-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 This line of the log indicates the problem:
Can't open a reference at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 1850. This is a Perl version incompatibility. It is trying to open a filehandle over a string then write the results to that string. This is not possible in versions of Perl older than 5.8. You need to upgrade your Perl to at least 5.8 for this to work. cheers, Richard Etai Jacob wrote: > Attached. > > On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote: >> >> On 13 Feb 2007, at 11:49, Etai Jacob wrote: >> >> > No errors. >> >> >> I meant ... could you send us the contents >> of this file while you are doing your query? >> >> we need to see what comes back from the >> database or webserver when you do it >> >> >> cheers, >> a. >> >> >> >> >> > >> > On 2/13/07, Arek Kasprzyk <[EMAIL PROTECTED]> wrote: >> >> >> >> On 13 Feb 2007, at 11:23, Etai Jacob wrote: >> >> >> >> > Hi, >> >> > >> >> > My answers below. >> >> >> >> Hi Etai, >> >> maybe we need a little bit more debugging there. >> >> Could you change the >> >> >> >> log4perl.threshold = FATAL >> >> >> >> to >> >> >> >> log4perl.threshold = WARN >> >> >> >> in biomart-perl/conf/log4perl.conf >> >> >> >> restart the server and see what you get >> >> in the error_log? >> >> >> >> >> >> cheers, >> >> a. >> >> >> >> >> >> >> >> > >> >> >> What do you mean by not seeing any results? Do you mean that you >> >> get >> >> >> an error message? >> >> > I don't get any error messages, not on the web browser (firefox or >> >> > explorer) and not in the error log file of the httpd. >> >> > >> >> > Or you see the results page but the table only has >> >> >> headings? >> >> > No heading. >> >> > >> >> > What happens exactly? >> >> > When pressing the "results" it waits a second and then when "Done" >> >> the >> >> > page stays blank (except the default GUI of the martview on the left >> >> > side of the page). >> >> > >> >> >> Could you try a query with no filters at all and just one or two >> >> >> attributes to see if you get results? >> >> > Yes I tried with many combinations. Nothing. >> >> > >> >> > I tried other biomart web interface, >> >> > http://www.dictybase.org/biomart/martview/, to see whether I have a >> >> > problem with the browser or JVM but it works fine. >> >> > >> >> > Thanks, >> >> > Etai >> >> > >> >> > >> >> >> Etai Jacob wrote: >> >> >> > Hi, >> >> >> > >> >> >> > I am trying to execute few basic queries using the biomart web >> >> >> > interface with the default configurations (as instructed in the >> >> >> > installation guide). >> >> >> > I don't get to see any results on the browser even though at the >> >> >> count >> >> >> > stage I see that there are relevant entries (i.e. 1/3967). >> >> >> > >> >> >> > What could be the problem? >> >> >> > Thanks, >> >> >> > Etai >> >> >> > >> >> >> -----BEGIN PGP SIGNATURE----- >> >> >> Version: GnuPG v1.4.2.2 (GNU/Linux) >> >> >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >> >> >> >> >> iD8DBQFF0YZf4C5LeMEKA/QRAnfjAJ4ryJaiBgNwabuiZNFijhNEvTsz8wCfa9bu >> >> >> 1QBsgL/hNLndGODDdK9wmu8= >> >> >> =Ro2C >> >> >> -----END PGP SIGNATURE----- >> >> >> >> >> >> >> >> >> >> >> >> ---------------------------------------------------------------------- >> >> -- >> >> ------- >> >> 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 >> >> ---------------------------------------------------------------------- >> >> -- >> >> ------- >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> ------- >> 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 >> ------------------------------------------------------------------------ >> ------- >> >> >> >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFF0bg64C5LeMEKA/QRAiTjAJ4ixlQdnQNACmyOg6Z+no6g4MZQ5wCgmdYd c5s2xRGIqli0z/fnDZ21/AE= =CWrs -----END PGP SIGNATURE-----
