHARACTER SET 'utf8'
 >     1064: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'references CHARACTER SET 'utf8'' at line 1

Which mysql version are you using? I'd like to check why mysql
complains about the syntax (which apparently works ok in versions 4.1
through 5.0).

regards,
Markus

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

[Refdb-users] Cannot create database in MySQL

[Torsten B. <br...@ph...>]

Hallöchen!

I installed RefDB 0.9.8 on an Ubuntu Server 8.04 running MySQL
(which was already there, as was an Apache).  The installation
showed no error messages, however, createdb fails with

    refdba: createdb references
    999:0 created:1 failed

The daemon says

    bronger@bob:~$ sudo refdbd -s -e 0 -l 7
    dbi_driver_dir went to:

    dbi is up using default driver dir
    Available libdbi database drivers:
    mysql
    sqlite
    Requested libdbi driver found
    Database directory:
    /var/lib/refdb/db
    application server started
    share extended notes by default
    use /tmp/refdbd_fifo19841 as fifo
    server waiting n_max_fd=4
    adding client 127.0.0.1 on fd 5
    server waiting n_max_fd=5
    try to read from client
    serving client on fd 5 with protocol version 5
    210-44-10-38
    send pseudo-random string to client
    parent removing client on fd 5
    server waiting n_max_fd=4
    createdb references -u root -w 07909**********
    dbi is up
    localhost
    root
    *****


    mysql
    /var/lib/refdb/db

    refdb
    connected to database server using database:
    refdb
    updated version file:
    /var/lib/refdb/db/DB_VERSION
    Main database looks ok:
    refdb
    localhost
    root
    *****


    mysql
    /var/lib/refdb/db
    UTF-8
    refdb
    connected to database server using database:
    refdb
    SELECT VERSION()
    CREATE DATABASE references CHARACTER SET 'utf8'
    1064: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'references CHARACTER SET 'utf8'' at line 1
    could not create reference database
    command processing done, finish dialog now
    child finished client on fd 5
    child exited with code 0
    server waiting n_max_fd=4

The MySQL database uses by default InnoDB with UTF8.

Can someone tell me what's going wrong?  Thank you!

Tschö,
Torsten.

-- 
Torsten Bronger, aquisgrana, europa vetus
                   Jabber ID: tor...@ja...

Re: [Refdb-users] svn install script issues

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

Hi Dan,

I can't comment about the script errors as I didn't write this one  
myself. I'll investigate as soon as time permits.

In any case, building from svn without that script is of course  
possible. All you need to do is to check out the sources:

svn co https://refdb.svn.sourceforge.net/svnroot/refdb/refdb/trunk refdb

This will create a new subdirectory refdb with the svn sources. cd  
into that directory, and run

./configure [your options]
make
make install

Whenever you want to update the sources, cd into the refdb directory and run

svn update

That's about it.

regards,
Markus

Quoting Daniel O'Donnell <dan...@ul...>:

> Hi all,
>
> I've been trying out the refdb-svn install script on an Ubuntu 8.04
> (i.e. debian variant) machine. I keep getting two errors after a
> successful build that I can't figure out:
>
>
>> sudo refdb-svn -h
>> /usr/local/bin/refdb-svn: 52: declare: not found
>> /usr/local/bin/refdb-svn: 559: Syntax error: "do" unexpected (expecting "}")
>
> (get the same whether I use sudo or not)
>
> I followed the instructions on the man pages and built a ~/.refdb-svnrc
> file with the appropriate debian peculiarities fixed, but still nothing.
>
> Anybody know what the issue is? Is there an easy way of building the svn
> version without the script?
>
> Thanks much!
>
> -dan
>
>
>
> --
> Daniel Paul O'Donnell, PhD
> Associate Professor of English
> Director, Digital Medievalist Project http://www.digitalmedievalist.org/
> Chair, Text Encoding Initiative http://www.tei-c.org/
>
> Department of English
> University of Lethbridge
> Lethbridge AB T1K 3M4
> Vox +1 403 329-2377
> Fax +1 403 382-7191
> Email: dan...@ul...
> WWW: http://people.uleth.ca/~daniel.odonnell/
>
>
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>



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

[Refdb-users] svn install script issues

[Daniel O'D. <dan...@ul...>]

Hi all,

I've been trying out the refdb-svn install script on an Ubuntu 8.04
(i.e. debian variant) machine. I keep getting two errors after a
successful build that I can't figure out:


> sudo refdb-svn -h
> /usr/local/bin/refdb-svn: 52: declare: not found
> /usr/local/bin/refdb-svn: 559: Syntax error: "do" unexpected (expecting "}")

(get the same whether I use sudo or not)

I followed the instructions on the man pages and built a ~/.refdb-svnrc
file with the appropriate debian peculiarities fixed, but still nothing.

Anybody know what the issue is? Is there an easy way of building the svn
version without the script?

Thanks much!

-dan



-- 
Daniel Paul O'Donnell, PhD
Associate Professor of English
Director, Digital Medievalist Project http://www.digitalmedievalist.org/
Chair, Text Encoding Initiative http://www.tei-c.org/

Department of English
University of Lethbridge
Lethbridge AB T1K 3M4
Vox +1 403 329-2377
Fax +1 403 382-7191
Email: dan...@ul...
WWW: http://people.uleth.ca/~daniel.odonnell/

Re: [Refdb-users] Ubuntu install question

[Dan O'D. <dan...@ul...>]

This of course is a real dependency, and hence not what I meant: I'd
hoped that 7.x was also possible, but I see it is not.

I've just built a clean box. On the weekend I'll try again the
installation and keep very careful notes.


On Mon, 2008-08-18 at 08:47 +0200, Markus Hoenicka wrote:
> Quoting dan...@ul...:
> 
> > I was wondering if it might not be a good idea to have a 'stable'   
> > branch of refdb--most of the dependency errors seem unimportant and   
> > I really wonder if the slightly older versions of the required files  
> >  that ship with ubuntu, for example, wouldn't in most cases work   
> > anyway. And it is not knowing which errors are important and which   
> > are not that causes me all the grief, any way.
> >
> 
> I'm afraid I'll need some more information about your dependency  
> hassles. IIRC the only dependency of RefDB in terms of libdbi versions  
> is that RefDB 0.9.6 through 0.9.9 require libdbi >= 0.8. Remember that  
> libdbi 0.7.3 which ubuntu apparently still ships is approx. three  
> years old. 0.7.3 does not support the extended character set encoding  
> stuff that RefDB has relied upon since about three years. The current  
> svn revisions of RefDB are built in a way that they can handle libdbi  
> versions 0.8.x through 1.0.x (not released yet, only available in cvs)  
> to avoid too strict version dependencies. That is, from my point of  
> view RefDB has been stable in terms of libdbi dependencies for about  
> three years and continues to do so - more than enough for packagers to  
> catch up.
> 
> Now in order to figure out why your builds fail, would you please list  
> the versions of libdbi, libdbi-drivers, and RefDB that you're trying  
> to install, including any configure settings that you apply. Also,  
> please append the error message (with sufficient context) that  
> indicates the build failure to your mail.
> 
> regards,
> Markus
> 
> 
> 
-- 
Daniel Paul O'Donnell
Chair, Text Encoding Initiative (http://www.tei-c.org/)
Director, Digital Medievalist Project
(http://www.digitalmedievalist.org/)
Associate Professor of English
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

vox: +1 (403) 329-2377
fax: +1 (403) 382-7191
email: dan...@ul...
homepage: http://people.uleth.ca/~daniel.odonnell/

Re: [Refdb-users] Ubuntu install question

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

Quoting dan...@ul...:

> I was wondering if it might not be a good idea to have a 'stable'   
> branch of refdb--most of the dependency errors seem unimportant and   
> I really wonder if the slightly older versions of the required files  
>  that ship with ubuntu, for example, wouldn't in most cases work   
> anyway. And it is not knowing which errors are important and which   
> are not that causes me all the grief, any way.
>

I'm afraid I'll need some more information about your dependency  
hassles. IIRC the only dependency of RefDB in terms of libdbi versions  
is that RefDB 0.9.6 through 0.9.9 require libdbi >= 0.8. Remember that  
libdbi 0.7.3 which ubuntu apparently still ships is approx. three  
years old. 0.7.3 does not support the extended character set encoding  
stuff that RefDB has relied upon since about three years. The current  
svn revisions of RefDB are built in a way that they can handle libdbi  
versions 0.8.x through 1.0.x (not released yet, only available in cvs)  
to avoid too strict version dependencies. That is, from my point of  
view RefDB has been stable in terms of libdbi dependencies for about  
three years and continues to do so - more than enough for packagers to  
catch up.

Now in order to figure out why your builds fail, would you please list  
the versions of libdbi, libdbi-drivers, and RefDB that you're trying  
to install, including any configure settings that you apply. Also,  
please append the error message (with sufficient context) that  
indicates the build failure to your mail.

regards,
Markus



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

Re: [Refdb-users] Ubuntu install question

[<dan...@ul...>]

I was wondering if it might not be a good idea to have a 'stable' branch of refdb--most of the dependency errors seem unimportant and I really wonder if the slightly older versions of the required files that ship with ubuntu, for example, wouldn't in most cases work anyway. And it is not knowing which errors are important and which are not that causes me all the grief, any way.

-----Original Message-----

From:  "Markus Hoenicka" <mar...@mh...>
Subj:  Re: [Refdb-users] Ubuntu install question
Date:  Sun 17 Aug 2008 14:44
Size:  2K
To:  dan...@ul...
cc:  ri...@ma..., ref...@li...

Daniel Paul O'Donnell writes:
 > I spent all day today on a fresh ubuntu install, but come to grief with
 > the libdbd dependencies. I simply can't get a working version of the 0.8
 > version and ubuntu ships with a 7.3 version. When building from source I
 > get a 
 > 
 > config.status: WARNING:  Makefile.in seems to ignore the --datarootdir
 > setting
 > 

AFAIK this warning is safe to ignore at this time, as it simply says
the Makefiles do not yet make use of a feature which was added to the
autotools just recently. I see this warning too on FreeBSD without
getting into trouble. This also explains why setting this variable
does not alter the results.

 > I've tried setting datarootdir, leaving it default, and nothing changes.
 > I've tried with and without --prefix set. I can see that the drivers are
 > in the right places, but I can never complete a build.

Just to make sure: do you manage to build and install libdbi and
libdbi-drivers 0.8.x?

What are exactly the error messages that indicate you can't build
RefDB? The only dependency at build time is a libdbi.a file in your
linker's search path. If you build libdbi from the sources without
fiddling with the prefix, the library files will end up in the
/usr/local hierarchy which, to the best of my knowledge, is not part
of the default library search path of Debian. You should be able to
fix this by setting LDFLAGS appropriately in your environment before
running configure and make.

 > 
 > I've tried building from source, and tried from the debs. Nothing works
 > for me.
 > 
 > I know this is a difficulty everybody is aware of and has tried to
 > address: but boy I wish there were an easier way to get refdb installed!
 > 

I had wished that packaging libdbi and RefDB would solve these
problems once and for all. But it seems were not there yet.

Please feel free to throw further details of your build problems my
way. I've got a spare box under my desk which currently runs a
stripped-down Debian. I could wipe that and use Ubuntu instead to help
you figure it out.

regards,
Markus

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

Re: [Refdb-users] Ubuntu install question

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

Daniel Paul O'Donnell writes:
 > I spent all day today on a fresh ubuntu install, but come to grief with
 > the libdbd dependencies. I simply can't get a working version of the 0.8
 > version and ubuntu ships with a 7.3 version. When building from source I
 > get a 
 > 
 > config.status: WARNING:  Makefile.in seems to ignore the --datarootdir
 > setting
 > 

AFAIK this warning is safe to ignore at this time, as it simply says
the Makefiles do not yet make use of a feature which was added to the
autotools just recently. I see this warning too on FreeBSD without
getting into trouble. This also explains why setting this variable
does not alter the results.

 > I've tried setting datarootdir, leaving it default, and nothing changes.
 > I've tried with and without --prefix set. I can see that the drivers are
 > in the right places, but I can never complete a build.

Just to make sure: do you manage to build and install libdbi and
libdbi-drivers 0.8.x?

What are exactly the error messages that indicate you can't build
RefDB? The only dependency at build time is a libdbi.a file in your
linker's search path. If you build libdbi from the sources without
fiddling with the prefix, the library files will end up in the
/usr/local hierarchy which, to the best of my knowledge, is not part
of the default library search path of Debian. You should be able to
fix this by setting LDFLAGS appropriately in your environment before
running configure and make.

 > 
 > I've tried building from source, and tried from the debs. Nothing works
 > for me.
 > 
 > I know this is a difficulty everybody is aware of and has tried to
 > address: but boy I wish there were an easier way to get refdb installed!
 > 

I had wished that packaging libdbi and RefDB would solve these
problems once and for all. But it seems were not there yet.

Please feel free to throw further details of your build problems my
way. I've got a spare box under my desk which currently runs a
stripped-down Debian. I could wipe that and use Ubuntu instead to help
you figure it out.

regards,
Markus

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

Re: [Refdb-users] Ubuntu install question

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

Quoting Markus Hoenicka <mar...@mh...>:

I can only advise you to build from
> the sources which should work without a hitch.
>

Forgot to mention that if you want to build RefDB from the sources,  
you'll also need the libdbd0-dev package.

regards,
Markus

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

Re: [Refdb-users] Ubuntu install question

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

Quoting ri...@ma...:

> Hello,
> If one looks here:
>
> http://refdb.sourceforge.net/debian/release/dists/
>
> there doesn't seem to be any package for "stable", which is why I used
> "testing" as the distro in my /etc/apt/sources.list
>

It is only now that I realize that the packages in this archive are  
outdated anyway. As with most open source projects, we depend on  
volunteers who build packages and/or archives for distros like Debian.  
Currently no one is actively maintaining these packages, so you'd  
actually have to build RefDB from the sources. This should work  
without any problems though.

As for the libdbi requirements, you'd best have a look at  
Debian-unstable which has the latest packages available. I don't know  
whether you can simply add Debian unstable to your sources.list. If  
not, you could still download the packages (libdbi0, libdbd-pgsql or  
libdbd-mysql) from the Debian site and install them with dpkg.

> It seems to me that simplifying the install process of refdb could
> increase its users base considerably. I was first interested in refdb
> about four years ago but felt quite intimidated by the installation
> process. I tried to get it running, but failed and gave up. Now four years
> later, and despite the fact that I use Emacs, that I would happily use the
> command line tools, that I manage postgresql databases and that I feel
> proficient using my Linux system, I still feel uncomfortable since I can't
> install the software on my machine after a few hours of trying various
> solutions. I consider myself a fairly proficient Linux user, not a
> developer, but I would welcome an easier way to get this running.
>

I do take this feedback seriously, and I'm feeling uncomfortable about  
not being able to provide a better user experience. But as I've  
mentioned above, we strongly depend on volunteers who provide  
packages. We had a very active maintainer for a while, but no one  
feels responsible at this time. I can only advise you to build from  
the sources which should work without a hitch.

regards,
Markus


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

Re: [Refdb-users] Ubuntu install question

[<ri...@ma...>]

Hello,
If one looks here:

http://refdb.sourceforge.net/debian/release/dists/

there doesn't seem to be any package for "stable", which is why I used
"testing" as the distro in my /etc/apt/sources.list


The dpkg tool uses .deb files, which worked great for me before for
installing things such as nx
(http://www.nomachine.com/download-package.php?Prod_Id=5). It does have a
force flag to allow installation despite unmet dependencies. So I
downloaded  the .deb file for refdb-server from here:

http://refdb.sourceforge.net/debian/release/dists/testing/main/source/refdb-server/


and ran dpkg with force flag to install it, and here is what I get:

**************************************************************************
bash>sudo dpkg -i refdb-server_0.9.8_i386.deb --ignore-depends=libdbd-sqlite
(Reading database ... 244125 files and directories currently installed.)
Preparing to replace refdb-server 0.9.8 (using
refdb-server_0.9.8_i386.deb) ...
Unpacking replacement refdb-server ...
dpkg: error processing --ignore-depends=libdbd-sqlite (--install):
 cannot access archive: No such file or directory
dpkg: dependency problems prevent configuration of refdb-server:
 refdb-server depends on libdbd-sqlite (>= 0.8.1-2); however:
  Package libdbd-sqlite is not installed.
 refdb-server depends on refdb-lib (>= 0.4.1-1); however:
  Package refdb-lib is not installed.
dpkg: error processing refdb-server (--install):
 dependency problems - leaving unconfigured
Errors were encountered while processing:
 --ignore-depends=libdbd-sqlite
 refdb-server
**************************************************************************

so it is still not working.

It seems to me that simplifying the install process of refdb could
increase its users base considerably. I was first interested in refdb
about four years ago but felt quite intimidated by the installation
process. I tried to get it running, but failed and gave up. Now four years
later, and despite the fact that I use Emacs, that I would happily use the
command line tools, that I manage postgresql databases and that I feel
proficient using my Linux system, I still feel uncomfortable since I can't
install the software on my machine after a few hours of trying various
solutions. I consider myself a fairly proficient Linux user, not a
developer, but I would welcome an easier way to get this running.

Thanks again for all the help.

Dan



> Martin Hicks writes:
>  > I think what I did on my sister's machine was to grab the debian
>  > packages from testing or unstable.
>  >
>
> That's what I'd suggest too. I'm not that familiar with the Debian
> tools, but at least dpkg should have a switch to force the
> installation regardless of unmet dependencies.
>
> regards,
> Markus
>
> --
> Markus Hoenicka
> mar...@ca...
> (Spam-protected email: replace the quadrupeds with "mhoenicka")
> http://www.mhoenicka.de
>

Re: [Refdb-users] Ubuntu install question

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

Martin Hicks writes:
 > I think what I did on my sister's machine was to grab the debian
 > packages from testing or unstable.
 > 

That's what I'd suggest too. I'm not that familiar with the Debian
tools, but at least dpkg should have a switch to force the
installation regardless of unmet dependencies.

regards,
Markus

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

Re: [Refdb-users] Ubuntu install question

[Martin H. <mo...@bo...>]

On Wed, Mar 19, 2008 at 03:28:02PM -0300, ri...@ma... wrote:
> Hi Markus,
> Thanks for the timely reply, that's why I love open source software.
> 
> I did mean libdbd-sqlite being version 0.7.1-3, not sqlite. I just checked
> for libdbd-pgsql and it is also at version 0.7.1-3.
> 
> I realise that this is not an Ubuntu mailing list, but I am stuck right
> now and don't know how to proceed. Here is what happens when I try to
> install refdb-server:
> 
> *************************************************************************
> bash>sudo aptitude install refdb-server
> 

I think what I did on my sister's machine was to grab the debian
packages from testing or unstable.

mh

-- 
Martin Hicks || mo...@bo... || PGP/GnuPG: 0x4C7F2BEE

Re: [Refdb-users] Ubuntu install question

[<ri...@ma...>]

Hi Markus,
Thanks for the timely reply, that's why I love open source software.

I did mean libdbd-sqlite being version 0.7.1-3, not sqlite. I just checked
for libdbd-pgsql and it is also at version 0.7.1-3.

I realise that this is not an Ubuntu mailing list, but I am stuck right
now and don't know how to proceed. Here is what happens when I try to
install refdb-server:

*************************************************************************
bash>sudo aptitude install refdb-server

Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading extended state information
Initializing package states... Done
Building tag database... Done
The following packages are BROKEN:
  refdb-server
The following NEW packages will be automatically installed:
  apache2-mpm-itk apache2-utils apache2.2-common docbook-xsl
docbook-xsl-doc-html libapr1
  libaprutil1 libperl-term-clui refdb-lib
The following NEW packages will be installed:
  apache2-mpm-itk apache2-utils apache2.2-common docbook-xsl
docbook-xsl-doc-html libapr1
  libaprutil1 libperl-term-clui refdb-lib
0 packages upgraded, 10 newly installed, 0 to remove and 0 not upgraded.
Need to get 4754kB of archives. After unpacking 23.5MB will be used.
The following packages have unmet dependencies:
  refdb-server: Depends: libdbd-sqlite (>= 0.8.1-2) but it is not installable
Resolving dependencies...
The following actions will resolve these dependencies:

Keep the following packages at their current version:
refdb-server [Not Installed]

Score is -9881

Accept this solution? [Y/n/q/?] Y
No packages will be installed, upgraded, or removed.
0 packages upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 0B of archives. After unpacking 0B will be used.
Do you want to continue? [Y/n/?] Y
Writing extended state information... Done
Reading package lists... Done
Building dependency tree
Reading state information... Done
Reading extended state information
Initializing package states... Done
Building tag database... Done
*************************************************************************

which basically does nothing.

Am I better off building from source here?
Cheers,

Daniel




>  > *************************************************************************
>  > ...
>  > The following packages have unmet dependencies:
>  >   refdb-server: Depends: libdbd-sqlite (>= 0.8.1-2) but it is not
> installable
>  > ...
>  > *************************************************************************
>  >
>  > sqlite on Ubuntu gutsy is at version 0.7.1-3.
>  >
>
> You mean libdbd-sqlite? Sqlite itself should rather be something like
> 3.5.x.
>
>
>  > I actually have both mysql and postgresql running on my machine. How
> can I
>  > configure refdb to use either of these instead of sqlite?
>  >
>
> The dependency on libdbd-sqlite is sort of a fake dependency. The
> RefDB package essentially depends on libdbi, but it is not functional
> without at least one database driver and its engine/library. Someone
> figured that it would be least intrusive to use sqlite as the default
> and added that as a dependency, just to make sure you can really start
> working.
>
> However, if you have one of mysql or postgresql installed anyway, you
> can safely ignore the dependency on libdbd-sqlite. You'll need the
> appropriate driver though (libdbd-mysql or libdbd-pgsql), and it may
> very well happen that these were not updated either.
>
> I don't know Ubuntu well enough, but as a Debian spin-off you should
> be able to install the latest Debian packages somehow. These are at
> 0.8.3 and should satisfy your dependencies.
>
> In any case, using a database engine other than sqlite is a
> post-install issue. I'm not familiar with what the Debian/Ubuntu
> install scripts do, but you should be able to run the refdb-init
> script again to set up the tool for a different database
> engine. Manual configuration and initialization is of course also
> possible as described in the manual. Feel free to get back if you need
> help at this point.
>
> regards,
> Markus
>
> --
> Markus Hoenicka
> mar...@ca...
> (Spam-protected email: replace the quadrupeds with "mhoenicka")
> http://www.mhoenicka.de
>

[Refdb-users] Ubuntu install question

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

Daniel Ricard writes:
 > *************************************************************************
 > ...
 > The following packages have unmet dependencies:
 >   refdb-server: Depends: libdbd-sqlite (>= 0.8.1-2) but it is not installable
 > ...
 > *************************************************************************
 > 
 > sqlite on Ubuntu gutsy is at version 0.7.1-3.
 > 

You mean libdbd-sqlite? Sqlite itself should rather be something like
3.5.x.


 > I actually have both mysql and postgresql running on my machine. How can I 
 > configure refdb to use either of these instead of sqlite?
 > 

The dependency on libdbd-sqlite is sort of a fake dependency. The
RefDB package essentially depends on libdbi, but it is not functional
without at least one database driver and its engine/library. Someone
figured that it would be least intrusive to use sqlite as the default
and added that as a dependency, just to make sure you can really start
working.

However, if you have one of mysql or postgresql installed anyway, you
can safely ignore the dependency on libdbd-sqlite. You'll need the
appropriate driver though (libdbd-mysql or libdbd-pgsql), and it may
very well happen that these were not updated either.

I don't know Ubuntu well enough, but as a Debian spin-off you should
be able to install the latest Debian packages somehow. These are at
0.8.3 and should satisfy your dependencies.

In any case, using a database engine other than sqlite is a
post-install issue. I'm not familiar with what the Debian/Ubuntu
install scripts do, but you should be able to run the refdb-init
script again to set up the tool for a different database
engine. Manual configuration and initialization is of course also
possible as described in the manual. Feel free to get back if you need
help at this point.

regards,
Markus

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

[Refdb-users] Ubuntu install question

[Daniel R. <ri...@ma...>]

Hello refdb-users,
I'm highly interested in using refdb but have encountered problems installing 
it on an i386 machine running Ubuntu gutsy.

I wanted to install using the packages in the Debian repository, so I added 
the following line to my /etc/apt/sources.list:

deb http://refdb.sourceforge.net/debian/svn testing main

and ran "sudo aptitude update". Now the different refdb packages are available 
for install but I keep getting a dependency problem with sqlite when trying 
to install refdb-server:

*************************************************************************
...
The following packages have unmet dependencies:
  refdb-server: Depends: libdbd-sqlite (>= 0.8.1-2) but it is not installable
...
*************************************************************************

sqlite on Ubuntu gutsy is at version 0.7.1-3.

I actually have both mysql and postgresql running on my machine. How can I 
configure refdb to use either of these instead of sqlite?

Thanks in advance for the help.

Daniel

[Refdb-users] Is refdb suitable for this?

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

Hi,

it depends. If you manage the "is referenced by" relationships
manually in your document, you could whip up something that does the
trick. refdb-publist [1] gets fairly close to what you need. The trick
is to assemble a document from several small bibliographies instead of
using just one like in a journal article.

However, if you want the bibliographic database to *store* these "is
referenced by" relationships, RefDB is not (yet) equipped to handle
this. I've suggested an improved data model [2] that would be able to
store such relationships, but this is not yet implemented.

Feel free to get back with more detailed questions if you feel that
RefDB is useful for your task.

regards,
Markus

[1] http://refdb.sourceforge.net/doc.html#refdb-publist
[2] http://refdb.sourceforge.net/rbib.html

Peter Elias writes:
 > Hello,
 > 
 > I plan to create and maintain a database of publications and citations 
 > in a small scientific institution. The database should list publications 
 > written by institution members and also publications which contain 
 > references to these publications. I need the ability to retrieve and 
 > format the output like this:
 > 
 > publication [...] is cited in:
 >    [1] ...
 >    [2] ...
 > publication [...] is cited in:
 >    [3] ...
 > etc.
 > 
 > Is refdb a suitable tool for this task? After looking to refdb manual, I 
 > was not able to tell.
 > 
 > Thanks,
 > Peter
 > 
 > -------------------------------------------------------------------------
 > This SF.net email is sponsored by: Microsoft
 > Defy all challenges. Microsoft(R) Visual Studio 2008.
 > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
 > _______________________________________________
 > Refdb-users mailing list
 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-users

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

[Refdb-users] Is refdb suitable for this?

[Peter E. <pet...@up...>]

Hello,

I plan to create and maintain a database of publications and citations 
in a small scientific institution. The database should list publications 
written by institution members and also publications which contain 
references to these publications. I need the ability to retrieve and 
format the output like this:

publication [...] is cited in:
   [1] ...
   [2] ...
publication [...] is cited in:
   [3] ...
etc.

Is refdb a suitable tool for this task? After looking to refdb manual, I 
was not able to tell.

Thanks,
Peter

[Refdb-users] experimental RTF support

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

Hi,

I've added some information about the experimental RTF support as well
as some example files to the RefDB homepage:

http://refdb.sourceforge.net/rtf.html

regards,
Markus

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

[Refdb-users] ANN: refdb-1.0.0-pre1 available for testing

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

Hi,

I've finished and uploaded a new prerelease of RefDB:

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

The full list of changes is appended below. I'd like to highlight
three noteworthy changes in this release:

1) RefDB now supports (with minor glitches) popular bibliography
   styles like AMA, APA, Chicago, Harvard, MLA, and Turabian

2) RefDB now supports bibliographies for RTF documents. The procedure
   is explained in the manual shipped with the prerelease, but in
   brief it works as follows: refdbnd creates a Makefile and a
   skeleton RTF document. Insert citations like [[Miller1999-X]] or
   [[Miller1999-X][Doe2001-X]] as plain text using your word
   processor, and then run "make". For an input file "foo.rtf" you'll
   get an output file "foo.refdb.rtf" which contains the bibliography
   and the formatted citations. I've tested this stuff with OpenOffice
   and AbiWord with success. I'd be glad to get feedback from other
   users as there are certainly some glitches.

3) RefDB now supports custom driver files for XML bibliographies. This
   is not as straightforward as you may think, but it is explained in
   the manual. The goal is to apply custom formatting to the parts of
   a XML document *not* managed by RefDB independent of other users,
   even independent of other documents.

There were no changes in the database schemas, so this release should
work with your existing 0.9.9 databases. The only problem you may run
into is the change of the content model of unpublished (UNPB)
references. Please see the UPGRADING file for instructions.

As always, feedback is more than welcome to further improve the tool.

regards,
Markus


Bugfixes:

- assorted stylesheet fixes for namespaced XML output

- fixed bibliography sorting order if author name is missing

- fixed a style export bug

- refdb-init no longer attempts to add schemas.xml as a style


Improvements:

- now creates bibliographies for RTF documents (still considered
  experimental)

- added styles for some common formats like AMA, APA, Chicago,
  Harvard, MLA, Turabian, as well as for the biomedical journals CHA-MC
  and JPET

- the web interface now supports result list paging, i.e. the query
  results and index searches no longer show the whole list of 5000+
  matches :-) but only a limited (configurable) number at a time. You
  can conveniently page forward or back using buttons.

- you can now provide driver files to the XML bibliography processing
  tools, e.g. to use custom formatting of the parts not managed by
  RefDB independent of other users on your system.


Backwards-incompatible changes:

- UNPB references are now considered not-yet-accepted INPR articles
  and thus use part data, just like JOUR. Previous versions have
  treated UNPB like an unpublished BOOK or RPRT. The current behaviour
  is more convenient for people who write more articles than books.


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

Re: [Refdb-users] TEI bibl, style data

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

Ralf Stephan writes:
 > > (http://refdb.sourceforge.net/doc.html), see especially chapter
 > > 10. RefDB will not process any <bibl> elements in the text.
 > 
 > Then, RefDB is not what I need. Do you know of a tool that could
 > at least help with it?
 > 

You should probably define what you expect from such a tool before you
can expect reasonable answers. But if you do not intend to store your
references in a database and rather want to keep them in the text,
RefDB is certainly not the tool you're looking for.

 > > Instead of doing all this manually, I'd suggest to have a look at
 > > refdbnd. Run this script in the directory which contains
 > > file.tei. When the script asks for the basename, you can pass the full
 > > name of your file. If all goes well, refdbnd will use appropriate
 > > values to process this document correctly. You can then just type
 > > "make pdf" or "make html" to process your document.
 > 
 > Both 'make pdf' and 'make html' give me
 > 
 > make: *** No rule to make target `file.short.xml', needed by `file.xml'.  Stop.
 > 
 > I only was curious what it would say.

I read from your previous paragraph that you do not intend to explore
this any further. Getting your special case to work might involve some
extra effort but I'm sure it is doable. However, at the risk of
disappointing your expectations: RefDB is not a tool that you throw a
random file at and magically get back a formatted bibliography. It
requires your document to stick to some conventions (within the limits
of the DTD/schema), and it may require some effort to familiarize
yourself with the usage and the limitations of the tool. So, as usual,
no free lunch :-(

regards,
Markus

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

Re: [Refdb-users] TEI bibl, style data

[Ralf S. <ra...@ar...>]

> (http://refdb.sourceforge.net/doc.html), see especially chapter
> 10. RefDB will not process any <bibl> elements in the text.

Then, RefDB is not what I need. Do you know of a tool that could
at least help with it?

> Instead of doing all this manually, I'd suggest to have a look at
> refdbnd. Run this script in the directory which contains
> file.tei. When the script asks for the basename, you can pass the full
> name of your file. If all goes well, refdbnd will use appropriate
> values to process this document correctly. You can then just type
> "make pdf" or "make html" to process your document.

Both 'make pdf' and 'make html' give me

make: *** No rule to make target `file.short.xml', needed by `file.xml'.  Stop.

I only was curious what it would say.


ralf