Hi Donghe,1- does the perl bin/configure.pl work with the registry file martDBLocation.xml ???
2- send us your registry file, there is somehting wrong with your parameters there,
Best, Syed [email protected] wrote:
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 330sorry 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! DongHi 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
