> 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
oops... the above file lives under biomart-perl/conf/ syed. > > 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. > ====================================== > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
