Morning Damian et al, Thanks for your response, i implemented your proposals up to step 3 (so far so good), where i ran into this error which seems classical looking at the past mart-dev mail archive: http://www.mail-archive.com/[email protected]/msg02259.html I did not find a solution offered on how to go about installing mod_deflate.so Any suggestion please? Thank you Nelson
The error i get in step 3: [nnde...@reactome2 biomart-perl]$ /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd -d $PWD -f /homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/conf/httpd.conf httpd: Syntax error on line 36 of /homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/conf/httpd.conf: Cannot load /homes/nndegwa/reactomes/Reactome/test/GKB/BioMart/apache/modules/mod_deflate.so into server: /homes/nndegwa/reactomes/Reactome/test/GKB/BioMart/apache/modules/mod_deflate.so: cannot open shared object file: No such file or directory > Hi Nelson, > > You definitely should not need to touch apache's httpd.conf file at all > and > it will be fine to run the reactome website and BioMart off the same > apache > unless performance becomes an issue. Put the httpd.conf file back how it > was > and instead edit conf/settings.conf in the biomart-perl directory to > change > the port from 80 to some other port but it sounds like you may have > already > changed it to 9002? > > Anyhow for now, once you have reinstated your httpd.conf file in the > biomart-perl directory do the following and let is know what errors you > get: > > (i) from the biomart-perl directory kill `cat logs/httpd.pid` > (ii) perl bin/configure.pl --clean -r conf/martReg.xml replacing the > martReg.xml with whatever your registry is called > (iii) /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/bin/httpd -d > $PWD > -f /homes/nndegwa/biomart-perl/conf/httpd.conf replacing the argument to > -f > with wherever your biomart-perl install is. You should be using the > biomart-perl httpd.conf. Below you were using the one in your apache > install. > (iv) if working point your browser to localhost:9002/biomart/martview > > Let us know how that goes. > > Cheers > Damian > > > On Tue, Mar 23, 2010 at 4:51 AM, <[email protected]> wrote: > >> Hi All, >> Firstly, i would like to thank all who took their time and offered >> really >> helpful suggestions to troubleshoot my task of installing Biomart 0.7 on >> 64 bit linux. >> May i mention that as i do not have root access to the machine am using, >> i >> installed my own - lets say most of the things (64 bit perl, apache, the >> works, edited .bashrc file to point to my installed perl and updated the >> required modules via cpan) >> I have made some progress so far: >> I have my local reactome website up and running - Biomart:query, link is >> my main worry. >> Successfully completed configuring MartView (section 1.4.3.2) >> I was able to start Martview (didn't attempt to stop it) - however a few >> interesting things happened here - so here i am with more questions >> >> NB: Both the reactome website (mostly written in perl) and Biomart are >> sharing the same Perl and apache i installed - not sure how bad this is. >> The first time i attempted to configure martview as shown below, i got >> the >> error shown >> >> [my_shell]$/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. >> >>> >> >>> >> >>> >> >> >> >> >> >> >> > >> > >> >> >> >
