Hi All, Firstly, i would like to thank all who took their time and offered really helpful suggestions to troubleshoot my task of installing Biomart 0.7 on 64 bit linux. May i mention that as i do not have root access to the machine am using, i installed my own - lets say most of the things (64 bit perl, apache, the works, edited .bashrc file to point to my installed perl and updated the required modules via cpan) I have made some progress so far: I have my local reactome website up and running - Biomart:query, link is my main worry. Successfully completed configuring MartView (section 1.4.3.2) I was able to start Martview (didn't attempt to stop it) - however a few interesting things happened here - so here i am with more questions
NB: Both the reactome website (mostly written in perl) and Biomart are sharing the same Perl and apache i installed - not sure how bad this is. The first time i attempted to configure martview as shown below, i got the error shown [my_shell]$/homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd -d $PWD -f /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/conf/httpd.conf The error that comes up is: (13)Permission denied: make_sock: could not bind to address 0.0.0.0:80 no listening sockets available, shutting down Unable to open logs I went ahead to edit httpd.conf file by commenting out the 'Listen 80' to '#Listen 80'. Now i get the following different error from previous above when i attempt to configure martview as in 2.4.4: [my_shell]$ /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd -d $PWD -f /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/conf/httpd.conf no listening sockets available, shutting down Unable to open logs So i threw in some arbitrary port number 'Listen 5555' and repeated the same command and this time round there was no more complaints. The following 'http://localhost:5555/' on my browser yields a bold "It works!" statement but 'http://localhost:5555/biomart/martview' says something else: '404 Not Found The requested URL /biomart/martview was not found on this server.' Another interesting thing is that 'http://localhost:9002/' on the browser brings up a nice logo and some info and a link to start Martview session " BioMart logo version 0.7 Start BioMart BioMart is a generic data management system which offers a range of advanced query interfaces and administration tools..... Start MartView session " When i click this link however i get the following error: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator, [no address given] and inform them of the time the error occurred, and anything you might have done that may have caused the error. More information about this error may be available in the server error log." So i head back to the biomart-perl/logs and the errors given are many, as shown below, i however tried to first rule out any require module errors by getting those modules required via cpan and the only one i did actually install was Time::HiRes, the rest according to CPAN were existing and up to date. In spite of this effort, the error logs remained exactly the same. [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] DynaLoader object version 1.08 does not match $DynaLoader::XS_VERSION 1.0802 at /homes/nndegwa/reactomes/Reactome/test/perl64/lib/DynaLoader.pm line 92., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Time/HiRes.pm line 7., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Util/TimeTracker.pm line 19., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN failed--compilation aborted at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Util/TimeTracker.pm line 22., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout/PatternLayout.pm line 14., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN failed--compilation aborted at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout/PatternLayout.pm line 14., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout.pm line 5., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN failed--compilation aborted at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Layout.pm line 5., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Logger.pm line 11., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN failed--compilation aborted at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl/Logger.pm line 11., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl.pm line 12., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN failed--compilation aborted at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl.pm line 12., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Compilation failed in require at /automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/cgi-bin/martview line 43., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] BEGIN failed--compilation aborted at /automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/cgi-bin/martview line 43., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Undefined subroutine &Log::Log4perl::Logger::cleanup called at /homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/Log/Log4perl.pm line 5., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] END failed--call queue aborted at /automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/cgi-bin/martview line 43., referer: http://localhost:9002/ [Tue Mar 23 11:36:31 2010] [error] [client 127.0.0.1] Premature end of script headers: martview, referer: http://localhost:9002/ This is the furthest i have got and would greatly appreciate your assistance. Thank you Kind Regards, Nelson PS: Sorry for the lengthy message, i hope it reveals the minimum information needed to troubleshoot. > [email protected] wrote: >> Hi James, >> I tried out Leandro's suggestion and still got the same error. >> I have notified him to see if he perhaps might offer some other >> suggestions. >> I would also like to know how you guys got round this issue - i would >> really appreciate. Thanks >> Nelson >> >> >> > Comment out "use CGI::Session::Driver::db_file;" in the BioMart::Web > module! >>> Leandro Hermida wrote: >>> >>>> Hi, >>>> >>>> Sorry to chime in in the middle, something is up with your Perl. >>>> Using the same Perl that have used to build your BioMart and run the >>>> BioMart configure script, try the following: >>>> >>>> perl -e 'use DB_File;' >>>> or >>>> perl -MDB_File >>>> >>>> do you get the same error? >>>> >>> Ensembl got round this issue by commenting the line out the use DB_File >>> in the mart code (along with a number of other tweaks we make) to >>> remove >>> this necessity - as we use MySQL sessions anyway. >>> >>> >>> >> >> >> > >
