Did you build your Apache with --enable-deflate (see instructions I sent you before)... looks like you didn't
-L On Wed, Mar 24, 2010 at 11:24 AM, <[email protected]> wrote: > 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 $PWD -f > >> /homes/nndegwa/reactomes/Reactome/test/httpd-2.2.15/conf/httpd.conf > >> > >> The error that comes up is: > >> (13)Permission denied: make_sock: could not bind to address > >> 0.0.0.0:80<http://0.0.0.0/> > >> no listening sockets available, shutting down > >> Unable to open logs > >> > >> I went ahead to edit httpd.conf file by commenting out the 'Listen 80' > >> to > >> '#Listen 80'. Now i get the following different error from previous > >> above > >> when i attempt to configure martview as in 2.4.4: > >> > >> [my_shell]$ > >> /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. > >> >>> > >> >>> > >> >>> > >> >> > >> >> > >> >> > >> > > >> > > >> > >> > >> > > > > >
