[BioMart Users] Biomart install error

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[BioMart Users] Biomart install error

Rosalind Cutts
Biomart install error Hi
I’m trying to set up biomart 0.7 on a new server on port 80 that has previously been running an apache web server.

Although the index page displays ok, I am getting the following error when trying to clicking on the biomart page

ERROR: caught BioMart::Exception::Session: new(): failed: load(): couldn't retrieve data: _tie_db_file(): couldn't tie '/home/biomart/db/server_80/biomart-perl/conf/sessions/cgisessions.db': Inappropriate ioctl for device

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 New button below.

Stacktrace:
  Exception::Class::Base::throw  /home/biomart/db/server_80/biomart-perl/lib/BioMart/Web.pm:386
  BioMart::Web::restore_session  /home/biomart/db/server_80/biomart-perl/lib/BioMart/Web.pm:1443
  BioMart::Web::handle_request  /home/biomart/db/server_80/biomart-perl/cgi-bin/martview:100
  (eval)  /home/biomart/db/server_80/biomart-perl/cgi-bin/martview:99
ModPerl::ROOT::ModPerl::Registry::home_biomart_db_server_80_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
  (eval)  /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
  ModPerl::RegistryCooker::run  /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
  ModPerl::RegistryCooker::default_handler  /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
  ModPerl::Registry::handler  -e:0
  (eval)  -e:0

Any idea what is going on here ?

Thanks


Ros Cutts
Barts Cancer Institute

 

 

 

 

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Re: [BioMart Users] Biomart install error

Syed Haider
Hi Rosalind,

When you run perl bin/configure.pl -r ... --clean,

please send us what you see in the console.

also, your conf/settings.conf

thanks,
Syed


On 26/01/2011 11:29, Rosalind Cutts wrote:

> Hi
> I’m trying to set up biomart 0.7 on a new server on port 80 that has previously been running an apache web server.
>
> Although the index page displays ok, I am getting the following error when trying to clicking on the biomart page
>
> ERROR: caught BioMart::Exception::Session: new(): failed: load(): couldn't retrieve data: _tie_db_file(): couldn't tie '/home/biomart/db/server_80/biomart-perl/conf/sessions/cgisessions.db': Inappropriate ioctl for device
>
> 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 New button below.
>
> Stacktrace:
>    Exception::Class::Base::throw  /home/biomart/db/server_80/biomart-perl/lib/BioMart/Web.pm:386
>    BioMart::Web::restore_session  /home/biomart/db/server_80/biomart-perl/lib/BioMart/Web.pm:1443
>    BioMart::Web::handle_request  /home/biomart/db/server_80/biomart-perl/cgi-bin/martview:100
>    (eval)  /home/biomart/db/server_80/biomart-perl/cgi-bin/martview:99
> ModPerl::ROOT::ModPerl::Registry::home_biomart_db_server_80_biomart_2dperl_cgi_2dbin_martview::handler /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
>    (eval)  /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
>    ModPerl::RegistryCooker::run  /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
>    ModPerl::RegistryCooker::default_handler  /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
>    ModPerl::Registry::handler  -e:0
>    (eval)  -e:0
>
> Any idea what is going on here ?
>
> Thanks
>
>
> Ros Cutts
> Barts Cancer Institute
>
>
>
>
> This email may contain information that is privileged, confidential or otherwise protected from disclosure.
> It must not be used by, or its contents copied or disclosed to, persons other than the addressee.
> If you have received this email in error please notify the sender immediately and delete the email.
> This message has been scanned for viruses.
>
>
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Re: [BioMart Users] Biomart install error

Rosalind Cutts
Here you go.

Thanks
Ros

perl bin/configure.pl --clean -r conf/registryDBPointer.xml

Do you want to install in API only mode [y/n] [n]:

Checking prerequisites ...[Looks good]

rm /home/biomart/db/server_80/biomart-perl/conf/templates/default/*.ttc
APACHE: /usr/sbin/httpd
HOST: 138.37.210.230
PORT: 80
PROXY:
LOCATION: biomart
APXS/2:

You can change the above configuration by editing
"biomart-perl/conf/settings.conf"



Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
configuration
Have Apache DSO-support and ModPerl library file present, configuring
ModPerl in httpd.conf.
Libdir /home/biomart/db/server_80/biomart-perl/lib is not in @INC, adding to
@INC



Connection parameters of [MSD PROTOTYPE (EBI UK)]    [ OK ]






[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... MSD PROTOTYPE (EBI UK) ... 001/001 ... msd
....................................... (RDBMS) martdb.ebi.ac.uk:3306
......... ->  upgrading to 0.6/0.7 ...  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
[1/1] Attribute Panel of Dataset.. :msd
[1/1] Filter Panel of Dataset..... :msd




On 26/01/2011 12:24, "Syed Haider" <[hidden email]> wrote:

> Hi Rosalind,
>
> When you run perl bin/configure.pl -r ... --clean,
>
> please send us what you see in the console.
>
> also, your conf/settings.conf
>
> thanks,
> Syed
>
>
> On 26/01/2011 11:29, Rosalind Cutts wrote:
>> Hi
>> I¹m trying to set up biomart 0.7 on a new server on port 80 that has
>> previously been running an apache web server.
>>
>> Although the index page displays ok, I am getting the following error when
>> trying to clicking on the biomart page
>>
>> ERROR: caught BioMart::Exception::Session: new(): failed: load(): couldn't
>> retrieve data: _tie_db_file(): couldn't tie
>> '/home/biomart/db/server_80/biomart-perl/conf/sessions/cgisessions.db':
>> Inappropriate ioctl for device
>>
>> 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 New button below.
>>
>> Stacktrace:
>>    Exception::Class::Base::throw
>> /home/biomart/db/server_80/biomart-perl/lib/BioMart/Web.pm:386
>>    BioMart::Web::restore_session
>> /home/biomart/db/server_80/biomart-perl/lib/BioMart/Web.pm:1443
>>    BioMart::Web::handle_request
>> /home/biomart/db/server_80/biomart-perl/cgi-bin/martview:100
>>    (eval)  /home/biomart/db/server_80/biomart-perl/cgi-bin/martview:99
>> ModPerl::ROOT::ModPerl::Registry::home_biomart_db_server_80_biomart_2dperl_cg
>> i_2dbin_martview::handler
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry
>> Cooker.pm:204
>>    (eval)  
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry
>> Cooker.pm:204
>>    ModPerl::RegistryCooker::run
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry
>> Cooker.pm:170
>>    ModPerl::RegistryCooker::default_handler
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry
>> .pm:31
>>    ModPerl::Registry::handler  -e:0
>>    (eval)  -e:0
>>
>> Any idea what is going on here ?
>>
>> Thanks
>>
>>
>> Ros Cutts
>> Barts Cancer Institute
>>
>>
>>
>>
>> This email may contain information that is privileged, confidential or
>> otherwise protected from disclosure.
>> It must not be used by, or its contents copied or disclosed to, persons other
>> than the addressee.
>> If you have received this email in error please notify the sender immediately
>> and delete the email.
>> This message has been scanned for viruses.
>>
>>

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