Hi Giulia I have seen your httpd.conf and surprisingly I can see the directives of mod_gzip, which refers to Apache 1.3x and Mod_perl 1 series setup. You mentioned, now you are using Apache 2 with mod_perl 2. Is it an old file you have sent, or this is the new file you are using with your new Apache 2/modperl 2 setup. If thats the case, try reconfiguring your biomart-perl setup so it generates httpd.conf as per new apache binary.
Cheers Syed On Mon, 2007-03-12 at 12:05 +0100, Giulia De Sario wrote: > Hi, > since the problem is still there I've tried to switch to a new > configuration... > as you can see from my biomart/apache logs > > [Sun Mar 11 19:08:03 2007] [notice] Apache/2.2.3 (Unix) mod_perl/2.0.3 > Perl/v5.8.0 configured -- resuming normal operations > > now I'm using apache2 and mod_perl2 but if you go on > > http://beagle01.ba.itb.cnr.it:5555/biomart/martview > > the page is not displayed correctly also if the apache server works (for > example you could start from > http://beagle01.ba.itb.cnr.it:5555/index.html ) > Maybe there is something related to the httpd.conf created by biomart > (it is in attach). > > Giulia. > > -----Messaggio originale----- > Da: Syed Haider [mailto:[EMAIL PROTECTED] > Inviato: giovedì 8 marzo 2007 13.34 > A: 'Giulia De Sario'; Arek Kasprzyk; 'BioMart mart-dev' > Oggetto: Re: Fwd: R: R: R: R: Segmentation fault > > Hi Giulia > The mod_gzip transmit error refers to your mod_gzip addition to apache > 1.3x. For debugging sake, I would suggest to remove apache and install > it without mod_gzip support. Its very good to have it eventually when > confirmed thats its mod_gzip. I had similar experience with mod_gzip and > finally got that to work after few tweaks. > > Do write how it goes. > > Good luck! > > Kind Regards > Syed > > On Thu, 2007-03-08 at 12:27 +0000, Arek Kasprzyk wrote: > > > > > > ______________________________________________________________________ > > > > > > > > Begin forwarded message: > > > > From: "Giulia De Sario" <[EMAIL PROTECTED]> > > Date: 8 March 2007 12:22:49 GMT > > To: "'Arek Kasprzyk'" <[EMAIL PROTECTED]> > > Subject: R: R: R: R: Segmentation fault > > > > This is the error ... > > > > [Thu Mar 8 13:03:26 2007] [error] mod_gzip: > > TRANSMIT_ERROR:104 > > [Thu Mar 8 13:08:38 2007] [error] [client 193.62.198.98] File > > does not > > exist: > /biotools/analysis-interfaces/biomart-perl/htdocs/favicon.ico > > > > -----Messaggio originale----- > > Da: Arek Kasprzyk [mailto:[EMAIL PROTECTED] > > Inviato: giovedì 8 marzo 2007 13.13 > > A: Giulia De Sario > > Cc: 'BioMart mart-dev' > > Oggetto: Re: R: R: R: Segmentation fault > > > > > > On 8 Mar 2007, at 12:07, Giulia De Sario wrote: > > > > Hi Arek, > > > > I have good news. > > I have forced the installation of mod_gzip and the > > restarted the > > biomart > > service and now I'm able to see the page > > > > http://beagle01.ba.itb.cnr.it:5555/biomart/martview > > > > Is it correct? > > I'll write you more details about the installation > > Thanks > > > > Hi Giulia, > > it looks very correct but it does not quite work correct > > yet :) > > Nothing happens when you click the 'Results' button. > > > > Could you look what happens in error_log when > > you click martview or even better, could you re-install > > BioMart > > and try it again? > > > > > > a. > > > > > > > > G > > > > -----Messaggio originale----- > > Da: Arek Kasprzyk [mailto:[EMAIL PROTECTED] > > Inviato: mercoledì 7 marzo 2007 14.38 > > A: Giulia De Sario > > Cc: 'BioMart mart-dev' > > Oggetto: Re: R: R: Segmentation fault > > > > > > On 7 Mar 2007, at 10:55, Giulia De Sario wrote: > > > > > > I don't if it could be an important > > information, but i have installed > > mod_perl in this way: > > > > cd /biotools/install/mod_perl-1.29 > > > > perl Makefile.PL USE_DSO=1 PERL_SECTIONS=1 > > cd /root/apache_1.3.34 > > > > ./configure > > --activate-module=src/modules/gzip/mod_gzip.c > > --activate-module=src/modules/php4/libphp4.a > > --activate-module=src/modules/perl/libperl.a > > --prefix=/var/www/ > > > > make > > > > make install > > > > Now I'm having the same problem non only with > > the daemon related at > > biomart, > > but also with the apache daemons running on > > port 80 > > > > > > Hi Giulia, > > yes it is clear that this is not a BioMart install > > problem but > > apache/mod_perl > > install problem. > > > > Do other people have idea how to best diagnose it/fix > > it? > > > > a. > > > > > > > > > ----------------------------------------------------------------------- > > - > > > > ------- > > Arek Kasprzyk > > EMBL-European Bioinformatics Institute. > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > Tel: +44-(0)1223-494606 > > Fax: +44-(0)1223-494468 > > > > > ----------------------------------------------------------------------- > > - > > > > ------- > > > > > > > > __________ Informazione NOD32 2100 (20070307) > > __________ > > > > Questo messaggio è stato controllato dal Sistema > > Antivirus NOD32 > > http://www.nod32.it > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > ------- > > Arek Kasprzyk > > EMBL-European Bioinformatics Institute. > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > Tel: +44-(0)1223-494606 > > Fax: +44-(0)1223-494468 > > > ------------------------------------------------------------------------ > > > > ------- > > > > > > > > > > __________ Informazione NOD32 2100 (20070307) __________ > > > > Questo messaggio è stato controllato dal Sistema Antivirus > > NOD32 > > http://www.nod32.it > > > > > > > > > > > > > ------------------------------------------------------------------------ > ------- > > Arek Kasprzyk > > EMBL-European Bioinformatics Institute. > > Wellcome Trust Genome Campus, Hinxton, > > Cambridge CB10 1SD, UK. > > Tel: +44-(0)1223-494606 > > Fax: +44-(0)1223-494468 > > > ------------------------------------------------------------------------ > ------- > > > > > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
