Hi Syed,
Thank you very much!! this problem seems solved, however, there is another
problem showing up, could you help me again? error_log says:
[error] Error in processing template error.tt: file error - cache failed
to write error.ttc: Error in tempfile() using /var/www/ht
ml/biomart-perl/conf/templates/default/XXXXXXXXXX: Parent directory
(/var/www/html/biomart-perl/conf/templates/default/) is not writable\n at
/usr/lib/perl5/
site_perl/5.8.8/i386-linux-thread-multi/Template/Document.pm line
295\n\n\nTrace begun at /var/www/html/biomart-perl/lib/BioMart/Web.pm line
267\nBioMart::We
b::process_template('BioMart::Web=HASH(0x81ec2e0c)', 'error.tt',
'HASH(0x84383194)') called at /var/www/html/biomart-perl/cgi-bin/martview
line 122\nModPerl:
:ROOT::ModPerl::Registry::var_www_html_biomart_2dperl_cgi_2dbin_martview::handler('Apache2::RequestRec=SCALAR(0x8421355c)')
called at /usr/lib/perl5/vendor_p
erl/5.8.8/i386-linux-thread-multi/ModPerl/RegistryCooker.pm line 203\neval
{...} at
/usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/ModPerl/Registry
Cooker.pm line
203\nModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0x84213610)')
called at /usr/lib/perl5/vendor_perl/5.8.8/i386-linux-thread-multi/Mod
Perl/RegistryCooker.pm line
169\nModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0x84213610)')
called at /usr/lib/perl5/vendor_perl/5.8.8/i3
86-linux-thread-multi/ModPerl/Registry.pm line
30\nModPerl::Registry::handler('ModPerl::Registry',
'Apache2::RequestRec=SCALAR(0x8421355c)') called at -e lin
e 0\neval {...} at -e line 0\n
Dong
> Hi Dong,
>
> the --clean option is a perl bin/configure.pl switch e.g
> perl bin/configure.pl -r conf/your_reg.xml --clean
> see docs for details.
>
> it seems that your httpd.conf needs a apache user directive, the user
> who has rights to start/stop apache. please manually add this to
> conf/httpd.conf and then start your apache. This is most likely the case.
>
> cheers
> Syed
>
>
> [email protected] wrote:
>> 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/
>>>
>>>
>>
>>
>
