Re: [mart-dev] Problem starting apache after installing biomart-perl

Tue, 07 Oct 2008 14:19:09 -0700 

Hi Glen,

please send me you httpd.conf,

thanks
syed




Damian Smedley wrote:


Hi Glen,
Sounds like the cached registry object never got created from your configure.pl. What do you get if you ls -l conf/cachedRegistries?
BTW are you planning on setting up an interesting BioMart at JAX. I am currently building a mouse resource portal here at the EBI using BioMart underneath so feel free if you need support from me. 

Best wishes,
Damian


On Tue, 7 Oct 2008, Glen Beane wrote:


I am trying to setup biomart-perl on OS X 10.5.
I am using the stock apache2, and have installed mod_perl from source. I am 
able to load mod_perl after modifying the standard apache2 .conf file.
I have installed all the prerequisite perl modules for biomart, and have run 
perl bin/configure.pl -r conf/registryURLPointer.xml

For now I am just testing biomart, so the biomart-perl folder is on my
desktop



Then I start up apache:
/usr/sbin/httpd -d /Users/gbeane/Desktop/biomart-perl/ -f
/Users/gbeane/Desktop/biomart-perl/conf/httpd.conf


Processing Cached Registry:
/Users/gbeane/Desktop/biomart-perl/conf/cachedRegistries/registryURLPointer. 
xml.cached

Syntax error on line 44 of
/Users/gbeane/Desktop/biomart-perl/conf/httpd.conf:
Can't call method "settingsParams" on an undefined value at
/Users/gbeane/Desktop/biomart-perl/lib/BioMart/Initializer.pm line 623.\n 




Can someone point me in the right direction to diagnose this error?



Here is the output from when I run the bin/configure.pl script:

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

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

Checking prerequisites ...[Looks good]
Subroutine BioMart::Web::Zlib::adler32 redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::crc32 redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::ZLIB_VERNUM redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20
Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at
/System/Library/Perl/5.8.8/Exporter.pm line 65.
at /Users/gbeane/Desktop/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 
20

APACHE: /usr/sbin/httpd
HOST: test.biomart.org
PORT: 9002
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 /Users/gbeane/Desktop/biomart-perl/lib is not in @INC, adding to @INC 

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




[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... MSD PROTOTYPE (EBI UK) ... 001/001 ... msd
....................................... (WEB) www.biomart.org:80
............ ->  upgrading to 0.6/0.7 ...  OK
default ... UNIPROT PROTOTYPE (EBI UK) ...  001/006 ... uniprot_location
.......................... (WEB) www.biomart.org:80 ............ ->
upgrading to 0.6/0.7 ...  OK
default ... UNIPROT PROTOTYPE (EBI UK) ...  002/006 ... uniprot_sequence
.......................... (WEB) www.biomart.org:80 ............ ->
upgrading to 0.6/0.7 ...  OK
default ... UNIPROT PROTOTYPE (EBI UK) ...  003/006 ...
uniprot_cell_component .................... (WEB) www.biomart.org:80
............ ->  upgrading to 0.6/0.7 ...  OK
default ... UNIPROT PROTOTYPE (EBI UK) ... 004/006 ... uniprot_biol_process ...................... (WEB) www.biomart.org:80 ............ -> upgrading 
to 0.6/0.7 ...  OK
default ... UNIPROT PROTOTYPE (EBI UK) ...  005/006 ... uniprot
................................... (WEB) www.biomart.org:80 ............ -> 
upgrading to 0.6/0.7 ...  OK
default ... UNIPROT PROTOTYPE (EBI UK) ... 006/006 ... uniprot_mol_function ...................... (WEB) www.biomart.org:80 ............ -> upgrading 
to 0.6/0.7 ...  OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 7/7
....(resolving) 100%
Building templates for visible datasets
.... 100%
Compiling templates for visible datasets
[1/2] Attribute Panel of Dataset.. :msd
[1/2] Filter Panel of Dataset..... :msd
[2/2] Attribute Panel of Dataset.. :uniprot
[2/2] Filter Panel of Dataset..... :uniprot

--
Glen L. Beane
Software Engineer
The Jackson Laboratory
Phone (207) 288-6153

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