-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I am confused.
(To SYED...: do you have any ideas? MartView/MartService on this user's own server is throwing exceptions like this: Can't open a reference at <blah blah>/lib/BioMart/Web.pm line 1850.) cheers, Richard Etai Jacob wrote: > Yes we have, the last version:( > > On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote: > Hmm. Well it must be a CPAN module then... not sure exactly as I've not > seen this problem before. The line I quoted is definitely the line that > is causing your results to be blank though. > > You could check to see if you have IO::Stringy installed from CPAN. It > provides the functions that back up the open() method. Let me know if it > is installed or not - if not, install it and retry the request (you'll > have to restart the MartView server after installing it). > > cheers, > Richard > > Etai Jacob wrote: >> We have perl 5.85 installed. > >> Thanks, >> Etai > >> On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote: >> 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 iD8DBQFF0fZ+4C5LeMEKA/QRAt4EAJ4ltiGnSyJS8Vt29E9etMxdwq50rQCfXqp6 YF5YbMLtsmwCxcPPAToHLl4= =PSH/ -----END PGP SIGNATURE-----
