Hi Syed, I installed apxs, still doesn't work. any other idea?
see the following message: ------- $ perl bin/configure.pl --update -r conf/spbase_annotation1022_6.xml Do you want to install in API only mode [y/n] [n]: n Checking prerequisites ...[Looks good] APACHE: /usr/sbin/httpd HOST: http://www.spbase.org PORT: 5430 PROXY: LOCATION: biomart APXS/2: /usr/sbin/apxs 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 /var/www/html/biomart-perl/lib is not in @INC, adding to @INC Optional setting for martUser in MartDBLocation location:mart_sea_urchin not defined - setting to default values !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! COULD NOT CONNECT TO DATABASE biomart_freeze5.CHECK YOUR SETTINGS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ERROR something wrong with your registry: Problems with the retrieval of dataset configuration Please check: that your mart Registry files contains correct connection params, that you are using the correct version on XML::Simple, that BioMart databases contain a populated meta_conf tables and that you have set martUser correctly if you are running in restricted data access mode (populated meta_conf__user__dm) Trace begun at /var/www/html/biomart-perl/bin/../lib/BioMart/Initializer.pm line 254 BioMart::Initializer::_init('BioMart::Initializer=HASH(0xa4aa82c)', 'registryFile', '/var/www/html/biomart-perl/conf/spbase_annotation1022_6.xml', 'action', 'update', 'mode', 'memory') called at /var/www/html/biomart-perl/bin/../lib/BioMart/Initializer.pm line 152 BioMart::Initializer::_new('BioMart::Initializer=HASH(0xa4aa82c)', 'registryFile', '/var/www/html/biomart-perl/conf/spbase_annotation1022_6.xml', 'action', 'update', 'mode', 'memory') called at /var/www/html/biomart-perl/bin/../lib/BioMart/RootI.pm line 64 BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/var/www/html/biomart-perl/conf/spbase_annotation1022_6.xml', 'action', 'update', 'mode', 'memory') called at /var/www/html/biomart-perl/bin/configureBioMart.pl line 331 eval {...} at /var/www/html/biomart-perl/bin/configureBioMart.pl line 330 > sorry to jump in guys, > > Donghe, > > you need to install apxs or apxs2 and then point to its path in > conf/settings.conf > > Cheers > Syed > > > [email protected] wrote: >> Hi Christina, >> >> I meet another problem: when I install Perl API and MartView together, >> the >> following error message shows up: >> >> >> $ perl bin/configure.pl -r conf/spbase_annotation1022_6.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 >> /var/www/html/biomart-perl/bin/configureBioMart.pl line 110. >> Use of uninitialized value in regexp compilation at >> /var/www/html/biomart-perl/bin/configureBioMart.pl line 112. >> >> rm /var/www/html/biomart-perl/conf/templates/default/*.ttcrm: cannot >> remove `/var/www/html/biomart-perl/conf/templates/default/*.ttc': No >> such >> file or directory >> >> APACHE: /usr/sbin/httpd >> HOST: http://www.spbase.org >> PORT: 5430 >> 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 >> Can't exec "/usr/sbin/apxs2": No such file or directory at >> /var/www/html/biomart-perl/bin/configureBioMart.pl line 176. >> Use of uninitialized value in scalar chomp at >> /var/www/html/biomart-perl/bin/configureBioMart.pl line 177. >> Use of uninitialized value in concatenation (.) or string at >> /var/www/html/biomart-perl/bin/configureBioMart.pl line 179. >> Libdir /var/www/html/biomart-perl/lib is not in @INC, adding to @INC >> >> Cached Registry Unavailable... >> >> Running Complete Clean... >> >> >> Optional setting for martUser in MartDBLocation location:mart_sea_urchin >> not defined - setting to default values >> >> >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> >> COULD NOT CONNECT TO DATABASE biomart_freeze5.CHECK YOUR SETTINGS >> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! >> >> >> do you have any idea about this problem? >> >> Thanks! >> >> Dong >> >> >>> Hi Dong: >>> >>> The readdir error occurs if you're using Perl 5.8.9 or 5.8.10. The >>> error >>> is not fatal, and the configuration will still complete. However, the >>> message also indicates that the perl module, Readonly, is missing. >>> Please >>> install this pre-requesite and let us know if you still have problems. >>> >>> Regards, >>> Christina >>> >>>> -----Original Message----- >>>> From: [email protected] >>>> [mailto:[email protected]] On Behalf Of [email protected] >>>> Sent: Monday, November 02, 2009 5:35 PM >>>> To: [email protected] >>>> Subject: [mart-dev] trouble with configuring the BioMart Perl API >>>> >>>> Hi, >>>> >>>> when I configure the Perl API, I got the following error >>>> message, does anybody know what's wrong with it? >>>> >>>> Thanks for your help >>>> >>>> Dong >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> >>>> biomart-perl]# perl bin/configure.pl -r conf/registryURLPointer.xml >>>> >>>> Do you want to install in API only mode [y/n] [n]: n >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> readdir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 286, <STDIN> line 1. >>>> closedir() attempted on invalid dirhandle DIR at >>>> bin/configure.pl line 287, <STDIN> line 1. >>>> >>>> Checking prerequisites ... please install the following modules: >>>> >>>> Readonly >>>> >>>> >>>> >> >> >
