Hi,
 
When I ran, it giave the following errors
/usr/local/apache2/bin/httpd -d $PWD -f $PWD/conf/httpd.conf
httpd: Syntax error on line 36 of /home/software/biomart-perl/conf/httpd.conf:
Cannot load /usr/local/apache2/modules/mod_deflate.so into server:
/usr/local/apache2/modules/mod_deflate.so: cannot open shared object file: No
such file or directory
 
Could you please let me know the reason? 

Thanks,
 
Ray
 
 
 

 
________________________________

From: Junjun Zhang [mailto:[email protected]]
Sent: Thu 12/3/2009 12:35 AM
To: Jing, Rui; Syed Haider
Cc: Arek Kasprzyk; [email protected]
Subject: RE: [mart-dev] errors when starting martview




> -----Original Message-----
> From: Jing, Rui [mailto:[email protected]]
> Sent: Thursday, December 03, 2009 12:13 AM
> To: Syed Haider
> Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
> Subject: RE: [mart-dev] errors when starting martview
>
> Hi Syed,
> 
> when I ran, it gave the following info.
> 
> > /common/home/software/biomart-perl/apache/bin/httpd -d $PWD -f
> $PWD/conf/httpd.conf
> Processing Cached Registry:
> /common/home/software/biomart-perl/conf/cachedRegistries/martD
> BLocation.xml.cach
> ed
> 
> then I try to visit biomart
> http://node01.com:8011/biomart-perl/martview
> it does not work.

It looks fine when you start apache. Please try this URL instead:

http://node01.com:8011/biomart/martview or just try this one
http://node01.com:8011/ (there is a link on this page that takes you to
martview).

That should work.

Cheers,
Junjun




> 
> Could you please let me know what the problem is?
> Thanks,
> 
> Ray
> 
> 
>
> ________________________________
>
> From: Syed Haider [mailto:[email protected]]
> Sent: Thu 11/26/2009 9:59 AM
> To: Jing, Rui
> Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
> Subject: Re: [mart-dev] errors when starting martview
>
>
>
>
>
> Jing, Rui wrote:
> > Hi Syed,
> >
> > Here is screen copy after execute b.
> > by the way, I installed my local biomart into
> /common/home/software/biomart-perl
> > (it is biomart-perl, do I need change settings.conf,
> LOCATION= biomart
> > to LOCATION=biomart-perl ?
>
> no biomart is just fine, thats what becomes the part of your
> URL, its not the location of biomart-perl on disk.
>
> could you also add the path to apxs or apxs2 in
> setttings.conf and redo the configure with --clean.
>
> once done, please let us know if that works, also send us the
> screen copy of terminal .
>
> thanks
> Syed
>
>
> >
> > [r...@node01 50]> perl bin/configure.pl -r conf/martDBLocation.xml
> > --clean Do you want to install in API only mode [y/n] [n]:
> n Checking
> > prerequisites ...[Looks good]
> > APACHE: /common/home/software/biomart-perl/apache/bin/httpd
> > HOST: localhost
> > PORT: 8011
> > PROXY:
> > LOCATION: biomart
> > APXS/2:
> > You can change the above configuration by editing
> > "biomart-perl/conf/settings.conf"
> >
> > Got usable Apache in
> > /common/home/software/biomart-perl/apache/bin/httpd,
> > probing for version & ModPerl configuration Have Apache DSO-support
> > and ModPerl library file present, configuring ModPerl
> in
> > httpd.conf.
> > Libdir /common/home/software/biomart-perl/lib is not in
> @INC, adding
> > to @INC Connection parameters of [My BioMart Database]  [ OK ]
> >
> > [NEW CONFIGURATION] .... WITH MEMORY [default] default ...
> My BioMart
> > Database ...... 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
> >
> > Thanks,
> >
> > Ray
> >
> > ________________________________
> >
> > From: Syed Haider [mailto:[email protected]]
> > Sent: Thu 11/26/2009 9:27 AM
> > To: Jing, Rui
> > Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
> > Subject: Re: [mart-dev] errors when starting martview
> >
> >
> >
> > a- please set the location param in conf/settings.conf to
> > location=biomart
> >
> > b- reconfigure the perl bin/configure.pl.... with --clean switch
> >
> > c- kill and restart apache and  then access the URL as:
> > http://node01.com:8011/biomart/martview
> >
> >
> > please send us what see in terminal after executing 'b'
> >
> > thanks
> > Syed
> >
> >
> >
> >
> > Jing, Rui wrote:
> >> Hi Syed,
> >>
> >> Great. It started.
> >> Processing Cached Registry:
> >>
> >
> /common/home/software/biomart-perl/conf/cachedRegistries/martD
> BLocation.xml.cach
> >> ed
> >>
> >> cat logs/httpd.pid
> >> 19006
> >>
> >> but when I visit hthttp://node01.com:8011/biomart-perl/martview
> >> <http://node01.com:8011/biomart-perl/martview>
> >> it gave error: Oops! This link appears to be broken from IE.
> >>
> >> I used martDBLocation.xml
> >> perl bin/configure.pl -r conf/martDBLocation.xml --clean
> >>
> >> settings.conf is:
> >>      5
> apacheBinary=/common/home/software/biomart-perl/apache/bin/httpd
> >>       6 serverHost=localhost
> >>       7 port=8011
> >>       8 # to use proxying set the proxy port below (even
> if its 80)
> >> and set serverHost as your proxy host
> >>       9 proxy=
> >>      10 # if apxs or apxs2 is not in default directory where httpd
> >> lives, you may set this param to point to apxs/2
> >>      11 apxs=
> >>      12 location=/common/home/software/biomart-perl
> >>      13
> >> 
> >> please advise what the problem is.
> >> Thanks,
> >>
> >> Ray
> >>
> >> ________________________________
> >>
> >> From: Syed Haider [mailto:[email protected]]
> >> Sent: Thu 11/26/2009 8:39 AM
> >> To: Jing, Rui
> >> Cc: Junjun Zhang; Arek Kasprzyk; [email protected]
> >> Subject: Re: [mart-dev] errors when starting martview
> >>
> >>
> >>
> >> Hi Rui,
> >>
> >>
> >> the only critical error is :
> >>
> >> Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf:
> >> Invalid command 'PerlOptions', perhaps misspelled or defined by a
> >> module not included in the server configuration
> >>
> >>
> >> you would need to see the onscreen instrcutions when you run:
> >>
> >> perl bin/configure.pl.....
> >>
> >> you probably dont have mod_perl or somehting configured correctly.
> >>
> >>
> >> Best,
> >> Syed
> >>
> >> Jing, Rui wrote:
> >>> Hi,
> >>>
> >>> When I am starting martview, there are some error and
> warn, please
> >>> advise
> how
> >> to
> >>> solve the problem.
> >>>
> >>> [r...@]> /software/biomart-perl/apache/bin/httpd -d $PWD -f
> >> $PWD/conf/httpd.conf
> >>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in
> >>> line 37 of /common/home/hge/software/biomart-perl/conf/httpd.conf.
> >>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in
> >>> line 45 of /common/home/hge/software/biomart-perl/conf/httpd.conf.
> >>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in
> >>> line 63 of /common/home/hge/software/biomart-perl/conf/httpd.conf.
> >>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in
> >>> line 73 of /software/biomart-perl/conf/httpd.conf.
> >>> Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf:
> >>> Invalid command 'PerlOptions', perhaps misspelled or defined by a
> >>> module not included in the server configuration
> >>>
> >>>
> >>> Thanks,
> >>>
> >>> Ray
> >>>
> >>>
> >>>
> >>>
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