Hi Syed, thanks again, I upgraded to 2.2.9 and the configuration seems to work fine:
[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: /home/juettemann/biomart/apache/bin/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 /home/juettemann/biomart/apache/bin/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 Processing Cached Registry: /home/juettemann/biomart/biomart-perl/conf/cachedRegistries/myRegistry.xml.cached ******************************** But apache still refuses to start, are these warnings a problem or do think the error is somewhere else: [EMAIL PROTECTED] /home/juettemann/biomart/biomart-perl: ../apache/bin/httpd -d $PWD -f /home/juettemann/biomart/biomart-perl/conf/httpd.conf Processing Cached Registry: /home/juettemann/biomart/biomart-perl/conf/cachedRegistries/myRegistry.xml.cached [Thu Jul 17 21:59:56 2008] [warn] Useless use of AllowOverride in line 126 of /home/juettemann/biomart/biomart-perl/conf/httpd.conf. [Thu Jul 17 21:59:56 2008] [warn] Useless use of AllowOverride in line 134 of /home/juettemann/biomart/biomart-perl/conf/httpd.conf. [Thu Jul 17 21:59:56 2008] [warn] Useless use of AllowOverride in line 153 of /home/juettemann/biomart/biomart-perl/conf/httpd.conf. [Thu Jul 17 21:59:56 2008] [warn] Useless use of AllowOverride in line 164 of /home/juettemann/biomart/biomart-perl/conf/httpd.conf. [Thu Jul 17 21:59:56 2008] [warn] Useless use of AllowOverride in line 180 of /home/juettemann/biomart/biomart-perl/conf/httpd.conf. I get a http.pid file, but it seems httpd starts and dies immediately. Cheers, Thomas On Thu, Jul 17, 2008 at 18:34, Syed Haider <[EMAIL PROTECTED]> wrote: > 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. > ====================================== > >
