[mart-dev] problem with biomart-0.7 on RedHat Linux AS4

Mirjam van den Hout - van Vroonhoven Thu, 03 Jul 2008 07:17:30 -0700

Dear all,


I'm trying to install biomart on a Redhat AS4 server, but apache fails
to start with the error message:

[EMAIL PROTECTED] biomart-perl]$ /usr/sbin/httpd -d $PWD -f$PWD/conf/httpd.conf

Processing Cached Registry:/usr/local/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached


  failed to resolve handler Apache::PerlSections

  [EMAIL PROTECTED] biomart-perl]$


I am using the RedHat default rpms for apache and mod_perl
  httpd-2.0.52-38.ent.2-x86_64
  mod_perl-1.99_16-4.5-x86_64
These are already running nicely on port 80 (as user apache), serving
some other content.  I want biomart to run on port 8000, as user
biomart.

I followed all the instructions carefully, installed a bunch of perl
modules, as instructed by configure.pl. I edited the settings.conf file
to have apache listen for biomart on port 8000, the first couple of
lines now read:

  [httpdSettings]
  apacheBinary=/usr/sbin/httpd
  serverHost=bioinf-intra.erasmusmc.nl
  port=8000

The output of the biomart configuration is:

[EMAIL PROTECTED] biomart-perl]$ perl bin/configure.pl -rconf/registryURLPointer.xml


  Do you want to install in API only mode [y/n] [n]:

  Checking prerequisites ...[Looks good]

Subroutine BioMart::Web::Zlib::adler32 redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20Subroutine BioMart::Web::Zlib::crc32 redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at/usr/lib/perl5/5.8.5/Exporter.pm line 65.at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pmline 20


  APACHE: /usr/sbin/httpd
  HOST: bioinf-intra.erasmusmc.nl
  PORT: 8000
  PROXY:
  LOCATION: biomart

You can change the above configuration by editing"biomart-perl/conf/settings.conf"

Got usable Apache in /usr/sbin/httpd, probing for version & ModPerlconfigurationHave Apache DSO-support and ModPerl library file present, configuringModPerl in httpd.conf.

  Libdir /usr/local/biomart/biomart-perl/lib is not in @INC, adding to @INC

  Cached Registry Unavailable...

  Running Complete Clean...

  Connection parameters of [MSD PROTOTYPE (EBI)]  [ OK ]
  Connection parameters of [UNIPROT PROTOTYPE (EBI)]      [ OK ]



  mkdir /usr/local/biomart/biomart-perl/conf/Cached
  mkdir /usr/local/biomart/biomart-perl/conf/Cached/default
  mkdir /usr/local/biomart/biomart-perl/conf/Cached/default/confTrees
  mkdir /usr/local/biomart/biomart-perl/conf/Cached/default/_portables
  mkdir /usr/local/biomart/biomart-perl/conf/Cached/default/XML

  [NEW CONFIGURATION] .... WITH MEMORY [default]

default ... MSD PROTOTYPE (EBI) ...... 001/001 ... msd....................................... (WEB) www.biomart.org:80............ -> upgrading to 0.6/0.7 ... OKdefault ... UNIPROT PROTOTYPE (EBI) .. 001/006 ... uniprot_location.......................... (WEB) www.biomart.org:80 ............ ->upgrading to 0.6/0.7 ... OKdefault ... UNIPROT PROTOTYPE (EBI) .. 002/006 ... uniprot_sequence.......................... (WEB) www.biomart.org:80 ............ ->upgrading to 0.6/0.7 ... OKdefault ... UNIPROT PROTOTYPE (EBI) .. 003/006 ...uniprot_cell_component .................... (WEB) www.biomart.org:80............ -> upgrading to 0.6/0.7 ... OKdefault ... UNIPROT PROTOTYPE (EBI) .. 004/006 ...uniprot_biol_process ...................... (WEB) www.biomart.org:80............ -> upgrading to 0.6/0.7 ... OKdefault ... UNIPROT PROTOTYPE (EBI) .. 005/006 ... uniprot................................... (WEB) www.biomart.org:80............ -> upgrading to 0.6/0.7 ... OKdefault ... UNIPROT PROTOTYPE (EBI) .. 006/006 ...uniprot_mol_function ...................... (WEB) www.biomart.org:80............ -> upgrading to 0.6/0.7 ... OK

  Setting possible links between datasets
  ....(scanning) 100%
  ....(linking) 100%
  ....(sorting) 100%
  ....(clustering) 7/7
  ....(resolving) 100%
  Building templates for visible datasets
  .... 100%
  Compiling templates for visible datasets
  [1/2] Attribute Panel of Dataset.. :msd
  [1/2] Filter Panel of Dataset..... :msd
  [2/2] Attribute Panel of Dataset.. :uniprot
  [2/2] Filter Panel of Dataset..... :uniprot

  [EMAIL PROTECTED] biomart-perl]$

Any help will be appreciated!


                                                Kind regards,


                                                Mirjam van den Hout
--
Dr. Mirjam van den Hout - van Vroonhoven
        system administrator/programmer, dept. of Bioinformatics
        Erasmus Medical Center, Rotterdam, The Netherlands
        Room Number Ee 15.32, phone +31-10-703 81 11
Web:    http://www.erasmusmc.nl/bioinformatics/
E-mail: [EMAIL PROTECTED]

[mart-dev] problem with biomart-0.7 on RedHat Linux AS4

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