That looks like an issue with the way we use threads that is not compatible with Java 1.5. It's on our buglist of things to fix.
Try installing Java 1.4 instead, and it should work fine. cheers, Richard On Tue, 2006-06-06 at 15:26 +0530, Pallavi Sarmah wrote: > Hi > > As I was nt being able to connect to the database, so I shifted all the > files to my laptop. Here I m being able to import msd_mart_4 bt I m nt > being able to connect to the server. > > When I give to command > /usr/local/apache/bin/httpd.conf -d biomart-web > > I get the following error msg > > Syntax error on line 11 of biomart-web/conf/httpd: > Invalid command '<Perl>', perhaps mis-spelled or defined by a module not > included in the server configuration. > > Now I have FC5, with the same files of biomart-web, it was working fine > in FC4 > > Regards, > > Pallavi > > -----Original Message----- > From: Arek Kasprzyk [mailto:[EMAIL PROTECTED] > Sent: Thursday, June 01, 2006 6:10 PM > To: Pallavi Sarmah > Cc: mart-dev (E-mail) > Subject: Re: [mart-dev] cannot connect to local database. > > > On 1 Jun 2006, at 05:58, Pallavi Sarmah wrote: > > > Hi > > Hi Pallavi, > > > I ve sent a mail on 30 th may. Since I have received no reply and also > > it didn't appear in the mail archive I m afraid it must have nt been > > delivered. I m forwarding the mail again. > > Waiting for a suggestion. > > this is because you sent your email directly to me rather than to > mart-dev :-) > It is always safer to send an email to the list because there are more > people > who could respond quickly. > > The problem you describe is best tested by writing a simple java class > which connects to the database just to check if this some sort of JDBC/ > db privileges problem or rather a BioMart problem (obviously run from > the > same machine and with the same connection string). Could you check > that and tell us if you are able to do it without BioMart code? We'll > then > look into this in more detail > > cheers, > a. > > > > > > > Thank you > > > > Regards, > > > > Pallavi > > -----Original Message----- > > From: Pallavi Sarmah > > Sent: Tuesday, May 30, 2006 12:07 PM > > To: 'Arek Kasprzyk' > > Subject: RE: [mart-dev] cannot connect to local database. > > > > Hi > > I am trying to install biomart locally in my machine. Bt I m nt being > > able to connect martj to a database. I ve msd_mart_4 table structures > > (without data) locally. I ve modified the defaultmartregistry file > both > > in martj n biomart-plib. But still I m nt being able to connect and > the > > error msg that I get is as follows > > > > Include a correct meta_version_version__main table > > entry:java.sql.SQLException:Invalid authorization specification > message > > from server: "Access denied for user > > 'root'@'localhost.localdomain'(using password:YES)" > > > > While root do have access to the database. I ve tried with other users > > bt still I get the same msg. I am also sending u the > > defaultmartregistry > > file for yr reference. > > > > <?xml version="1.0" encoding="UTF-8" ?> > > <!DOCTYPE MartRegistry (View Source for full doctype...)> > > - <MartRegistry> > > <MartDBLocation name="Local BioMart" > > displayName="Local BioMart Database" > > databaseType="mysql" > > host="localhost" > > port="3306" > > database="msd_mart_4" > > schema="msd_mart_4" > > includeDatasets="" > > user="root" > > password="pallu" > > visible="1" > > default="" > > martUser="" > > /> > > </MartRegistry> > > > > > > > > Regards, > > > > Pallavi > > > > > > > > > ------------------------------------------------------------------------ > > ------- > Arek Kasprzyk > EMBL-European Bioinformatics Institute. > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > Tel: +44-(0)1223-494606 > Fax: +44-(0)1223-494468 > ------------------------------------------------------------------------ > > ------- > > > -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416
