Hi, Sorry to chime in in the middle, something is up with your Perl. Using the same Perl that have used to build your BioMart and run the BioMart configure script, try the following:
perl -e 'use DB_File;' or perl -MDB_File do you get the same error? -leandro On Fri, Mar 19, 2010 at 4:59 PM, <[email protected]> wrote: > Hi Allan et al, > Thanks for your suggestion, I have gone ahead and tried to connect to an > existing database which is known to work (Reactome database), and it does > give the same error. > If it is any consolation, my local Reactome website installation is > working fine, and for the Biomart installation everything goes well up > until this point. Are there other checks i could do to possibly identify > the source of the problem? Thank you > Kind Regards, > Nelson > > > On Fri, Mar 19, 2010 at 4:42 PM, <[email protected]> wrote: > >> Hi All, > >> I went ahead and decided to do away with Biomart 0.6 as advised and > >> started installing Biomart 0.7 on my 64 bit linux. > >> Now as i follow the "3.3 Setting up MartView" section of the user-docs > >> (after being referred to this section by the BioMart 0.7 Quick Install > >> Guide), i created my own registry file in the biomart-perl/conf > >> directory > >> as specified in section 3.3 of that document and when i tried to > >> configure > >> MartView, i got the error below: > >> I have checked that i have the DB_File module, that the DB_File.so > >> exists > >> and that i have the XSLoader.pm in that path. > >> I already created the database and checked it exists in mysql. The .xml > >> file i used is shown below as well as the settings.conf file i edited. > >> I will greatly appreciate your assistance. Thanks > >> Nelson > >> > >> The ERROR while configuring MartView: > > > > > > > > It is likely the you may have left out some Perl module(s) and that is > > why configure.pl -r is complaining or perhaps you may have > > misconfigured biomart somehow. > > To eliminate possible sources of error, you may first want to simply > > connect to an existing database which is known to work, it you are > > able to connect and browse the other databases, then it may be some > > misconfiguration in your Biomart installation. > > > > > > Allan . > > > > >
