Just my two cents. The following error may be caused by missing DBI and/or DBD::mysql perl module.
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > COULD NOT CONNECT TO DATABASE biomart_freeze5.CHECK YOUR SETTINGS > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Regards, Junjun > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Syed Haider > Sent: Thursday, November 05, 2009 4:25 PM > To: [email protected] > Cc: Christina Yung; [email protected] > Subject: Re: [mart-dev] trouble with configuring the BioMart Perl API > > 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 > >>> > >>> > >>> > > > > >
