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 >> >> >> >
