Hi Syed, Yes, I found some errors when I isntalled mod_perl. Here is the errors message. If you have a chance, could you please have a look at what the problem might be? Thanks, > perl Makefile.PL \ > PREFIX=/usr/local/apache2 \ MP_APXS=/usr/local/apache2/bin/apxs errors: Use of uninitialized value in length at /usr/lib/perl5/5.8.8/ExtUtils/Command/MM.pm line 134. /usr/bin/perl -Iblib/lib -I/home/software/biomart-perl/apache/source/mod_perl-2.0.4/Apache-Test/lib -MModPerl::BuildMM -e ModPerl::BuildMM::glue_pod WrapXS/APR/Date/Date.pm /home/software/biomart-perl/apache/source/mod_perl-2.0.4/docs/api/APR/Date.pod blib/lib/APR/Date.pm Manifying blib/man3/APR::Date.3pm Use of uninitialized value in length at /usr/lib/perl5/5.8.8/ExtUtils/Command/MM.pm line 134. /usr/bin/perl -Iblib/lib -I/home/software/biomart-perl/apache/source/mod_perl-2.0.4/Apache-Test/lib -MModPerl::BuildMM -e ModPerl::BuildMM::glue_pod WrapXS/APR/Pool/Pool.pm /home/software/biomart-perl/apache/source/mod_perl-2.0.4/docs/api/APR/Pool.pod blib/lib/APR/Pool.pm Manifying blib/man3/APR::Pool.3pm Use of uninitialized value in length at /usr/lib/perl5/5.8.8/ExtUtils/Command/MM.pm line 134. /usr/bin/perl -Iblib/lib -I/home/software/biomart-perl/apache/source/mod_perl-2.0.4/Apache-Test/lib -MModPerl::BuildMM -e ModPerl::BuildMM::glue_pod WrapXS/APR/Base64/Base64.pm /home/software/biomart-perl/apache/source/mod_perl-2.0.4/docs/api/APR/Base64.pod blib/lib/APR/Base64.pm
Ray ________________________________ From: Syed Haider [mailto:[email protected]] Sent: Sat 12/5/2009 6:52 PM To: Jing, Rui Cc: Junjun Zhang; [email protected] Subject: Re: [mart-dev] errors when starting martview Hi Ray, As per exception, this is most likely due to the absence or incorrect configuration of mod_perl. please check that. Cheers Syed Jing, Rui wrote: > Hi Syed, > > I installed mod_deflate.so. when I ran , it has the following errors: > >> /usr/local/apache2/bin/httpd -d $PWD -f $PWD/conf/httpd.conf > Processing Cached Registry: > /home/software/biomart-perl/conf/cachedRegistries/martDBLocation.xml.cached > Syntax error on line 37 of /home/software/biomart-perl/conf/httpd.conf: > failed to resolve handler `Apache2::PerlSections': Can't locate > Apache2/PerlSections.pm in @INC (@INC contains: /home/software/biomart-perl/lib > /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi > /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi > /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi > /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 > /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 > /usr/lib/perl5/site_perl > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi > /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi > /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi > /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi > /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 > /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 > /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi > /usr/lib/perl5/5.8.8 . /home/software/biomart-perl) at (eval 115) line 3.\n > > Could you please let me know the problems? > Thanks, > > Ray > > ________________________________ > > From: Syed Haider [mailto:[email protected]] > Sent: Fri 12/4/2009 1:54 PM > To: Jing, Rui > Cc: Junjun Zhang; [email protected] > Subject: Re: [mart-dev] errors when starting martview > > > > Hi Ray, > > you apaache needs the following module: > > mod_deflate.so > > as stated in the exception. > > Cheers > Syed > > > Jing, Rui wrote: >> Hi, >> >> When I ran, it giave the following errors >> /usr/local/apache2/bin/httpd -d $PWD -f $PWD/conf/httpd.conf >> httpd: Syntax error on line 36 of /home/software/biomart-perl/conf/httpd.conf: >> Cannot load /usr/local/apache2/modules/mod_deflate.so into server: >> /usr/local/apache2/modules/mod_deflate.so: cannot open shared object file: No >> such file or directory >> >> Could you please let me know the reason? >> >> Thanks, >> >> Ray >> >> >> >> >> >> ________________________________ >> >> From: Junjun Zhang [mailto:[email protected]] >> Sent: Thu 12/3/2009 12:35 AM >> To: Jing, Rui; Syed Haider >> Cc: Arek Kasprzyk; [email protected] >> Subject: RE: [mart-dev] errors when starting martview >> >> >> >> >>> -----Original Message----- >>> From: Jing, Rui [mailto:[email protected]] >>> Sent: Thursday, December 03, 2009 12:13 AM >>> To: Syed Haider >>> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >>> Subject: RE: [mart-dev] errors when starting martview >>> >>> Hi Syed, >>> >>> when I ran, it gave the following info. >>> >>>> /common/home/software/biomart-perl/apache/bin/httpd -d $PWD -f >>> $PWD/conf/httpd.conf >>> Processing Cached Registry: >>> /common/home/software/biomart-perl/conf/cachedRegistries/martD >>> BLocation.xml.cach >>> ed >>> >>> then I try to visit biomart >>> http://node01.com:8011/biomart-perl/martview >>> it does not work. >> It looks fine when you start apache. Please try this URL instead: >> >> http://node01.com:8011/biomart/martview or just try this one >> http://node01.com:8011/ (there is a link on this page that takes you to >> martview). >> >> That should work. >> >> Cheers, >> Junjun >> >> >> >> >>> Could you please let me know what the problem is? >>> Thanks, >>> >>> Ray >>> >>> >>> >>> ________________________________ >>> >>> From: Syed Haider [mailto:[email protected]] >>> Sent: Thu 11/26/2009 9:59 AM >>> To: Jing, Rui >>> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >>> Subject: Re: [mart-dev] errors when starting martview >>> >>> >>> >>> >>> >>> Jing, Rui wrote: >>>> Hi Syed, >>>> >>>> Here is screen copy after execute b. >>>> by the way, I installed my local biomart into >>> /common/home/software/biomart-perl >>>> (it is biomart-perl, do I need change settings.conf, >>> LOCATION= biomart >>>> to LOCATION=biomart-perl ? >>> no biomart is just fine, thats what becomes the part of your >>> URL, its not the location of biomart-perl on disk. >>> >>> could you also add the path to apxs or apxs2 in >>> setttings.conf and redo the configure with --clean. >>> >>> once done, please let us know if that works, also send us the >>> screen copy of terminal . >>> >>> thanks >>> Syed >>> >>> >>>> [r...@node01 50]> perl bin/configure.pl -r conf/martDBLocation.xml >>>> --clean Do you want to install in API only mode [y/n] [n]: >>> n Checking >>>> prerequisites ...[Looks good] >>>> APACHE: /common/home/software/biomart-perl/apache/bin/httpd >>>> HOST: localhost >>>> PORT: 8011 >>>> PROXY: >>>> LOCATION: biomart >>>> APXS/2: >>>> You can change the above configuration by editing >>>> "biomart-perl/conf/settings.conf" >>>> >>>> Got usable Apache in >>>> /common/home/software/biomart-perl/apache/bin/httpd, >>>> probing for version & ModPerl configuration Have Apache DSO-support >>>> and ModPerl library file present, configuring ModPerl >>> in >>>> httpd.conf. >>>> Libdir /common/home/software/biomart-perl/lib is not in >>> @INC, adding >>>> to @INC Connection parameters of [My BioMart Database] [ OK ] >>>> >>>> [NEW CONFIGURATION] .... WITH MEMORY [default] default ... >>> My BioMart >>>> Database ...... 001/001 ... msd >>>> ....................................... (RDBMS) >>> martdb.ebi.ac.uk:3306 >>> ......... >>>> -> upgrading to 0.6/0.7 ... OK >>>> Setting possible links between datasets >>>> ....(scanning) 100% >>>> ....(linking) 100% >>>> ....(sorting) 100% >>>> ....(clustering) 1/1 - 0 remain >>>> ....(resolving) 100% >>>> Building templates for visible datasets .... 100% Compiling >>> templates >>>> for visible datasets [1/1] Attribute Panel of Dataset.. :msd [1/1] >>>> Filter Panel of Dataset..... :msd >>>> >>>> Thanks, >>>> >>>> Ray >>>> >>>> ________________________________ >>>> >>>> From: Syed Haider [mailto:[email protected]] >>>> Sent: Thu 11/26/2009 9:27 AM >>>> To: Jing, Rui >>>> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >>>> Subject: Re: [mart-dev] errors when starting martview >>>> >>>> >>>> >>>> a- please set the location param in conf/settings.conf to >>>> location=biomart >>>> >>>> b- reconfigure the perl bin/configure.pl.... with --clean switch >>>> >>>> c- kill and restart apache and then access the URL as: >>>> http://node01.com:8011/biomart/martview >>>> >>>> >>>> please send us what see in terminal after executing 'b' >>>> >>>> thanks >>>> Syed >>>> >>>> >>>> >>>> >>>> Jing, Rui wrote: >>>>> Hi Syed, >>>>> >>>>> Great. It started. >>>>> Processing Cached Registry: >>>>> >>> /common/home/software/biomart-perl/conf/cachedRegistries/martD >>> BLocation.xml.cach >>>>> ed >>>>> >>>>> cat logs/httpd.pid >>>>> 19006 >>>>> >>>>> but when I visit hthttp://node01.com:8011/biomart-perl/martview >>>>> <http://node01.com:8011/biomart-perl/martview> >>>>> it gave error: Oops! This link appears to be broken from IE. >>>>> >>>>> I used martDBLocation.xml >>>>> perl bin/configure.pl -r conf/martDBLocation.xml --clean >>>>> >>>>> settings.conf is: >>>>> 5 >>> apacheBinary=/common/home/software/biomart-perl/apache/bin/httpd >>>>> 6 serverHost=localhost >>>>> 7 port=8011 >>>>> 8 # to use proxying set the proxy port below (even >>> if its 80) >>>>> and set serverHost as your proxy host >>>>> 9 proxy= >>>>> 10 # if apxs or apxs2 is not in default directory where httpd >>>>> lives, you may set this param to point to apxs/2 >>>>> 11 apxs= >>>>> 12 location=/common/home/software/biomart-perl >>>>> 13 >>>>> >>>>> please advise what the problem is. >>>>> Thanks, >>>>> >>>>> Ray >>>>> >>>>> ________________________________ >>>>> >>>>> From: Syed Haider [mailto:[email protected]] >>>>> Sent: Thu 11/26/2009 8:39 AM >>>>> To: Jing, Rui >>>>> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >>>>> Subject: Re: [mart-dev] errors when starting martview >>>>> >>>>> >>>>> >>>>> Hi Rui, >>>>> >>>>> >>>>> the only critical error is : >>>>> >>>>> Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf: >>>>> Invalid command 'PerlOptions', perhaps misspelled or defined by a >>>>> module not included in the server configuration >>>>> >>>>> >>>>> you would need to see the onscreen instrcutions when you run: >>>>> >>>>> perl bin/configure.pl..... >>>>> >>>>> you probably dont have mod_perl or somehting configured correctly. >>>>> >>>>> >>>>> Best, >>>>> Syed >>>>> >>>>> Jing, Rui wrote: >>>>>> Hi, >>>>>> >>>>>> When I am starting martview, there are some error and >>> warn, please >>>>>> advise >>> how >>>>> to >>>>>> solve the problem. >>>>>> >>>>>> [r...@]> /software/biomart-perl/apache/bin/httpd -d $PWD -f >>>>> $PWD/conf/httpd.conf >>>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>>> line 37 of /common/home/hge/software/biomart-perl/conf/httpd.conf. >>>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>>> line 45 of /common/home/hge/software/biomart-perl/conf/httpd.conf. >>>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>>> line 63 of /common/home/hge/software/biomart-perl/conf/httpd.conf. >>>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>>> line 73 of /software/biomart-perl/conf/httpd.conf. >>>>>> Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf: >>>>>> Invalid command 'PerlOptions', perhaps misspelled or defined by a >>>>>> module not included in the server configuration >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Ray >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is addressed. 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