Hi Thomas, The problem
undefined symbol: ap_get_server_banner is because of incompatible mod_perl and apache. The above-mentioned function is a replacement for a deprecate function in new mod_perl and changed only couple of months ago. for details see: http://www.mail-archive.com/[EMAIL PROTECTED]/msg00505.html You either need to upgrade apache to version >= 2.2.4 or downgrade mod_perl, which ever is convenient. cheers syed On Thu, 2008-07-17 at 12:36 -0700, Thomas Juettemann wrote: > Hi Syed, > > thanks so much for your help, it works now. The problem was > DBD::mysql, reinstalling fixed it. > I figured it out by adding RaiseError=>1 to the DBI->connect. > > The configuration went fine, but when starting Apache I get this error: > > [bischet] ~/biomart/biomart-perl: /usr/sbin/httpd -d $PWD -f $PWD > conf/httpd.conf > > Processing Cached Registry: > /home/juettemann/biomart/biomart-perl/conf/cachedRegistries/myRegistry.xml.cached > > /usr/sbin/httpd: symbol lookup error: > /home/juettemann/biomart/apache/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi/auto/Apache2/ServerUtil/ServerUtil.so: > undefined symbol: ap_get_server_banner > > Any ideas for this? > > Cheers, > Thomas > > On Thu, Jul 17, 2008 at 05:23, Syed Haider <[EMAIL PROTECTED]> wrote: > > Hi Thomas, > > > > I entered your machine to investigate the problem. There is something > > wrong with perl DBI there. I have left a script testDBI.pl under > > biomart-perl/scripts directory. This should work (output: connected > > successfully) if your DBI is functional, which isnt at the moment. > > Please try to find out where you installed the module and whats wrong > > with it. When this script works, then go back to install and configure - > > hopefully should work then. > > > > > > syed > > > > >> > >> On 15/07/2008, Thomas Juettemann <[EMAIL PROTECTED]> wrote: > >> > Hi Syed, > >> > > >> > yes, the tables contain data, some examples: > >> > > >> > mysql> select * from meta_conf__dataset__main limit 1; > >> > +----------------+---------+--------------+-------------+----------+---------+---------+---------------------+ > >> > | dataset_id_key | dataset | display_name | description | type | > >> > visible | version | modified | > >> > +----------------+---------+--------------+-------------+----------+---------+---------+---------------------+ > >> > | 1 | bischet | BISChet | | TableSet | > >> > 1 | | 2008-07-15 15:45:15 | > >> > +----------------+---------+--------------+-------------+----------+---------+---------+---------------------+ > >> > 1 row in set (0.00 sec) > >> > > >> > mysql> select * from meta_conf__interface__dm limit 1; > >> > +----------------+-----------+ > >> > | dataset_id_key | interface | > >> > +----------------+-----------+ > >> > | 1 | default | > >> > +----------------+-----------+ > >> > > >> > mysql> select * from meta_template__template__main limit 1; > >> > +----------------+----------+ > >> > | dataset_id_key | template | > >> > +----------------+----------+ > >> > | 1 | bischet | > >> > +----------------+----------+ > >> > > >> > > >> > Cheers, > >> > Thomas > >> > > >> > On Tue, Jul 15, 2008 at 16:51, Syed Haider <[EMAIL PROTECTED]> wrote: > >> >> Hi Thomas, > >> >> the exceptions you are getting by starting apache are meaningless until > >> >> the configure goes fine, which isnt in this case. Could you please > >> >> confirm > >> >> if you do have at least one record in your __main table of the mart and > >> >> also if the meta tables have record in them ? > >> >> > >> >> thanks > >> >> syed > >> >> > >> >> > >> >> > >> >>> Hi all, > >> >>> > >> >>> I am still having trouble connecting to the database (I checked out > >> >>> the most recent biomart-perl). I ran MartEditor and exporter the naive > >> >>> settings (got all meta-tables) > >> >>> Syed, the myRegistry.xml I sent you is still up-to-date, in case you > >> >>> want to check again. > >> >>> > >> >>> /usr/sbin/httpd -d $PWD -f > >> >>> /home/juettemann/biomart/biomart-perl/conf/httpd.conf > >> >>> > >> >>> Cached Registry Unavailable... > >> >>> > >> >>> Running Complete Clean... > >> >>> Optional setting for martUser in MartDBLocation location:bischet not > >> >>> defined - setting to default values > >> >>> > >> >>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > >> >>> > >> >>> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS > >> >>> > >> >>> > >> >>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > >> >>> Syntax error on line 44 of > >> >>> /home/juettemann/biomart/biomart-perl/conf/httpd.conf: > >> >>> 8\xe9c\t\x01 > >> >>> > >> >>> httpd.conf: > >> >>> 42 LoadModule authz_host_module > >> >>> /usr/lib/httpd/modules/mod_authz_host.so > >> >>> 43 <Perl> > >> >>> 44 use lib > >> >>> '/home/juettemann/biomart/biomart-perl/lib'; > >> >>> 45 require "BioMart/Web/SiteDefs.pm"; > >> >>> > >> >>> I tried to remove all whitespaces preceeding/trailing from line 44, > >> >>> just in case something hidden in there. > >> >>> > >> >>> > >> >>> [bischet] ~/biomart/biomart-perl: perl bin/configure.pl -r > >> >>> conf/myRegistry.xml > >> >>> > >> >>> Do you want to install in API only mode [y/n] [n]: > >> >>> > >> >>> Checking prerequisites ...[Looks good] > >> >>> > >> >>> APACHE: /usr/sbin/httpd > >> >>> HOST: localhost > >> >>> PORT: 80 > >> >>> PROXY: > >> >>> LOCATION: biomart > >> >>> > >> >>> You can change the above configuration by editing > >> >>> "biomart-perl/conf/settings.conf" > >> >>> > >> >>> Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl > >> >>> configuration > >> >>> Have Apache DSO-support and ModPerl library file present, configuring > >> >>> ModPerl in httpd.conf. > >> >>> Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC > >> >>> Libdir /home/juettemann/biomart/biomart-perl/lib is not in @INC, adding > >> >>> to > >> >>> @INC > >> >>> > >> >>> Cached Registry Unavailable... > >> >>> > >> >>> Running Complete Clean... > >> >>> Optional setting for martUser in MartDBLocation location:bischet not > >> >>> defined - setting to default values > >> >>> > >> >>> > >> >>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > >> >>> > >> >>> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS > >> >>> > >> >>> > >> >>> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > >> >>> ERROR something wrong with your registry: Problems with the retrieval > >> >>> of dataset configuration > >> >>> Please check: > >> >>> that your mart Registry files contains correct > >> >>> connection > >> >>> params, > >> >>> that you are using the correct version on XML::Simple, > >> >>> that BioMart databases contain a populated meta_conf > >> >>> tables and > >> >>> that you have set martUser correctly if you are running > >> >>> in restricted data > >> >>> access mode (populated meta_conf__user__dm) > >> >>> > >> >>> Trace begun at > >> >>> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm > >> >>> line 254 > >> >>> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xb227ea4)', > >> >>> 'registryFile', > >> >>> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action', > >> >>> 'cached', 'mode', 'memory') called at > >> >>> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm > >> >>> line 377 > >> >>> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xb227ea4)', > >> >>> 'registryFile', > >> >>> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action', > >> >>> 'cached', 'mode', 'memory') called at > >> >>> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm > >> >>> line 328 > >> >>> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xb227ea4)', > >> >>> 'registryFile', > >> >>> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action', > >> >>> 'cached', 'mode', 'memory') called at > >> >>> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm > >> >>> line 168 > >> >>> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xb227ea4)', > >> >>> 'registryFile', > >> >>> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action', > >> >>> 'cached', 'mode', 'memory') called at > >> >>> /home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line > >> >>> 64 > >> >>> BioMart::RootI::new('BioMart::Initializer', 'registryFile', > >> >>> '/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action', > >> >>> 'cached', 'mode', 'memory') called at > >> >>> /home/juettemann/biomart/biomart-perl/bin/configureBioMart.pl line 328 > >> >>> eval {...} at > >> >>> /home/juettemann/biomart/biomart-perl/bin/configureBioMart.pl > >> >>> line 327 > >> >>> > >> >>> Cheers, > >> >>> Thomas > >> >>> > >> >> > >> >> > >> >> ====================================== > >> >> Syed Haider. > >> >> EMBL-European Bioinformatics Institute > >> >> Wellcome Trust Genome Campus, Hinxton, > >> >> Cambridge CB10 1SD, UK. > >> >> ====================================== > >> >> > >> >> > >> > > > -- > > ====================================== > > Syed Haider. > > EMBL-European Bioinformatics Institute > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > ====================================== > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
