refdb-users — List for RefDB users

Re: [Refdb-users] ANN: refdb-0.9.8-pre2 available

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

Hi,

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

 > Build dies horribly on my system when making refdbdgetref:

Big oops. The file was lacking two includes which I've added
now. Could you please test revision 141?

regards
Markus

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

Re: [Refdb-users] ANN: refdb-0.9.8-pre2 available

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

Hi Markus,

> I've uploaded yet another prerelease of RefDB, built from repository ve=
rsion 140.

Build dies horribly on my system when making refdbdgetref:
-------------------------------------------------------------------------=
-------------
david@hezmana:refdb-0.9.8-pre2$ ./autogen.sh
/usr/share/aclocal/libmcrypt.m4:17: warning: underquoted definition of=20
AM_PATH_LIBMCRYPT
run info '(automake)Extending aclocal'
or see http://sources.redhat.com/automake/automake.html#Extending%20acloc=
al
/usr/share/aclocal/libart.m4:11: warning: underquoted definition of=20
AM_PATH_LIBART
/usr/share/aclocal/glib.m4:8: warning: underquoted definition of=20
AM_PATH_GLIB
david@hezmana:refdb-0.9.8-pre2$ ./configure --prefix=3D/usr=20
--disable-clients --disable-doc s
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
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 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 ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for bash... /bin/bash
checking for ld used by GCC... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for shared library run path origin... /bin/sh:=20
=2E/conf/config.rpath: No such file or directory
done
checking for iconv... yes
checking for library containing dlopen... -ldl
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 how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/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 for socklen_t... yes
checking for ANSI C header files... (cached) 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
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

Configuration summary:
will build server
will build man pages

What you should do next:
- run "make" to build RefDB.
- run "make install" as root to install everything.
- create the main database and the configuration files. Either run the
refdb-init shell script as root, or peruse the handbook if you
prefer a manual installation.

david@hezmana:refdb-0.9.8-pre2$ make
Making all in etc

<snip.../>

if gcc -DPACKAGE_NAME=3D\"\" -DPACKAGE_TARNAME=3D\"\" -DPACKAGE_VERSION=3D=
\"\"=20
-DPACKAGE_STRING=3D\"\" -DPACKAGE_BUGREPORT=3D\"\" -DPACKAGE=3D\"refdb\" =

-DVERSION=3D\"0.9.8-pre2\" -D_GNU_SOURCE=3D1 -DHAVE_ICONV=3D1 -DSTDC_HEAD=
ERS=3D1=20
-DHAVE_SYS_TYPES_H=3D1 -DHAVE_SYS_STAT_H=3D1 -DHAVE_STDLIB_H=3D1=20
-DHAVE_STRING_H=3D1 -DHAVE_MEMORY_H=3D1 -DHAVE_STRINGS_H=3D1=20
-DHAVE_INTTYPES_H=3D1 -DHAVE_STDINT_H=3D1 -DHAVE_UNISTD_H=3D1=20
-DHAVE_SOCKLEN_T=3D1 -DSTDC_HEADERS=3D1 -DHAVE_FCNTL_H=3D1 -DHAVE_LIMITS_=
H=3D1=20
-DHAVE_SYS_FILE_H=3D1 -DHAVE_SYS_TIME_H=3D1 -DHAVE_SYS_IOCTL_H=3D1=20
-DHAVE_SYSLOG_H=3D1 -DHAVE_UNISTD_H=3D1 -DTIME_WITH_SYS_TIME=3D1=20
-DRETSIGTYPE=3Dvoid -DHAVE_STRFTIME=3D1 -DHAVE_MKFIFO=3D1 -DHAVE_GETHOSTN=
AME=3D1=20
-DHAVE_SELECT=3D1 -DHAVE_SOCKET=3D1 -DHAVE_STRCSPN=3D1 -DHAVE_STRSTR=3D1 =

-DHAVE_STRTOLL=3D1 -DHAVE_ATOLL=3D1 -I. -I. -DSYSCONFDIR=3D\"/usr/etc/ref=
db\"=20
-DULLSPEC=3D\"%llu\" -g -O2 -MT refdbdgetref.o -MD -MP -MF=20
".deps/refdbdgetref.Tpo" -c -o refdbdgetref.o refdbdgetref.c; \
then mv -f ".deps/refdbdgetref.Tpo" ".deps/refdbdgetref.Po"; else rm -f=20
".deps/refdbdgetref.Tpo"; exit 1; fi
refdbdgetref.c: In function =91assemble_author_subselect=92:
refdbdgetref.c:96: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:100: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:143: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:227: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c: In function =91assemble_keyword_subselect=92:
refdbdgetref.c:390: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:473: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c: In function =91assemble_link_subselect=92:
refdbdgetref.c:649: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:732: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c: In function =91getref=92:
refdbdgetref.c:995: warning: incompatible implicit declaration of=20
built-in function =91strlen=92
refdbdgetref.c:1076: warning: incompatible implicit declaration of=20
built-in function =91strncpy=92
refdbdgetref.c:1295: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1298: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1301: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1304: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1307: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1406: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1411: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1414: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1419: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1463: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1466: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1469: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1472: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1573: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1578: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1582: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1586: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1694: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1697: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1700: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1816: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1822: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1939: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1942: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1945: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1961: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1964: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:1967: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:2320: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:2442: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:2446: warning: incompatible implicit declaration of=20
built-in function =91strcpy=92
refdbdgetref.c:2449: warning: incompatible implicit declaration of=20
built-in function =91strstr=92
refdbdgetref.c:2483: warning: incompatible implicit declaration of=20
built-in function =91strdup=92
refdbdgetref.c:2645: warning: passing argument 2 of =91iconv=92 from=20
incompatible pointer type
refdbdgetref.c:2646: error: =91errno=92 undeclared (first use in this fun=
ction)
refdbdgetref.c:2646: error: (Each undeclared identifier is reported only =

once
refdbdgetref.c:2646: error: for each function it appears in.)
refdbdgetref.c:2646: error: =91EILSEQ=92 undeclared (first use in this fu=
nction)
refdbdgetref.c:2649: error: =91E2BIG=92 undeclared (first use in this fun=
ction)
refdbdgetref.c:2652: error: =91EINVAL=92 undeclared (first use in this fu=
nction)
make[2]: *** [refdbdgetref.o] Error 1
make[2]: Leaving directory `/home/david/tmp/temp/refdb-0.9.8-pre2/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/david/tmp/temp/refdb-0.9.8-pre2/src'
make: *** [all-recursive] Error 1
david@hezmana:refdb-0.9.8-pre2$
-------------------------------------------------------------------------=
-------------

Regards,
David.

[Refdb-users] ANN: refdb-0.9.8-pre2 available

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

Hi,

I've uploaded yet another prerelease of RefDB, built from repository
version 140:

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

The bugfixes and improvements are listed below. Another reason for
this prerelease is that I've upgraded my development platform to
FreeBSD 6.1. As we've seen in the past, upgrades of the autotools
sometimes cause build failures on other platforms. I'd like to
encourage everyone with a little time on their hands to build both the
prerelease archive as well as the SVN version 140 to identify these
build problems as early as possible.

regards,
Markus

Bugfixes:

- queries for UR and L1-L4 fields now work again

- en2ris now properly imports the start and end page information from
  newer EndNote versions

- strings extending the length of limited size fields in t_refdb are
  now properly truncated during data import


Improvements:

- the refdba:listuser command now checks for the required database
  argument

- improved manpage layout by using new DocBook stylesheet capabilities
  when available, and workarounds for older stylesheet versions

- configure now simplifies the task of building modularized RefDB
  packages. You can now build server, clients, and doc packages
  separately. Additionally, you can switch off building docs and
  manpages to build the RefDB binaries from the SVN sourceson systems
  without an XML/DocBook toolchaiin

- the code that generates citation keys from author names was improved
  by using iconv to transliterate foreign characters. 



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

[Refdb-users] FYI - docbook-xsl 1.70.1 now in Debian testing

[Michael(tm) S. <sm...@xm...>]

Thanks to an non-maintainer upgrade by Daniel Leidert, there's now
an up-to-date Debian package of the DocBook XSL stylesheets.

  http://packages.debian.org/testing/text/docbook-xsl

Many fixes and improvements were made between v1.70.1 and the
previous version that was available for Debian (v1.68.1). So
upgrading is strongly recommended.

  --Mike

[Refdb-users] FYI - docbook-xsl 1.70.1 now in Debian testing

[Michael(tm) S. <sm...@si...>]

Thanks to an non-maintainer upgrade by Daniel Leidert, there's now
an up-to-date Debian package of the DocBook XSL stylesheets.

  http://packages.debian.org/testing/text/docbook-xsl

Many fixes and improvements were made between v1.70.1 and the
previous version that was available for Debian (v1.68.1). So
upgrading is strongly recommended.

  --Mike

[Refdb-users] ANN: new debian svn packages (refdb-doc temporarily unavailable)

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

The packages 'refdb-clients' and 'refdb-server' have been rebuilt to 
remove a dependency that was preventing their proper install.  Thanks to 
Dominik for catching the problem and reporting it.

The package 'refdb-doc' has been temporarily removed from the svn 
repository while a build problem is fixed.

Regards,
David.

[Refdb-users] ANN: Change in debian refdb dependencies

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

Until now a number of perl libraries required by RefDB were not provided 
as debian packages.  These libraries had to be installed by hand from an 
archive provided at <refdb.sourceforge.net/download.html> .  These perl 
libraries are now packaged in the debian package 'refdb-lib' which is 
part of the svn refdb repository.  The svn refdb-clients and 
refdb-server packages now depend on refdb-lib so the new package will be 
automatically installed next time you install/update refdb svn.

I believe all the requirements to run svn refdb have now been 
debianised.  Given the dependencies in place, to fully install refdb all 
you now need do is add the appropriate line to /etc/apt/sources.list and 
issue the command:
    apt-get install refdb-clients refdb-server

Add 'refdb-doc' to the package list if you want the documentation.

The pre-release refdb repository will be similarly modified next time 
Markus posts a new pre-release.

Regards,
David.

Re: [Refdb-users] RefDB::Log in debian-packages

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

Hi Dominik,

> which debian package provides the RefDB/Log.pm? Where is it installed? How 
> would I get this path into my @INC?

Until now there has been no debian package supplying RefDB/Log.pm 
(referred to as the RefDB::Log module in perl nomenclature).  Thanks for 
pointing out this defect.  You previously had to install it, along with 
some other perl modules, from the archive RefDB-perlmod.tar.gz made 
provided by Markus (follow links from 
http://refdb.sourceforge.net/download.html).

You were right to wonder what debian package contained this perl 
library.  Since it is required to run some of the tools in the refdb 
package it should be supplied in debian form, i.e., a debian package.

The RefDB::Log module (and other required perl modules) are now provided 
by the debian package 'refdb-lib'.  I will shortly make an announcement 
to the refdb-users list giving package details.

To explain the @INC variable I would have to write a mini-essay on Perl 
library installation and, not being a perl guru, I'd likely get it 
wrong.  Let the refdb-lib package handle it for you.

Regards,
David.

[Refdb-users] ANN: new svn refdb packages are split

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

New svn refdb packages (revision 127) are available from the usual refdb 
repository.

** IMPORTANT **
The svn version of refdb is now packaged into three debs:
    'refdb-clients',
    'refdb-server',  and
    'refdb-doc'.

This enables refdb to be installed easily as a distributed application.  
If you are running it on a standalone computer make sure to install both 
client and server packages.

The manual, tutorial and schema documentation are installed by the doc 
package.  Help indexing systems (such as 'dwww' or 'dhelp') will 
register this documentation under 'refdb-doc', not 'refdb' as with the 
previous unitary package.

All other refdb-related applications packaged as debs now depend only on 
the 'refdb-clients' package.  This one-off change in dependencies should 
be handled smoothly by any sufficiently sophisticated package manager 
('aptitude' is known to handle it without error).

The current pre-release version of refdb remains a unitary package.  The 
next pre-release will be packaged in a similar manner to the svn version.

Regards,
David.

[Refdb-users] en2ris drops end page

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

Hi,

Dominik Reusser writes:
 > I would like to import some endnote ris export into refdb.
 > 
 > I'm surprised that en2ris just drops the ending page from my entries e.g.:
 > 
 > endnote.ris contains:
 > SP  - 526-529 
 > en2ris produces:
 > SP  - 526
 > 

Unfortunately the EndNote RIS export is a bit whacky. The output
appears to depend on both the version and on the platform. I've
modelled en2ris after test data provided by a user who ran EndNote on
a Mac maybe two years ago. The test data contained this if a page
range was exported:

SP  - 526-529 
EP  - 526-529 

That is, both the start page and the end page tags contained the same
range, instead of single values. en2ris therefore removed the end
page from the first line, and the start page from the second line.

You're apparently using an EndNote version that does not show this bug
(although the export still does not make proper use of the EP
tag). I've changed the code so it always converts SP lines with a
range into a SP and an EP line. This way you won't lose the EP info
even if the original data contain only a single SP line. In case of
the data that contain both a SP and an EP line, you'd get a duplicate
EP line, but this would not cause any harm when adding the data to the
database.

regards,
Markus

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

[Refdb-users] en2ris drops end page

[Dominik R. <dre...@un...>]

I would like to import some endnote ris export into refdb.

I'm surprised that en2ris just drops the ending page from my entries e.g.:

endnote.ris contains:
SP  - 526-529=20
en2ris produces:
SP  - 526

Why dropping this piece of information, if it is in a valid format (255=20
characters) according to the manual? Yes, I see that this is not just the=20
starting page... Even better would be to create an end page entry (EP)  fro=
m=20
the number after the dash.=20

I ran sed on the initial file to fix this problem=20
(sed 's/^SP  - \([1-9]*\)-\([1-9]*\)/SP  - \1\nEP  - \2/')
which produces the EP entries.
I was quite surprised that en2ris removes these lines...

Is there any reason to this?

Regards
Dominik
=2D-=20
Dominik Reusser
Universit=C3=A4t Potsdam

Re: [Refdb-users] Out of memory

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

Jeremy Malcolm writes:
 > Thanks, you were right.  It wasn't running out of memory, it was that 
 > one of the new documents somehow didn't have a title. *kickself*
 > 

Do you remember the type of that reference? I reckon it qualifies as
a bug if RefDB returns an out of memory error because a reference
lacks a title.

regards,
Markus

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

Re: [Refdb-users] Out of memory

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

Markus Hoenicka wrote:
> 
> First of all you should make sure that your box is really running out of memory.
> Did you try and run "top" while transforming your document? This should give a
> clue whether RefDB really hits the ceiling.
> 
> If not, one of the publications that you added since the builds were still
> working may cause problems. Could you create a test document with those
> references that you added lately? Maybe it is a RefDB bug (or unexpected
> reference data or style data or whatever) rather than missing memory.

Thanks, you were right.  It wasn't running out of memory, it was that 
one of the new documents somehow didn't have a title. *kickself*

What I'll be looking into next is how to integrate RefDB support into 
DocBookWiki, which I'm using to host my thesis online (see 
http://www.malcolm.id.au/thesis/).  Since DocBookWiki doesn't support 
RefDB the references don't appear in the Wiki version, only in the 
downloads.  I'll post back here if I have any success.

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

[Refdb-users] RefDB rpm available for Mandriva

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

St=E9phane T=E9letch=E9a writes:
 > I've uploaded it yesterday but since Mandriva has suffered some hw=20=

 > failures (it was really warm in France the last two weeks), it may b=
e=20
 > delayed on some mirrors.
 >=20

I'd like to provide concise information on the RefDB web page how to
install RefDB on RPM-based Linuxes. Not being familiar with anything
Linuxish except Debian, I'd like to get some external help. Would you
like to provide something along the lines of:

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

which now includes usable instructions for Debian and FreeBSD. I'd
like to see a section about RPMs too. Any help is greatly appreciated.

regards,
Markus

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

Re: [Refdb-users] Out of memory

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

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

> What can I do, apart from getting more memory, about a fatal "out of
> memory" error from refdbib when formatting a largish (424 publications)
> bibliography?
>
> I'm using refdbd 0.9.7-pre4 on Mac OS X 10.3.9, which was working fine
> with a slightly smaller bibliography.
>

First of all you should make sure that your box is really running out of memory.
Did you try and run "top" while transforming your document? This should give a
clue whether RefDB really hits the ceiling.

If not, one of the publications that you added since the builds were still
working may cause problems. Could you create a test document with those
references that you added lately? Maybe it is a RefDB bug (or unexpected
reference data or style data or whatever) rather than missing memory.

If you're really running out of memory, I'd have to rethink the code that
creates the bibliography in order to send the data as chunks.

regards,
Markus

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

[Refdb-users] Out of memory

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

Hello again,

What can I do, apart from getting more memory, about a fatal "out of 
memory" error from refdbib when formatting a largish (424 publications) 
bibliography?

I'm using refdbd 0.9.7-pre4 on Mac OS X 10.3.9, which was working fine 
with a slightly smaller bibliography.

The last few lines the server printed on log level 7 were:

SELECT 
thesis.t_author.author_name,thesis.t_author.author_lastname,thesis.t_author.author_firstname,thesis.t_author.author_middlename,thesis.t_author.author_suffix,thesis.t_xauthor.xauthor_role 
FROM thesis.t_author, thesis.t_xauthor WHERE 
thesis.t_author.author_id=thesis.t_xauthor.author_id AND 
thesis.t_xauthor.xauthor_type='primary' AND thesis.t_xauthor.refdb_id=22 
ORDER BY t_xauthor.xauthor_position
out of memory
child exited with code 0

The last thing the client printed was "SERIESTITLE formatting failed".

Thanks.

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

[Refdb-users] RefDB::Log in debian-packages

[Dominik R. <dre...@un...>]

Hi,=20
which debian package provides the RefDB/Log.pm? Where is it installed? How=
=20
would I get this path into my @INC?

I get the following error:

$ en2ris theresa.en.ris > theresa.ris
Can't locate RefDB/Log.pm in @INC (@INC=20
contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /=
usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/l=
ocal/lib/site_perl .)=20
at /usr/bin/en2ris line 34.
BEGIN failed--compilation aborted at /usr/bin/en2ris line 34.


I've installed the following

$ dpkg -l *refdb*
Desired=3DUnknown/Install/Remove/Purge/Hold
| Status=3DNot/Installed/Config-files/Unpacked/Failed-config/Half-installed
|/ Err?=3D(none)/Hold/Reinst-required/X=3Dboth-problems (Status,Err:upperca=
se=3Dbad)
||/ Name             Version          Description
+++-=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D-=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D-=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D
ii  libperl-refdb-ca 1.1-1            Provides methods used by RefDB da
ii  libperl-refdb-ma 1.2-1            Provides methods used by RefDB sty
ii  refdb            0.9.8-pre1-1     Reference database and bibliography t
ii  refdb-cache      1.1-1            RefDB reference database cache for ra
un  refdb-makestyle  <none>           (no description available)

Regards
Dominik

=2D-=20
Dominik Reusser
Universit=C3=A4t Potsdam

Re: [Refdb-users] getref hangs

[Dominik R. <dre...@un...>]

Hi,

Am Thursday, 10. August 2006 12:52 schrieb Markus Hoenicka:
> Hi,
>
> Dominik Reusser <dre...@un...> was heard to say:
> > > Could you please provide the exact command that you issued to invoke
> > > getref?
> >
> > either getref
>
> This one is definitely going to hang. If you don't provide an argument,
> refdbc will attempt to read a query string from stdin, which makes you
> think RefDB hangs.
>
> > or getref :ID:=7
> > or getref :ID:<5
>
> But these should of course work ok. If they don't, there is something
> wrong.
>
> > Linux aare 2.6.17-1-686 #1 SMP Sat Jul 29 15:32:47 UTC 2006 i686
> > GNU/Linux
>
> [...]
>
> > serverip	localhost
> > dbsport
> > dbserver	mysql
>
> This is the only weird thing I've found in your config. dbsport should not
> be empty. Did you remove the correct value (3306) manually, or did the
> build system fail somehow to provide the correct value? I don't think this
> explains your getref failures, but I'd be surprised if this won't screw up
> things eventually.

I corrected the dpsport entry and after rebooting, the problem was fixed.

Thank you for your support
Dominik

Re: [Refdb-users] getref hangs

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

Hi,

Dominik Reusser <dre...@un...> was heard to say:

> > Could you please provide the exact command that you issued to invoke
> > getref?
>
> either getref

This one is definitely going to hang. If you don't provide an argument, refdbc
will attempt to read a query string from stdin, which makes you think RefDB
hangs.

> or getref :ID:=7
> or getref :ID:<5
>

But these should of course work ok. If they don't, there is something wrong.

> Linux aare 2.6.17-1-686 #1 SMP Sat Jul 29 15:32:47 UTC 2006 i686 GNU/Linux
[...]
> serverip	localhost
> dbsport
> dbserver	mysql

This is the only weird thing I've found in your config. dbsport should not be
empty. Did you remove the correct value (3306) manually, or did the build
system fail somehow to provide the correct value? I don't think this explains
your getref failures, but I'd be surprised if this won't screw up things
eventually.

Your configuration does look ok otherwise, so I'm at a loss what is going wrong
here. Has anyone else seen similar failures before? Specifically when using a
Linux SMP kernel?

The only additional debug info that you could provide is if you run both refdbc
and refdbd with log level 7. Does the client provide any additional information
if you run getref?

If this does not get us any further, is there a chance to provide a ssh login on
your box? A regular user account is all I'd need to have a closer look using
gdb.

regards,
Markus


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

Re: [Refdb-users] getref hangs

[Dominik R. <dre...@un...>]

Am Wednesday, 9. August 2006 23:21 schrieb Markus Hoenicka:
> Hi,
>
> Dominik Reusser writes:
>  > And this is the corresponding log file (getau first, which works, then
>  > getref which just hangs):
>
> Could you please provide the exact command that you issued to invoke
> getref?=20

either getref=20
or getref :ID:=3D7
or getref :ID:<5

> It is not clear from the log what you were asking for. Last=20
> time the getref command was reported to hang on this list turned out
> to be a user error. Could you please provide the output of refdb-bug
> as well?

Linux aare 2.6.17-1-686 #1 SMP Sat Jul 29 15:32:47 UTC 2006 i686 GNU/Linux
RefDB binaries and scripts in the path:
/usr/bin/refdbd
/usr/bin/refdba
/usr/bin/refdbc
/usr/bin/refdbib
/usr/bin/bib2ris
and their version numbers:
refdbd 0.9.8-pre1
refdba 0.9.8-pre1
refdbc 0.9.8-pre1
refdbib 0.9.8-pre1
/usr/bin/refdb-bug: line 41: nmed2ris: command not found
bib2ris 0.9.8-pre1
DSSSL engines in the path:
and their version numbers:

$REFDBLIB is /usr/share/refdb
global refdbd config file:
refdblib /usr/share/refdb
serverip	localhost
dbsport	=09
dbserver	mysql
dbpath		/var/lib/refdb/db
port	9734
logfile /var/log/refdbd.log
logdest file
loglevel info
pidfile		/var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan t
db_encoding=09
in_encoding	UTF-8

global refdba config file:
serverip	127.0.0.1
port	9734
pager	less
username	joeuser
passwd	<protected>
logdest file
loglevel info
logfile /var/log/refdba.log

global refdbc config file:
serverip	127.0.0.1
port	9734
pager	less
username	joeuser
passwd	<protected>
logdest file
loglevel info
logfile /var/log/refdbc.log
cssurl /usr/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8

global refdbc config file (cgi):

global refdbib config file:

global nmed2ris config file:

global bib2ris config file:

$HOME is /home/dreusser
user refdba config file:

user refdba config file (hidden):

user refdbc config file:

user refdbc config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       hykli
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbib config file:

user refdbib config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       refdb_test
pager           less
toencoding      ISO-8859-1

user nmed2ris config file:

user nmed2ris config file (hidden):

user bib2ris config file:

user bib2ris config file (hidden):
logfile bib2ris.log
logdest 2
loglevel 7
nsf_abstract N2
nsf_url UR
nsf_url2 UR
nsf_pdf AV
nsf_keywords KW
nsf_owner U2
nsf_comment U3
nsf_issn SN

>
> regards,
> Markus

=2D-=20
Dominik Reusser
Universit=E4t Potsdam
Institut f=FCr Geo=F6kologie
Karl-Liebknecht-Strasse 24-25
14476 Golm

Tel: 0331 977 21 11
=46ax: 0331 977 20 92

http://www.uni-potsdam.de/u/Geooekologie/index.html

[Refdb-users] getref hangs

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

Hi,

Dominik Reusser writes:
 > And this is the corresponding log file (getau first, which works, then getref 
 > which just hangs):

Could you please provide the exact command that you issued to invoke
getref? It is not clear from the log what you were asking for. Last
time the getref command was reported to hang on this list turned out
to be a user error. Could you please provide the output of refdb-bug
as well?

regards,
Markus

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

[Refdb-users] getref hangs

[Dominik R. <dre...@un...>]

My refdbd hangs when I issue a getref command. Everything else works. I know a 
similar bug was reported about one year ago, but it is not clear, whether the 
problem was resolved then.


Here my setup:
You are served by: refdb 0.9.8-pre1
Client IP: 127.0.0.1
Connected via mysql driver (dbd_mysql v0.8.1)
to: 5.0.22-Debian_4-log
db version: 1
serverip: localhost
timeout: 180
dbs_port:
logfile: /var/log/refdbd.log
logdest: 0
loglevel: 7
remoteadmin: off
pidfile: /var/run/refdbd.pid


And this is the corresponding log file (getau first, which works, then getref 
which just hangs):
++
refdbd -s -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
mysql
pgsql
sqlite
sqlite3
Requested libdbi driver found
Database directory:
/var/lib/refdb/db
application server started
share extended notes by default
use /tmp/refdbd_fifo6047 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 4
210-13-79-16
send pseudo-random string to client
parent removing client on fd 5
server waiting n_max_fd=4
selectdb hykli -u dominik -w XXXXXXXXXXX
dbi is up
localhost
dominik
XXXXXX


mysql
/var/lib/refdb/db

refdb
connected to database server using database:
refdb
could not open version file:
/var/lib/refdb/db/DB_VERSION
Main database looks ok:
refdb
localhost
dominik
XXXXXX


mysql
/var/lib/refdb/db

refdb
connected to database server using database:
refdb
localhost
dominik
XXXXXX


mysql
/var/lib/refdb/db

hykli
connected to database server using database:
hykli
SELECT meta_app,meta_type,meta_dbversion from t_meta
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
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 4
021-63-17-18
send pseudo-random string to client
parent removing client on fd 5
server waiting n_max_fd=4
getau  -u dominik -w XXXXXXXXX -E ISO-8859-1 -d hykli
dbi is up
localhost
dominik
XXXXXX
hykli

mysql
/var/lib/refdb/db
ISO-8859-1
refdb
connected to database server using database:
refdb
Main database looks ok:
refdb
localhost
dominik
XXXXXX
hykli

mysql
/var/lib/refdb/db
ISO-8859-1
hykli
SELECT meta_app,meta_type,meta_dbversion from t_meta
connected to database server using database:
hykli
SELECT VERSION()
SELECT DISTINCT t_author.author_name FROM t_author, t_xauthor WHERE 
t_author.aut hor_id=t_xauthor.author_id AND t_xauthor.xauthor_type='primary' 
AND t_author.aut hor_name RLIKE '.*' ORDER BY t_author.author_name
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
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 4
120-61-46-11
send pseudo-random string to client
parent removing client on fd 5
server waiting n_max_fd=4
error
child finished client on fd 5
child exited with code 1
server waiting n_max_fd=4


Dominik Reusser

[Refdb-users] ANN: refdb-release deb now at version 0.9.8-pre1

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

The subject header of the previous message header was incorrect.

A new version (0.9.8-pre1) of the RefDB pre-release Debian package is now available.

Regards,
David.

Re: [Refdb-users] ANN: refdb-release deb now at version 0.9.7-pre1

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

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

> A new version of the RefDB pre-release Debian package is now available.
>

I guess the subject line should read "0.9.8-pre1".

regards,
Markus

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

[Refdb-users] ANN: refdb-release deb now at version 0.9.7-pre1

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

A new version of the RefDB pre-release Debian package is now available.

Regards,
David.