> -----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.) >
Yeah, I know whats this all about. Its a warning not causing any harm due passing a string to a file which sometimes is not assigned a value. Will be fixed soon. I dont sense if this should cause any serious troubles. Cheers Syed > 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----- > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
