refdb-users — List for RefDB users

[Refdb-users] Problem: main database is too old or corrupt

[<do...@gm...>]

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Re: [Refdb-users] trouble installing refdb: make says 'refdb.cat.in: No such file or directory'

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

Ulf Martin <ulf...@we...> was heard to say:

> OK. Now I understand: you have to be in the *same* directory as the
> 'configure' file. Remember: I first made a 'build' directory, cd-ed into
> it and ran '../configure' (two dots). This is what I usually do, as you
> can clean up things with 'rm -r *' if necessary without doing harm to
> other files...
>

Ah I see. A while ago the sources and the build system were indeed in a state
where you could build RefDB outside of the source tree. I understand that this
is desirable, but obviously a few dependencies on absolute file locations crept
back in. I'll try to clean up the Makefiles as far as possible.

> Now 'make' runs much further, but still exits somewhere:
>
> UMac:~/Desktop/refdb/refdb-0.9.7-pre2 uma$ make
> [...]
> Making all in doc
> ../scripts/statgen.pl docbook > refdb-manual-statustable.xml
> Creating PDF manual...
> xsltproc -o refdb-manual.fo --nonet --xinclude
> ../doc/include/manual-fo.xsl refdb-manual.xml
> I/O error : Attempt to load network entity
> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
> warning: failed to load external entity
> "http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl"
> compilation error: file ../doc/include/manual-fo.xsl line 12 element import
> xsl:import : unable to load
> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
> make[1]: *** [refdb-manual.pdf] Error 5
> make: *** [all-recursive] Error 1
>
> Note: I *can* access the 'http://[...]/docbook.xsl' from the terminal:
>
> UMac:~/Desktop/refdb/refdb-0.9.7-pre2 uma$ curl
> http://docbook.sourceforge.net/release/xsl/current/fo/docbook.xsl
> <?xml version='1.0'?>
> <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
>                 xmlns:exsl="http://exslt.org/common"
>                 xmlns:fo="http://www.w3.org/1999/XSL/Format"
>                 xmlns:ng="http://docbook.org/docbook-ng"
>                 xmlns:db="http://docbook.org/ns/docbook"
>                 exclude-result-prefixes="db ng exsl"
>                 version='1.0'>
> [...]
>
> Also, the local the local 'docbook.xsl' was obviously found too:
>
> UMac:~/Desktop/refdb/refdb-0.9.7-pre2 uma$ ./configure
> --with-tei-xsl=/Users/uma/_/xml/tei/stylesheet
> --with-classpath-root=/Users/uma/_/bin/java/xmltools
> --with-db-server=mysql --with-docbook-xsl=/Users/uma/_/xml/docbook
> [...]
> checking for /Users/uma/_/xml/docbook/fo/docbook.xsl... yes
> DocBook XSL stylesheets found
> [...]
>

Please give me some leeway in all things related to the documentation. The
transition from SGML to XML was all but smooth, and there may still be rough
edges. Your best bet is to avoid building the docs at all. The prerelease
tarball contains the prebuilt documentation, and you better not touch it.

As for the specific error that you see, I believe that the XSLT processors
cannot execute the import statements without the help of an XML catalog. Either
I'd have to make the build system replace the URLs with absolute paths if you
use the --with-docbook-xsl switch, or you'd have to set up an XML catalog which
resolves the URLs to local paths.

regards,
Markus



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

Re: [Refdb-users] trouble installing refdb: make says 'refdb.cat.in: No such file or directory'

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

Ulf Martin <ulf...@we...> was heard to say:

> UMac:~/Desktop/refdb uma$ ls -al refdb-0.9.7-pre2.tar.gz
> -rw-r--r--  1 uma  uma  2711453  8 Feb 10:55 refdb-0.9.7-pre2.tar.gz
>

Great. When I check the archive here, I get this output:

$ tar -tzf refdb-0.9.7-pre2.tar.gz | grep refdb.cat.in
refdb-0.9.7-pre2/dsssl/refdb.cat.in

I don't see why make should complain that this file is missing on your box. Did
you manually verify that the file is unpacked and accessible?

regards,
Markus

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

Re: [Refdb-users] /usr/local/bin/runbib: line 319: 12645 Bus error

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

Jeremy Malcolm <Je...@Ma...> was heard to say:

> Do I need to update my style file when upgrading to 0.9.7-pre2?
>

Which version did you use previously?

> I get "/usr/local/bin/runbib: line 319: 12645 Bus error" on the command
> line when running runbib, and refdbd with logging turned up to 7 logs this:
>

This usually points to some sort of memory corruption. I checked the getref
command with valgrind while fixing the client-server dialog problem, but I'll
repeat this with the getbib command as soon as time permits. Creating
bibliographies (even with your style) works on my box.

regards,
Markus

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

Re: [Refdb-users] Adduser problem

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

Hi,

Z F <mai...@ya...> was heard to say:

> > This is probably the way to go. I'm not aware of any
> > incompatibilities that
> > might arise.
>
> I have forced the installation of libdbd-mysql without libmysqlclient12
> and made symbolic links libmysqlclient12 -> libmysqlclient15. After
> that
> when I start refdbd, it thinks that it loaded the mysql driver.
>
> When I do viewstat from refdba, I get this message from refdbd:
>
> connected to database server using database:
> refdb
> The requested variable type does not match what libdbi thinks it should
> be
> main database is too old or corrupt
>
>

I stand corrected. There do seem to be incompatibilities.

> Do you think it is fixable? Or should I simply install mysql4 for now?
> And the problem of upgrading to mysql5 will find me latter :-)
> Another thing is that one could build a debian package for
> libdbd-mysql.
> I have never built a debian package before. I could try...
>

I'm not sure whether using symlinks from libmysqlclient12 to 15 are really
appropriate to force the libdbi installation. The libdbi mysql driver was
linked agaist the 12.a file but is now dynamically linked against the 15.so
library. Apparently this is not going to work. I think you'd have to rebuild
the libdbi mysql driver using the new libmysqlclient15-dev package before
attempting to connect to mysqld 5.x.

I see two options:

1) downgrade MySQL to 4.x (mysql-server, mysql-client, libmysqlclient,
libmysqlclient-dev...)

2) Deinstall the RefDB and libdbi packages, upgrade everything cleanly to MySQL
5.x (same packages as above), and then build libdbi and RefDB from the sources.
FreeBSD and Debian are the platforms that saw most of the development and
packaging work ever done with RefDB and libdbi, so you should be able to build
both out of the box.

It is always appreciated if someone attempts to provide packages. David used to
be very helpful in the past but he seems to be occupied by other tasks right
now. libdbi and libdbi-drivers contain debian subdirectories which should allow
to build .debs with a minimum amount of fiddling. The corresponding files for
RefDB have not yet been integrated into the sources, unfortunately.

regards,
Markus

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

Re: [Refdb-users] trouble installing refdb: make says 'refdb.cat.in: No such file or directory'

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

Hi,

Ulf Martin <ulf...@we...> was heard to say:

> sed 's%<pkgdatadir>%/usr/local/share/refdb%' < refdb.cat.in > refdb.cat
> /bin/sh: line 1: refdb.cat.in: No such file or directory
> make[1]: *** [refdb.cat] Error 1
> make: *** [all-recursive] Error 1
>

Could you please check the size of the tar.gz archive that you downloaded? I
just tried to verify the presence of refdb.cat.in by downloading the
refdb-latest.tar.gz archive from the web page. The archive was truncated. I
downloaded it again using scp (I can do this as the project admin) and it came
out ok. The archive size should be 2711453 byte. I suspect SourceForge is
experiencing some http problems again.


>
> Here is the complete output of the ../configure && make run
> (another note: configure obviously does not find 'batik-rasterizer'
> although 'classpath-root' is explicitly specified and has a softlink
> 'batik-rasterizer.jar' to the 'batik-rasterizer.jar' proper):
>

You should not worry about this. batik-rasterizer is only required to build the
user manual from the XML sources, i.e. when you try to build RefDB from the CVS
sources. The tarball contains prebuilt documentations. In any case, the
configure script looks for a shell script called "batik-rasterizer" which in
turn invokes java with the proper CLASSPATH. The classpath-root setting is
relevant only for the java tools used in the XML transformations, as the
refdbxml shell script invokes the XML and FO processors directly and therefore
needs to know where the jars are.

regards,
Markus

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

[Refdb-users] Re: trouble installing refdb: make says 'refdb.cat.in: No such file or directory

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

Ulf Martin wrote:
> I have some trouble installing RefDB on a Mac (OS X 10.3.9):
> 'make' stops with this message:
> 
> sed 's%<pkgdatadir>%/usr/local/share/refdb%' < refdb.cat.in >
 > refdb.cat
> /bin/sh: line 1: refdb.cat.in: No such file or directory
> make[1]: *** [refdb.cat] Error 1
> make: *** [all-recursive] Error 1
> 
> Any tips? Tell me if you need more infos, please. Thank you all!
> (Installing this software is really a challenge for a stupid Mac user
> who has just started occupying himself with all this XML stuff...)

Try installing 0.9.7-pre1 instead, it seemed pretty stable on Mac though 
still with some bugs.  I'm having more trouble with pre2.

-- 
JEREMY MALCOLM <Je...@Ma...> - lawyer, IT consultant and actor.
Internet and Open Source specialist. Web site: http://www.malcolm.id.au.
Disclaimer: http://www.terminus.net.au/disclaimer.html. GPG key: finger.

[Refdb-users] /usr/local/bin/runbib: line 319: 12645 Bus error

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

Do I need to update my style file when upgrading to 0.9.7-pre2?

I get "/usr/local/bin/runbib: line 319: 12645 Bus error" on the command 
line when running runbib, and refdbd with logging turned up to 7 logs this:

SELECT ID, STYLE, BIBLIOFIRSTINDENT, BIBLIOBLOCKINDENT, FONTSIZE FROM 
refdb.CITSTYLE WHERE JOURNAL='Murdoch.Law.'
SELECT PUBTYPE, QSTYLE, XSTYLE, YSTYLE, ZSTYLE, QALTERNATESTYLE, 
XALTERNATESTYLE, YALTERNATESTYLE, ZALTERNATESTYLE, PUBDATESTYLE, 
PUBDATESECSTYLE, PUBDATEALLSTYLE, TITLESTYLE, BOOKTITLESTYLE, 
SERIESTITLESTYLE, ALLTITLESTYLE, JOURNALNAMESTYLE, VOLUMESTYLE, 
ISSUESTYLE, PAGESSTYLE, PUBLISHERSTYLE, PUBPLACESTYLE, REFNUMBERSTYLE, 
QABBREVIATEFIRSTSTYLE, QABBREVIATESUBSEQSTYLE, XABBREVIATEFIRSTSTYLE, 
XABBREVIATESUBSEQSTYLE, YABBREVIATEFIRSTSTYLE, YABBREVIATESUBSEQSTYLE, 
ZABBREVIATEFIRSTSTYLE, ZABBREVIATESUBSEQSTYLE, 
QAUTHORNAMESNAMEFIRSTINITIALSTYLE, XAUTHORNAMESNAMEFIRSTINITIALSTYLE, 
YAUTHORNAMESNAMEFIRSTINITIALSTYLE, ZAUTHORNAMESNAMEFIRSTINITIALSTYLE, 
QAUTHORNAMESNAMEOTHERINITIALSTYLE, XAUTHORNAMESNAMEOTHERINITIALSTYLE, 
YAUTHORNAMESNAMEOTHERINITIALSTYLE, ZAUTHORNAMESNAMEOTHERINITIALSTYLE, 
SERIALSTYLE, ADDRESSSTYLE, USERDEF1STYLE, USERDEF2STYLE, USERDEF3STYLE, 
USERDEF4STYLE, USERDEF5STYLE, MISC1STYLE, MISC2STYLE, MISC3STYLE, 
NOTESSTYLE, ABSTRACTSTYLE, LINK0STYLE, LINK1STYLE, LINK2STYLE, 
LINK3STYLE, LINK4STYLE, PAGESPAGERANGESTYLE FROM refdb.REFSTYLE WHERE 
refdb.REFSTYLE.CITSTYLEID=0
An invalid or out-of-range index was passed to libdbi
CREATE TEMPORARY TABLE getbibtemp (id BIGINT NOT NULL 
AUTO_INCREMENT,dbname VARCHAR(64),orig_id BIGINT,entry_id 
BLOB,article_title BLOB,author_concat BLOB,periodical 
VARCHAR(255),volume VARCHAR(255),issue VARCHAR(255),startpage 
VARCHAR(255),pubyear SMALLINT,monthday VARCHAR(16),citation_pos 
INT,xref_pos INT,multi_id BLOB,sorted_pos INT DEFAULT 
1,author_abbrevlist BLOB,year_uni_suffix VARCHAR(16),title_as_author 
SMALLINT DEFAULT 0,PRIMARY KEY (id))
XML parse error
An invalid or out-of-range index was passed to libdbi

-- 
JEREMY MALCOLM <Je...@Ma...> - lawyer, IT consultant and actor.
Internet and Open Source specialist. Web site: http://www.malcolm.id.au.
Disclaimer: http://www.terminus.net.au/disclaimer.html. GPG key: finger.

[Refdb-users] trouble installing refdb: make says 'refdb.cat.in: No such file or directory'

[Ulf M. <ulf...@we...>]

Dear RefDB Users!

I have some trouble installing RefDB on a Mac (OS X 10.3.9):
'make' stops with this message:

sed 's%<pkgdatadir>%/usr/local/share/refdb%' < refdb.cat.in > refdb.cat
/bin/sh: line 1: refdb.cat.in: No such file or directory
make[1]: *** [refdb.cat] Error 1
make: *** [all-recursive] Error 1

Any tips? Tell me if you need more infos, please. Thank you all!
(Installing this software is really a challenge for a stupid Mac user
who has just started occupying himself with all this XML stuff...)

Cheers, Ulf.

Here is the complete output of the ../configure && make run
(another note: configure obviously does not find 'batik-rasterizer'
although 'classpath-root' is explicitly specified and has a softlink
'batik-rasterizer.jar' to the 'batik-rasterizer.jar' proper):

UMac:~/Desktop/refdb/refdb-0.9.7-pre2 uma$ mkdir build
UMac:~/Desktop/refdb/refdb-0.9.7-pre2 uma$ cd build
UMac:~/Desktop/refdb/refdb-0.9.7-pre2/build uma$ ../configure
--with-tei-xsl=/Users/uma/_/xml/tei/stylesheet
--with-classpath-root=/Users/uma/_/bin/java/xmltools
--with-db-server=mysql --with-docbook-xsl=/Users/uma/_/xml/docbook
checking build system type... powerpc-apple-darwin7.9.0
checking host system type... powerpc-apple-darwin7.9.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
Configuration files will assume mysql as database engine
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for openjade... /sw/bin/openjade
checking for bash... /bin/bash
checking for perl... /usr/bin/perl
checking for xsltproc... /usr/bin/xsltproc
checking for xmlcatalog... /usr/bin/xmlcatalog
checking for dtdparse... no
checking for dtdformat... no
checking for sgrep... no
checking for tidy... no
checking for batik-rasterizer... no
checking for tputs in -ltermcap... yes
checking for readline in -lreadline... yes
checking for libreadline version... new
checking for ld used by GCC... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for shared library run path origin... .././conf/config.rpath:
.././conf/config.rpath: No such file or directory
done
checking for iconv... yes
checking how to link with libiconv... -liconv
checking for library containing dlopen... none required
checking for library containing lt_dlopen... -lltdl
checking for dbi_initialize in -ldbi... yes
checking for library containing compress... -lz
checking for library containing setsockopt... none required
checking for library containing gethostbyname... none required
checking for XML_ParserCreate in -lexpat... yes
checking for bt_initialize in -lbtparse... yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking syslog.h usability... yes
checking syslog.h presence... yes
checking for syslog.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for pid_t... yes
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking return type of signal handlers... void
checking for strftime... yes
checking for working mkfifo... yes
checking for gethostname... yes
checking for select... yes
checking for socket... yes
checking for strcspn... yes
checking for strstr... yes
checking for strtoll... yes
checking for atoll... yes
checking for /Users/uma/_/xml/docbook/fo/docbook.xsl... yes
DocBook XSL stylesheets found
checking for /Users/uma/_/xml/tei/stylesheet/p4/fo/tei.xsl... yes
TEI XSL stylesheets found
checking for Perl version... 5.008001
checking for Perl module RefDB::Prefs... RefDB::Prefs
checking for Perl module XML::Parser... XML::Parser
checking for Perl module MARC::Record... MARC::Record
checking for Perl module MARC::Charset... MARC::Charset
checking for Perl module Text::Iconv... Text::Iconv
configure: creating ./config.status
config.status: creating src/Makefile
config.status: creating scripts/Makefile
config.status: creating etc/Makefile
config.status: creating doc/Makefile
config.status: creating dtd/Makefile
config.status: creating declarations/Makefile
config.status: creating examples/Makefile
config.status: creating styles/Makefile
config.status: creating phpweb/Makefile
config.status: creating dsssl/Makefile
config.status: creating dsssl/refdb/Makefile
config.status: creating dsssl/refdb/html/Makefile
config.status: creating dsssl/refdb/print/Makefile
config.status: creating dsssl/refdb/lib/Makefile
config.status: creating xsl/Makefile
config.status: creating xsl/refdb/Makefile
config.status: creating xsl/refdb/common-refdb/Makefile
config.status: creating xsl/refdb/docbk-refdb-xsl/Makefile
config.status: creating xsl/refdb/docbk-refdb-xsl/docbk-fo/Makefile
config.status: creating xsl/refdb/docbk-refdb-xsl/docbk-html/Makefile
config.status: creating xsl/refdb/docbk-refdb-xsl/docbk-xhtml/Makefile
config.status: creating xsl/refdb/docbk-refdb-xsl/docbk-lib/Makefile
config.status: creating xsl/refdb/tei-refdb-xsl/Makefile
config.status: creating xsl/refdb/tei-refdb-xsl/tei-fo/Makefile
config.status: creating xsl/refdb/tei-refdb-xsl/tei-html/Makefile
config.status: creating xsl/refdb/tei-refdb-xsl/tei-lib/Makefile
config.status: creating man/Makefile
config.status: creating Makefile
config.status: executing depfiles commands

Please check the above output for missing Perl modules. It is safe
to make and make install anyway, but some of the Perl scripts will
fail to run if the required modules are not installed. Please consult
the manual where to get the modules from.

If you manage to compile (or even run) RefDB on a not yet supported
platform or distribution, please do not hesitate to pride yourself
on this achievement. This is best done by sending an email to the
RefDB mailing list <ref...@li...> or to the
maintainer <mho...@us...>. Thanks.

Your configuration:
Database engine: mysql
will build clients
will build server
will build docs
UMac:~/Desktop/refdb/refdb-0.9.7-pre2/build uma$ make
Making all in declarations
make[1]: Nothing to be done for `all'.
Making all in dsssl
Making all in refdb
Making all in html
make[3]: Nothing to be done for `all'.
Making all in lib
make[3]: Nothing to be done for `all'.
Making all in print
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
make[2]: Nothing to be done for `all-am'.
sed 's%<pkgdatadir>%/usr/local/share/refdb%' < refdb.cat.in > refdb.cat
/bin/sh: line 1: refdb.cat.in: No such file or directory
make[1]: *** [refdb.cat] Error 1
make: *** [all-recursive] Error 1
UMac:~/Desktop/refdb/refdb-0.9.7-pre2/build uma$ make -v
GNU Make version 3.79, by Richard Stallman and Roland McGrath.
Built for powerpc-apple-darwin7.0
Copyright (C) 1988, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99
        Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

Report bugs to <bug...@gn...>.

UMac:~/Desktop/refdb/refdb-0.9.7-pre2/build uma$

Re: [Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Dear Markus,

--- Markus Hoenicka <mar...@mh...> wrote:

> Hi,
> 
> Z F <mai...@ya...> was heard to say:
> 
> > I indeed have two versions of libmysqlclient. I did not notice
> > it before. As it turns out, the libdbd-mysql debian package from
> >
> > refdb.sourceforge.net
> >
> > requires libmysqlclient12 (which is an old one). Maybe it is
> > a typo on the dependency list and the inteneded one should have
> > been libmysqlclient15? This would be the easiest solution :-)
> 
> Unfortunately it is not a typo. I'm not the maintainer of the Debian
> packages,
> but I was briefly involved in the discussion about which MySQL client
> library
> is the right one to link to. The Debian folks wanted 12 as the
> default MySQL
> version at that time was 4.x. We may have to create new packages that
> work with
> MySQL 5.x, but I can't do this myself. David, are you alive?
> 
> > Could you confirm/refute this? If I am right, I will simply
> > force the installation of libdbd-mysql without libmysqlclient12.
> >
> 
> This is probably the way to go. I'm not aware of any
> incompatibilities that
> might arise.

I have forced the installation of libdbd-mysql without libmysqlclient12
and made symbolic links libmysqlclient12 -> libmysqlclient15. After
that
when I start refdbd, it thinks that it loaded the mysql driver.

When I do viewstat from refdba, I get this message from refdbd:

connected to database server using database:
refdb
The requested variable type does not match what libdbi thinks it should
be
main database is too old or corrupt


mysql log says this:
060207 14:14:57       5 Connect     root@chaos on refdb
                      5 Query       SHOW CREATE DATABASE refdb
                      5 Query       SET NAMES 'ISO-8859-1'
                      5 Query       SELECT meta_dbversion from t_meta
                      5 Quit       

Do you think it is fixable? Or should I simply install mysql4 for now?
And the problem of upgrading to mysql5 will find me latter :-)
Another thing is that one could build a debian package for
libdbd-mysql.
I have never built a debian package before. I could try...


Lazar

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Re: [Refdb-users] Adduser problem

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

Hi,

Z F <mai...@ya...> was heard to say:

> I indeed have two versions of libmysqlclient. I did not notice
> it before. As it turns out, the libdbd-mysql debian package from
>
> refdb.sourceforge.net
>
> requires libmysqlclient12 (which is an old one). Maybe it is
> a typo on the dependency list and the inteneded one should have
> been libmysqlclient15? This would be the easiest solution :-)

Unfortunately it is not a typo. I'm not the maintainer of the Debian packages,
but I was briefly involved in the discussion about which MySQL client library
is the right one to link to. The Debian folks wanted 12 as the default MySQL
version at that time was 4.x. We may have to create new packages that work with
MySQL 5.x, but I can't do this myself. David, are you alive?

> Could you confirm/refute this? If I am right, I will simply
> force the installation of libdbd-mysql without libmysqlclient12.
>

This is probably the way to go. I'm not aware of any incompatibilities that
might arise.

>
> A side note. I can not understand how I could connect to the
> database using the root account. Now, actually, I can not :-)
>

I can't understand this either, unless your database root account was not
password-protected. Maybe MySQL 5.0 won't complain in this particular case.

regards,
Markus

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

Re: [Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Hello Markus,

--- Markus Hoenicka <mar...@mh...> wrote:

 
> That rings a bell. MySQL has changed the password hashing algorithm
> lately. I
> suspect you accidentally link against a 4.x client library while the
> server
> expects the passwords in the 5.0 format. Please check whether you
> need to
> upgrade your libmysqlclient and/or libmysqlclient-dev packages. You
> may also
> have two versions installed in parallel, so you may have to remove
> the older
> version. The MySQL manual has a few more options how to work around
> this
> problem, see here:
> 
> http://dev.mysql.com/doc/refman/5.0/en/old-client.html
> 

I indeed have two versions of libmysqlclient. I did not notice
it before. As it turns out, the libdbd-mysql debian package from 

refdb.sourceforge.net

requires libmysqlclient12 (which is an old one). Maybe it is
a typo on the dependency list and the inteneded one should have
been libmysqlclient15? This would be the easiest solution :-)
Could you confirm/refute this? If I am right, I will simply
force the installation of libdbd-mysql without libmysqlclient12.


A side note. I can not understand how I could connect to the
database using the root account. Now, actually, I can not :-)

Thanks for your help

Lazar


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Re: [Refdb-users] Adduser problem

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

Hi,

Z F <mai...@ya...> was heard to say:


> The mysql error message which I get when using refdbc to connect is
> this:
>
> 5 Connect     Client does not support authentication protocol requested
> by server; consider upgrading MySQL client
>
> I have mysql 5.0
>

That rings a bell. MySQL has changed the password hashing algorithm lately. I
suspect you accidentally link against a 4.x client library while the server
expects the passwords in the 5.0 format. Please check whether you need to
upgrade your libmysqlclient and/or libmysqlclient-dev packages. You may also
have two versions installed in parallel, so you may have to remove the older
version. The MySQL manual has a few more options how to work around this
problem, see here:

http://dev.mysql.com/doc/refman/5.0/en/old-client.html

regards,
Markus

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

Re: [Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Dear Markus

--- Markus Hoenicka <mar...@mh...> wrote:
> If you can connect through mysql --protocol=tcp but not with refdbc,
> you should
> see one of these error messages:
> 
> Access denied for user '%s'@'%s' to database '%s'
> Access denied for user '%s'@'%s' (using password: %s)
> 
> The latter message indicates whether or not a password was sent to
> mysqld. To
> the best of my knowledge MySQL also issues an error if you have a
> user account
> w/o password but try to connect with a password.

The mysql error message which I get when using refdbc to connect is
this:

5 Connect     Client does not support authentication protocol requested
by server; consider upgrading MySQL client

I have mysql 5.0

> If nothing else helps, could you please send me the results of
> 
> select * from db
> select * from host
> select * from user
> 
> after opening the database mysql as root?

The attached file contains the output of the commands above.
the host table is empty, the others have something...

Can you see where I made a mistake in configuration? :-)

Thanks for your kind help

Lazar

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[Refdb-users] ANN: refdb-0.9.7-pre2 available for download

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

Hi all,

please grab the latest prerelease at the usual location:

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

This prerelease was clearly triggered by the recently discovered bug
in the client/server dialog. See here for a description:

http://sourceforge.net/mailarchive/forum.php?thread_id=9641554&forum_id=1798

However, there were a few more changes that make a new prerelease seem
worthwhile (see below for a detailed list). A large part of these
changes are related to the manual which is now built from XML sources,
which are also used to build the man pages. The changes to the code
proper are fairly small and by no means of an experimental nature. Due
to the abovementioned bug I recommend to upgrade to this
prerelease. I'll try to wrap up a new release fairly soon unless the
prerelease causes any problems.

regards,
Markus


- the XML headers now contain a larger selection of predefined
  entities

- FIRSTSPCM (without a dot) was added to the *NAMEORDER values

- support for multi-head tex citations was added

- import and export fixes for CONF, HEAR, and ELEC types

- replaced SGML manual sources by XML sources

- replaced handcrafted man pages by DocBook output

- the logic of the configure switch to build docs was reversed: docs
  are now built by default (this is required to install the prebuilt
  docs), but if you run into problems when building from the CVS
  sources you can disable the docs by means of the --disable-docs
  switch

- fixed a crash in the bibliography generation code when an URL was
  missing

- print empty part title instead of none to make the output comply
  with the DTD

- fixed possible segfaults if the automatic keyword scan ran without
  any keywords

- fixed client/server dialog mishap in refdbc:getref, refdbc:getnote
  and getbib


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

[Refdb-users] Advisory: possible data loss during data export

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

Hi,

much to my regret I have to report a serious problem with the data
export from RefDB when using the getref command. A bug in the
client/server protocol implemented in 0.9.6-pre2 and later, 0.9.6
(release), and 0.9.7-preX may cause the client/server dialog to hang
if the transmitted datasets have a particular size (between 4096 and
4100 bytes). This affects all output formats, but is most likely to
occur in risx output as this format is the most verbose. Most RIS
datasets are smaller than 4096 byte.

The symptoms are an "error" entry in the refdbd log and a misleading
"ok" message in the refdbc client instead of a command summary when
the refdbc:getref command finishes. When making backups, please always
use RIS/risx *and* SQL dumps to be on the safe side.

I've fixed the faulty code, but I'd like to take my time to review
similar sections in the source code as other commands may be affected
as well. I'll update the CVS repository frequently in the next days,
but I'll announce a new prerelease as soon as I feel I've caught all
related problems.

regards,
Markus

-- 
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mar...@ca...
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Re: [Refdb-users] 0.9.6-pre2 to 0.9.6 update troubles

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

Markus Hoenicka writes:
 > Before doing weird things, I'd like to find out which datasets were lost and
 > why. The overall number of rows and size of data are not accurate enough to get
 > a clean picture. What I'd be interested in  is the number of datasets in t_refdb
 > in the databases regenerated from the SQL dump and from the XML dump. You can
 > find out yourself using the mysql client, but I'd suggest you send me both dump
 > files off-list for further analysis. I'll be able to convert the SQL dump to a
 > database that 0.9.6 can connect to, with the possible data loss mentioned
 > above. But from that we can probably move on.
 > 

Ok, resuscicating the data from the SQL dump was fairly trivial. It is
possible to build 0.9.6-pre2 with the current libraries, so I made a
RIS dump with this version, loaded it into a 0.9.7-pre2 database, and
made a risx dump to convert it to XML data after fixing the problem
mentioned below.

Not so trivial was the analysis of the problem. I suspected a memory
corruption but valgrind didn't think so. Finally I tracked down a
problem with the client/server protocol that caused the dialog to hang
if the length of a dataset sent by the server was between 4096 and
4100 bytes. Everything smaller and larger would work ok which is one
of the reasons why I didn't spot this problem earlier. I'll send an
advisory in a separate mail as this bug can cause data loss. Please
refer to this advisory for further information.

regards,
Markus

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

Re: [Refdb-users] 0.9.6-pre2 to 0.9.6 update troubles

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

Hi,

Per-Anders Glans <PA...@lb...> was heard to say:

> I figured the update from 0.9.6-pre2 to 0.9.6 should be a small one and
> fairly painless. Not so.

Actually no. There have been quite a few non-trivial changes in the database
schema. E.g. 0.9.6-pre3 introduced support for multiple UR and L1-L4 fields per
dataset which required an additional table in the reference databases.

> *  Used 'addref -t risx database.xml' in refdbc to repopulate the
> databases.
>
> Initially this looked fine, until I realised that not all references
> had been added...
>
> Looking through the backup files, I noticed that all the references
> from the .xml files seems to have been loaded. The problem must have
> occured when doing the dump from 0.9.6-pre2.
>

This comes close to a desaster for RefDB, because the last thing a database
should do is to lose data.

> To get around this problem I attempted to create one of the databases
> in refdba, but load the sql dump via the mysql client. The database
> repopulated by loading the xml file has 26559 rows, a Data length of
> 1.96 MB and an Index length of 1.14 MB. The database loaded from the
> sql dump has 35592 rows, a Data length of 2.68 MB and in Index length
> of 1.51 MB. Some references must have gotten lost when doing the
> risx dump, but they are probably present in the sql dump. However,
> when I try to connect to a database created by refdba, but populated
> from the sql dump, refdbc says
>
> refdbc: selectdb newdatabase
> not a RefDB database
>
> When the new database has been created, the listdb command in both
> refdba and refdbc lists it. After I've tried to populate it from the
> sql dump, the database is no longer listed.
>

This is the "correct" behaviour as refdbd checks the version stamp in t_meta and
finds out that the database format is not compatible with your currently
installed version of RefDB. As I've mentioned above, the schema has changed,
and just adding the SQL dump will not be able to recreate the structure
required for 0.9.6 databases. You could massage the SQL database sufficiently
to allow 0.9.6 to connect to it, but you'd lose all UR and L1-L4 data.

> Is there any way to make refdb talk to the (hopefully) complete
> database? What makes the database suddenly not be a RefDB database?
> Or is there another way to use the sql dump to get my complete set
> of references back?
>

This depends on the data. One strategy might be to manually change the database
that you created from the SQL dump in a way that 0.9.6 can connect to it, and
then update the references using the XML data. This would add the UR and L1-L4
data back to those datasets contained in the XML data.

Before doing weird things, I'd like to find out which datasets were lost and
why. The overall number of rows and size of data are not accurate enough to get
a clean picture. What I'd be interested in  is the number of datasets in t_refdb
in the databases regenerated from the SQL dump and from the XML dump. You can
find out yourself using the mysql client, but I'd suggest you send me both dump
files off-list for further analysis. I'll be able to convert the SQL dump to a
database that 0.9.6 can connect to, with the possible data loss mentioned
above. But from that we can probably move on.

regards,
Markus


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

Re: [Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

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

Jeremy Malcolm <Je...@Ma...> was heard to say:

> Yes, many thanks - though the reference that messed up your code was a
> fault on my part, now also corrected!
>

The upside is that this reference uncovered a serious bug in my code. Feel free
to throw more incorrect references at RefDB :-)

> s/\.<\/othername>/<\/othername>/g
> s/ --- /\&mdash;/
> s/\'<title/\&lsquo;<title/
> s/title>\'/title>\&rsquo;/
> s/ \(<title[ A-Za-z=\"]*>\)/ \1<emphasis>/
> s/<\/title>\([, <]\)/<\/emphasis><\/title>\1/
>

I don't recall all details of your formatting problems. I'm currently back to
using the Openjade/Jadetex toolchain for a few documents and had to find out
that italics and boldface work in HTML and RTF output, but not in PDF or
Postscript output. This points to an incompatibility between the current
DocBook stylesheets and Jadetex. The dsl driver files appear to work ok as the
RTF output does show italics and boldface properly. Can you confirm this? If
yes, I'd have to bug the docbook-apps folks.

regards,
Markus

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http://www.mhoenicka.de

Re: [Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

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

Markus Hoenicka wrote:
>  > <bibliomixed id="IDMALCOLM2005PRIVACY-ISSUES-" role="ELEC">
>  > 
> 
> This is indeed the dataset that caused the hiccup. It is an electronic
> citation without an URL (is that intended?). refdbd accidentally freed
> the query result in this case, screwing up a few things. While it
> still did generate a valid bibliography on FreeBSD, it is likely to
> crash on other systems.
> 
> In any case, the fix is simple. I've attached a diff for
> backend-dbiba.c. The fixed version is also available in CVS. Please
> let me know if this fixes your problem.

Yes, many thanks - though the reference that messed up your code was a 
fault on my part, now also corrected!

BTW, for all of the problems or limitations I experienced earlier (RefDB 
not italicising titles, not allowing the use of entities I needed, and 
inserting a period after the middle initials of authors), I have 
constructed workarounds using a very simple sed script through which I 
pipe basename.bib.sgml:

s/\.<\/othername>/<\/othername>/g
s/ --- /\&mdash;/
s/\'<title/\&lsquo;<title/
s/title>\'/title>\&rsquo;/
s/ \(<title[ A-Za-z=\"]*>\)/ \1<emphasis>/
s/<\/title>\([, <]\)/<\/emphasis><\/title>\1/

That means that RefDB is now working as well as I really need it to. :-)

-- 
JEREMY MALCOLM <Je...@Ma...> - lawyer, IT consultant and actor.
Internet and Open Source specialist. Web site: http://www.malcolm.id.au.
Disclaimer: http://www.terminus.net.au/disclaimer.html. GPG key: finger.

[Refdb-users] 0.9.6-pre2 to 0.9.6 update troubles

[Per-Anders G. <PA...@lb...>]

Hi Markus and list,

Thanks for all the hard work that's being put into this software package.
I have been running refdb for almost a year now and am generally very 
happy with it. 

I figured the update from 0.9.6-pre2 to 0.9.6 should be a small one and
fairly painless. Not so. I am running a Debian testing/unstable system
and I had the debianised version of 0.9.6-pre2 installed. libdbi is at
version 0.8.1-1. My sql server is MySQL 5.0. 

*  I backed up my databases by doing a 

refdbc: getref -t risx -o database.xml :ID:>0

on each of them.

*  I also dumped the databases via mysqldump

~$ mysqldump --opt database > database.sql

just in case.

*  I removed the refdb via

~$ sudo apt-get remove refdb

*  Configured, make && make install refdb-0.9.6

*  Quickly realised that the databases couldn't be used as they were,
but had to be recreated. Used mysql to drop them and refdba to 
recreate them.

*  Used 'addref -t risx database.xml' in refdbc to repopulate the 
databases.

Initially this looked fine, until I realised that not all references
had been added...  

Looking through the backup files, I noticed that all the references 
from the .xml files seems to have been loaded. The problem must have
occured when doing the dump from 0.9.6-pre2.

To get around this problem I attempted to create one of the databases 
in refdba, but load the sql dump via the mysql client. The database
repopulated by loading the xml file has 26559 rows, a Data length of
1.96 MB and an Index length of 1.14 MB. The database loaded from the 
sql dump has 35592 rows, a Data length of 2.68 MB and in Index length
of 1.51 MB. Some references must have gotten lost when doing the 
risx dump, but they are probably present in the sql dump. However,
when I try to connect to a database created by refdba, but populated
from the sql dump, refdbc says 

refdbc: selectdb newdatabase
not a RefDB database

When the new database has been created, the listdb command in both 
refdba and refdbc lists it. After I've tried to populate it from the 
sql dump, the database is no longer listed.

Is there any way to make refdb talk to the (hopefully) complete 
database? What makes the database suddenly not be a RefDB database?
Or is there another way to use the sql dump to get my complete set 
of references back?

Any help greatly appreciated.

Thanks,

Anders


-- 
Per-Anders Glans, Ph.D.
--------------------------------------------------------------------
Novel Materials Laboratory, Boston University Physics Department
Office: (510) 486-7336 (at the ALS, Lawrence Berkeley Nat. Lab.)
mailto:gl...@bu...                      http://nml.bu.edu

Re: [Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

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

Hi,

Jeremy Malcolm writes:

 > Actually refdbib still exits with an error (refdbd just says "child 
 > exited with code 0", but I get "error" on refdbib's console).  It does 
 > now produce a partial bibliography file, though.  It gets as far as this 
 > bibliomixed entry before quitting:
 > 
 > <bibliomixed id="IDMALCOLM2005PRIVACY-ISSUES-" role="ELEC">
 > 

This is indeed the dataset that caused the hiccup. It is an electronic
citation without an URL (is that intended?). refdbd accidentally freed
the query result in this case, screwing up a few things. While it
still did generate a valid bibliography on FreeBSD, it is likely to
crash on other systems.

In any case, the fix is simple. I've attached a diff for
backend-dbiba.c. The fixed version is also available in CVS. Please
let me know if this fixes your problem.

regards,
Markus

Re: [Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

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

Hi Jeremy,

Jeremy Malcolm writes:
 > Good point - it seems to fail as soon as you have 128 entries or more. 
 > That's why I didn't get the error until I had completed another chapter 
 > with more references in it!  I'm using MySQL and so this sounds very 
 > much like a TINYINT problem to me, however there are no TINYINTs in my 
 > databases...

I can reproduce the problem here, but I see different
error messages. I don't get a libdbi error but only RefDB
errors. However, the problem also occurs at dataset 128 when using
your test data.

You've got a nice hypothesis, but the number 128 seems to be a funny
coincidence. refdbd stumbles over the citation key
"IETF2005SENDER-ID-AUTH". One obscure and under-documented feature
of RefDB is that you can generate bibliographies from data in
different databases. For references from non-default databases the ID
value must be preceded by the database name and a dash. E.g.

otherdb-IDIETF2005

specifies a dataset with the citation key IETF2005 in the database
"otherdb".

Going back to your data, refdbd thinks that "IDIETF2005SENDER" is the
database to pull the reference with the citation key "-AUTH"
from. This has to fail miserably unless you happen to have a database
and a dataset with these names.

I recommend to avoid the string "-ID" in your citation keys to work
around this problem. I'll try to figure out whether refdbd can
generate a somewhat more helpful error message.

regards,
Markus

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

Re: [Refdb-users] new (potental) user with problems (debian/sid)

[Dot D. <do...@gm...>]

On 2/1/06, Z F <mai...@ya...> wrote:
> Dear Dot Deb,
>
> Try installing the libreadline4 manually either by
> apt-get install libreadline4 or download the package and use
> dpkg -i packagename.
>
> Debian unstable has libreadline4 version 4.3-18
> With best wishes,
>
> Lazar

=09Uhmmm, I'm probably missing something but ...
=09this is what I get from my box:

krsna:~# apt-get update
Get:1 http://http.us.debian.org sid Release.gpg [189B]
Hit http://http.us.debian.org sid Release
Hit http://http.us.debian.org sid/main Packages
Hit http://http.us.debian.org sid/contrib Packages
Hit http://http.us.debian.org sid/non-free Packages
Fetched 1B in 1s (1B/s)
Reading package lists... Done
krsna:~# apt-get install libreadline4
Reading package lists... Done
Building dependency tree... Done
Package libreadline4 is not available, but is referred to by another
package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
  readline-common
E: Package libreadline4 has no installation candidate
krsna:~#

=09Any idea?

=09augh

Re: [Refdb-users] new (potental) user with problems (debian/sid)

[Z F <mai...@ya...>]

Dear Dot Deb,

Try installing the libreadline4 manually either by
apt-get install libreadline4 or download the package and use
dpkg -i packagename.

Debian unstable has libreadline4 version 4.3-18
With best wishes,

Lazar

--- Dot Deb <do...@gm...> wrote:

>         Hi everybody,
> 
>         I'm new to this list and I start with an installation
> problem.
> 
>         I wanted to install refdb on a debian/sid but I came across a
>         problem since the beginning. Here is briefly what I did:
> 
>         1. put refdb repositories in /etc/apt/sources.list
> deb http://refdb.sourceforge.net/debian/release unstable main
> deb http://refdb.sourceforge.net/debian/addons unstable main
> 
>         2. apt-get update + apt-get install refdb
> [...]
> The following packages have unmet dependencies:
>   refdb: Depends: libreadline4 (>= 4.3-1) but it is not installable
> E: Broken packages
> 
>         I know that in debian/sid libreadline4 is replaced by
>         readline-common: apt-get install libreadline4, says:
> [...]
> However the following packages replace it:
>   readline-common
> 
>         Is it possible for the debian package maintainer to update
> this
>         information?
> 
>         Thank you,
>         augh
> 
> 
> -------------------------------------------------------
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> 


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