Hi Richard, could you let me know how to use --clean option in detail? I checked the error_log which says:
[warn] pid file /var/www/html/biomart-perl/logs/httpd.pid overwritten -- Unclean shutdown of previous Apache run? [Tue Jan 13 15:55:44 2009] [alert] getpwuid: couldn't determine user name from uid 4294967295, you probably need to modify the User directive [Tue Jan 13 15:55:44 2009] [alert] getpwuid: couldn't determine user name from uid 4294967295, you probably need to modify the User directive [Tue Jan 13 15:55:44 2009] [notice] Apache/2.2.6 (Unix) mod_perl/2.0.2 Perl/v5.8.8 configured -- resuming normal operations [Tue Jan 13 15:55:44 2009] [alert] Child 24664 returned a Fatal error... Apache is exiting! do you have any idea from this information? Thanks! Dong > Also it might be worth checking the contents of the conf/httpd.conf file > to see if it has correctly populated it with the correct port numbers etc. > > If it hasn't, rerun bin/configure.pl with the --clean option to force it > to regenerate httpd.conf properly. > > cheers, > Richard > > [email protected] wrote: >> Hi Syed, >> >> Actually, the host name 'mandolin.caltech.edu' is already in the >> /etc/hosts file and the web server works well. I follow your suggestion >> to >> try 127.0.0.1, the same trouble happened. could you give me other >> suggestion? >> Thank you! >> >> Dong >> >> >>> Hi Dong, >>> >>> your apache startup error says it all, the apache server doesnt >>> recognise your host name (the one which you are specifying in >>> settings.conf). You need to modify the /etc/hosts file on your system >>> and then restart apache server. Once done, reconfigure BioMart (only >>> perl bin/configure.pl....) and restart your apache. A good test would >>> be to put 127.0.0.1 in settings.conf and configure Biomart, restart >>> apache and see if you can access the webserver on >>> http://127.0.0.1:5430/biomart/martview >>> >>> Stepwise solution can be seen here: >>> >>> http://digitaldeviation.com/articles/apache-articles/apache-error-could-not-reliably-determine-servers-fully-qualified-domain-na >>> >>> Good Luck!, >>> Syed >>> >>> >>> >>> [email protected] wrote: >>>> Hi Syed, >>>> >>>> here is the output after configure: >>>> >>>> # 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] >>>> >>>> APACHE: /usr/sbin/httpd >>>> HOST: http://mandolin.caltech.edu >>>> PORT: 5430 >>>> PROXY: >>>> LOCATION: biomart >>>> >>>> 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 >>>> >>>> Processing Cached Registry: >>>> /var/www/html/biomart-perl/conf/cachedRegistries/spbase_annotation1022_6.xml.cached >>>> >>>> # /usr/sbin/httpd -d $PWD -f $PWD/conf/httpd.conf >>>> >>>> Processing Cached Registry: >>>> /var/www/html/biomart-perl/conf/cachedRegistries/spbase_annotation1022_6.xml.cached >>>> >>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in line >>>> 131. >>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in line >>>> 139. >>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in line >>>> 158. >>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in line >>>> 169. >>>> [Tue Jan 13 10:00:26 2009] [warn] Useless use of AllowOverride in line >>>> 185. >>>> httpd: Could not reliably determine the server's fully qualified >>>> domain >>>> name, using mandolin.caltech.edu for ServerName >>>> >>>> ------------------------------------------------------------------------ >>>> attached are the httpd.conf and settings.conf. >>>> >>>> Thank you very much for your help! >>>> >>>> Dong >>>> >>>> >>>>> Hi Dong, >>>>> >>>>> please send me the following: >>>>> >>>>> - conf/httpd.conf >>>>> - on screen output when you run perl bin/configure.pl...... >>>>> - conf/settings.conf >>>>> >>>>> >>>>> thanks >>>>> Syed >>>>> >>>>> >>>>> [email protected] wrote: >>>>> >>>>>> Hi Friends: >>>>>> >>>>>> I successfully set up a mart in one of my machines, then, I moved >>>>>> whole >>>>>> mart database into another machine, and the configuring ("perl >>>>>> bin/configure.pl -r conf/annotation1022_6.xml", "/usr/sbin/httpd -d >>>>>> $PWD >>>>>> -f $PWD/conf/httpd.conf")seems work, however, when point web browser >>>>>> to >>>>>> the corresponding URL, I got a error: "Firefox can't establish a >>>>>> connection to the server at mandolin.caltech.edu:5430." does this >>>>>> mean >>>>>> mart is not portable? do I have to build mart at each machine >>>>>> separately? >>>>>> or I missed some httpd configuration? >>>>>> Thanks! >>>>>> >>>>>> Dong >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >> >> >> > > -- > Richard Holland, BSc MBCS > Finance Director, Eagle Genomics Ltd > M: +44 7500 438846 | E: [email protected] > http://www.eaglegenomics.com/ >
