-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 iD8DBQFF0dAy4C5LeMEKA/QRAtyfAJ9jNMd2dnd/L/fAJ4uTRPywG/9LUgCdF+NC 4Z+xRpWGjZFHrKdZ2PcQSmc= =8UCj -----END PGP SIGNATURE-----
