---------- Forwarded message ----------
From: Etai Jacob <[EMAIL PROTECTED]>
Date: Feb 8, 2007 12:52 PM
Subject: Re: [mart-dev] Problems with executing martview
To: Syed Haider <[EMAIL PROTECTED]>
this is the output when running configure.pl:
perl bin/configure.pl --clean -r conf/DGV_registry.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
Use of uninitialized value in string ne at
/home/etai/.html/biomart/biomart-perl/bin/configureBioMart.pl line 83.
Use of uninitialized value in regexp compilation at
/home/etai/.html/biomart/biomart-perl/bin/configureBioMart.pl line 85.
rm /home/etai/.html/biomart/biomart-perl/conf/templates/default/*.ttc
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n
Checking several common Apache locations...done.
Select either one of the detected httpd paths on the list, OR enter
the path you wish to use:
/usr/sbin/httpd
[1]:
Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
configuration
Enter the server host OR default [dell5.compugen.co.il]:
Enter the server port OR default [5555]:
Enter proxy OR default :
Enter the required script location OR default [biomart]:
Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
Libdir /home/etai/.html/biomart/biomart-perl/lib is not in @INC, adding to @INC
Optional setting for martUser in MartDBLocation location:DGV not
defined - setting to default values
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... DGV ...................... 001/001 ... variation
................................. (RDBMS) dell7:3306
.................... OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
.... 100%
this is the output when I am running the martview from the commandline:
cgi-bin/martview.cgi
Subroutine BioMart::Web::Zlib::adler32 redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
Subroutine BioMart::Web::Zlib::crc32 redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at
/opt/compugen/perl/5.8.5/lib/5.8.5/Exporter.pm line 65.
at /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web/Zlib.pm line 20
ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
"settingsParams" on an undefined value at
/home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 116.
Stacktrace:
Exception::Class::Base::new cgi-bin/martview.cgi:80
Content-Type: text/html; charset=ISO-8859-1
<br/><br/><br/>
YOUR SITE HEADER HERE
<br/><br/><br/><br/>
<div id="mart_containerpanel">
<p>
ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
"settingsParams" on an undefined value at
/home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 116.<br
/>
</p>
<p>
If you repeatedly get directed to this error page, there may be a
problem with your
current session parameters. To clear your session and start with a
clean slate, please
click the button below.
</p>
<form name="mainform" action="martview" method="post"
enctype="multipart/form-data">
<input type="submit" name="newsession" value="New Session" />
</form>
<p>
Stacktrace:<br /> Exception::Class::Base::new cgi-bin/martview.cgi:80<br />
</p>
</div> <!-- martpanel closes -->
<!-- : footer.tt,v 1.2 2006/11/23 15:59:13 syed Exp -->
<!--
<br><br>
      <font ="" size="1" >YOUR SITE FOOTER HERE</font>
<br>
-->
Thanks!
On 2/8/07, Syed Haider <[EMAIL PROTECTED]> wrote:
On Thu, 2007-02-08 at 11:55 +0200, Etai Jacob wrote:
Hi Etai
> Hi,
> I have installed biomart and did the following before executing martview:
>
> 1) Define your mart in MartBuilder
> 2) Use MartBuilder to generate SQL that will create the mart out of your
> source data. Run that SQL.
> 3) Connect to the created mart using MartEditor and configure the
> attributes and filters you want (the Naive option will do this for you
> with sensible defaults)
> 4) Export the config from MartEditor so that it is saved in your mart
> 5) Create a registry XML file that describes how to find your newly
> configured mart
> 6) Run bin/configure.pl using the registry XML and --clean
Looks as if your registry is not getting configured properly. Could be
due to incorrect xmls representing your marts (I am not talking about
registry.xml file). Could you please have a look at the on-screen
messages while you are configuring your martview and see if there is
somehting wrong there. Might help us understanding your problem in a
better way.
Kind regards
Syed
> 7) Start up MartView
>
> as described in [[mart-dev] martview problems, Jennifer Siepen]
>
> The registry.xml file:
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
> <virtualSchema name="default" visible="1" default="1">
> <MartDBLocation
> name = "DGV"
> displayName = "DGV"
> databaseType = "mysql"
> host = "dell7"
> port = "3306"
> database = "DGV"
> schema = "DGV"
> user = "****"
> password = "****"
> visible = "1"
> default = ""
> includeDatasets = ""
> />
> </virtualSchema>
> </MartRegistry>
>
> I keep getting the error (web):
>
> ERROR: caught BioMart::Exception: non-BioMart die(): Can't call method
> "settingsParams" on an undefined value at
> /home/etai/.html/biomart/biomart-perl/lib/BioMart/Web.pm line 116.
>
> If you repeatedly get directed to this error page, there may be a
> problem with your current session parameters. To clear your session
> and start with a clean slate, please click the button below.
>
> Stacktrace:
> Exception::Class::Base::new
> /home/etai/.html/biomart/biomart-perl/cgi-bin/martview.cgi:80
>
> Running the martview from command line results with the same error.
> I followed each step as described in ([mart-dev] martview problems,
> Jennifer Siepen) but I am still getting the same error.
>
> Any suggestions are happily welcome.
>
> Thanks,
> Etai
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
