Yes we have, the last version:(
On 2/13/07, Richard Holland <[EMAIL PROTECTED]> wrote:
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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
>>> >> >> >
>>> >> >>
>>
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