Hi Allan COuld you please try the clean check-out with out changing the default directory name from biomart-perl to biomart-test2. Open the file log4perl.conf, set the
log4perl.threshold = FATAL to log4perl.threshold = WARN This time, when you begin the process with perl bin/configure.pl -r conf/martDBLocation.xml --clean Could you please note down complete onscreen information. Start your server. What comes in the browser window ? If it doesnt work/throws an error, send me the onscreen information you saved and your error_log. Many thanks Syed. > Hi, > I did change the "httpd path" during configuration to point to httpd, now > I am getting an error of a different kind (see below). > (I would like to mention that am running ubuntu just incase this could > bring more light into the issue) > > [Fri Mar 23 11:55:01 2007] [notice] Apache/2.2.4 (Unix) mod_perl/2.0.3 > Perl/v5.8.8 configured -- resuming normal operations > [Fri Mar 23 11:55:06 2007] [error] [client 127.0.0.1] Use of uninitialized > value in concatenation (.) or string at > /usr/lib/perl5/ModPerl/RegistryCooker.pm line 636.\n, referer: > http://localhost:5555/ > [Fri Mar 23 11:55:12 2007] [notice] caught SIGTERM, shutting down > > > Allan. > > Richard Holland wrote: > >>-----BEGIN PGP SIGNED MESSAGE----- >>Hash: SHA1 >> >>Hi. >> >>I noticed this bit: >> >><snip> >> >>Select either one of the detected httpd paths on the list, OR enter the >>path you wish to use: >> /usr/sbin/apache >> /usr/sbin/apache2 >>[1]: /caprisa/usr/local/apache2/bin/apachectl >> >></snip> >> >>It looks like you've given it the path to apachectl rather than apache. >> >>It needs to know the path to the apache binary itself (sometimes also >>called httpd or apache2), not the apachectl binary. >> >>Although I can't say exactly what would happen if you gave it the >>apachectl binary, as I've never tried it, its safer to try again with >>the correct one before going any further. >> >>Also, to do an absolutely clean reconfiguration after problems like >>this, you need to append the '--clean' switch to the call to >>configure.pl, eg.: >> >> perl bin/configure.pl -r martRegistry.xml --clean >> >>If you don't use the --clean switch then it will attempt to reuse the >>cached compiled configuration from your previous attempt, which >>potentially could cause problems if the previous attempt failed. >> >>cheers, >>Richard >> >>[EMAIL PROTECTED] wrote: >> >> >>>Hi Syed, >>>I did a clean reconfiguration this time I received a warning during >>>configuration as follows. >>> >>> >>>>perl bin/configure.pl -r conf/martDBLocation.xml >>>> >>>> >>>Do you want to install in API only mode [y/n] [n]: >>> >>>Checking prerequisites ...[Looks good] >>> >>> >>>DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n >>>Checking several common Apache locations...done. >>> >>>Select either one of the detected httpd paths on the list, OR enter the >>>path you wish to use: >>> /usr/sbin/apache >>> /usr/sbin/apache2 >>>[1]: /caprisa/usr/local/apache2/bin/apachectl >>>Got usable Apache in /caprisa/usr/local/apache2/bin/apachectl, probing >>> for >>>version & ModPerl configuration >>>Have Apache DSO-support and ModPerl library file present, configuring >>>ModPerl in httpd.conf. >>> >>>Enter the server host OR default [ruth]: >>> >>>Enter the server port OR default [5555]: >>> >>>Enter proxy OR default : >>> >>>Enter the required script location OR default [biomart]: >>>Libdir /home/ruby/prj/biomart/biomart-test2/lib is not in @INC, adding >>> to >>>@INC >>> >>>Processing Cached Registry: >>>/home/ruby/prj/biomart/biomart-test2/conf/cachedRegistries/martDBLocation.xml.cached >>> >>> >>> >>>Then I receive an error when I try accessing the web application as >>> follows. >>> >>>[Thu Mar 22 17:32:06 2007] [error] [client 127.0.0.1] Use of >>> uninitialized >>>value in concatenation (.) or string at >>>/usr/lib/perl5/ModPerl/RegistryCooker.pm line 636.\n, referer: >>>http://localhost:5555/ >>> >>>Am attaching the current conf/httpd.conf >>> >>> >>>Allan. >>> >>> >>> >>>>Hi Allan >>>>I can see that there are configuration directives completely missing >>>>from your httpd.conf. >>>> >>>>Please do a clean check out, and reconfigure again. >>>> >>>>Cheers >>>>Syed >>>> >>>> >>>>On Thu, 2007-03-22 at 17:01 +0200, allank wrote: >>>> >>>> >>>>>Hi all, >>>>>I am experiencing an error running Biomart 0.5, the web browser >>>>> reports >>>>>internal server error a look at the logs (of my biomart-perl >>>>> directory) >>>>>shows a "No such file or directory: exec of .. cgi-bin/martview. >>>>>The configuration process(perl bin/configure.pl -r >>>>>conf/myRegisteration.xml) goes through successfully, but I get an >>>>>internal server error when I try accessing the web resource of my >>>>> newly >>>>>installed biomart via a browser. >>>>> >>>>>Allan. >>>>> >>>>> >>>>> >>>>-- >>>>====================================== >>>>Syed Haider. >>>>EMBL-European Bioinformatics Institute >>>>Wellcome Trust Genome Campus, Hinxton, >>>>Cambridge CB10 1SD, UK. >>>>====================================== >>>> >>>> >>>> >>>> >>-----BEGIN PGP SIGNATURE----- >>Version: GnuPG v1.4.2.2 (GNU/Linux) >>Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org >> >>iD8DBQFGAq7x4C5LeMEKA/QRArTdAJ9erpZ0hdmzonM8imx066IXY4+nxQCghUqi >>e5H/l5K0CWuZfiYZV4kDaeU= >>=/ot6 >>-----END PGP SIGNATURE----- >> >> > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
