Hi: You'r right; I have recompiled mod_perl + apache + php; Now the appplication is running.
Ty -----Original Message----- From: Michael Reece [mailto:[EMAIL PROTECTED] Sent: Monday, August 06, 2007 6:49 PM To: Rojas, Fernando (CIAT) Cc: Mason-Users Subject: Re: [Mason] Can't locate object method "search" via package it looks to me like you need to recompile mod_perl + apache. your environment looks very broken, and i would not rely on those symlinks! On Aug 6, 2007, at 1:37 PM, Rojas, Fernando ((CIAT)) wrote: > I have some differences in the @INC for each environment: > > For Web Environment I have: > > $VAR1 = '/usr/lib/perl5/5.8.0/i386-linux-thread-multi'; > $VAR2 = '/usr/lib/perl5/5.8.0'; > $VAR3 = '/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi'; > $VAR4 = '/usr/lib/perl5/site_perl/5.8.0'; > $VAR5 = '/usr/lib/perl5/site_perl'; > $VAR6 = '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi'; > $VAR7 = '/usr/lib/perl5/vendor_perl/5.8.0'; $VAR8 = '/usr/lib/perl5/ > vendor_perl'; > $VAR9 = '.'; > $VAR10 = '/usr/local/apache/'; > $VAR11 = '/usr/local/apache/lib/perl'; > > And for the PERL Environment I have: > > $VAR1 = '/usr/local/lib/perl5/5.8.5/i686-linux'; > $VAR2 = '/usr/local/lib/perl5/5.8.5'; > $VAR3 = '/usr/local/lib/perl5/site_perl/5.8.5/i686-linux'; > $VAR4 = '/usr/local/lib/perl5/site_perl/5.8.5'; > $VAR5 = '/usr/local/lib/perl5/site_perl'; > $VAR6 = '.'; > > All my modules are located at: /usr/local/lib/perl5/site_perl/5.8.5 > > But I have some links in: /usr/lib/perl5/site_perl/5.8.0 in this way: > > lrwxrwxrwx 1 root root 39 Aug 3 10:39 IO -> /usr/ > local/lib/perl5/site_perl/5.8.5/IO > lrwxrwxrwx 1 root root 41 Aug 3 10:39 DBIx -> / > usr/local/lib/perl5/site_perl/5.8.5/DBIx > lrwxrwxrwx 1 root root 40 Aug 3 10:38 Sub -> /usr/ > local/lib/perl5/site_perl/5.8.5/Sub > lrwxrwxrwx 1 root root 41 Aug 3 10:38 Test -> / > usr/local/lib/perl5/site_perl/5.8.5/Test > lrwxrwxrwx 1 root root 47 Aug 3 10:38 i686-linux - > > /usr/local/lib/perl5/site_perl/5.8.5/i686-linux > lrwxrwxrwx 1 root root 42 Aug 3 10:37 Error -> / > usr/local/lib/perl5/site_perl/5.8.5/Error > lrwxrwxrwx 1 root root 42 Aug 3 10:37 Cache -> / > usr/local/lib/perl5/site_perl/5.8.5/Cache > lrwxrwxrwx 1 root root 42 Aug 3 10:37 Devel -> / > usr/local/lib/perl5/site_perl/5.8.5/Devel > lrwxrwxrwx 1 root root 46 Aug 3 10:36 Exception - > > /usr/local/lib/perl5/site_perl/5.8.5/Exception > lrwxrwxrwx 1 root root 43 Aug 3 10:36 Bundle -> / > usr/local/lib/perl5/site_perl/5.8.5/Bundle > lrwxrwxrwx 1 root root 43 Aug 3 10:36 Apache -> / > usr/local/lib/perl5/site_perl/5.8.5/Apache > lrwxrwxrwx 1 root root 41 Aug 3 10:35 HTML -> / > usr/local/lib/perl5/site_perl/5.8.5/HTML > lrwxrwxrwx 1 root root 42 Aug 2 09:46 Class -> / > usr/local/lib/perl5/site_perl/5.8.5/Class > lrwxrwxrwx 1 root root 42 Aug 1 17:26 ESTdb -> / > usr/local/lib/perl5/site_perl/5.8.5/ESTdb > lrwxrwxrwx 1 root root 46 Aug 1 15:27 UNIVERSAL - > > /usr/local/lib/perl5/site_perl/5.8.5/UNIVERSAL > lrwxrwxrwx 1 root root 41 Jul 31 14:16 Data -> / > usr/local/lib/perl5/site_perl/5.8.5/Data > lrwxrwxrwx 1 root root 58 Jul 31 11:40 version.pm - > > /usr/local/lib/perl5/site_perl/5.8.5/i686-linux/version.pm > lrwxrwxrwx 1 root root 40 Jul 31 11:36 Ima -> /usr/ > local/lib/perl5/site_perl/5.8.5/Ima > > Could be this the error.?? > Can't I use Links here.?? > How can I change my @INC in the web environment for point to same as > the Perl Environment?? > > Thank you for help . > > > -----Original Message----- > From: Michael Reece [mailto:[EMAIL PROTECTED] > Sent: Monday, August 06, 2007 12:31 PM > To: Rojas, Fernando (CIAT) > Cc: Mason-Users > Subject: Re: [Mason] Can't locate object method "search" via package > > is there anything peculiar about your Class::DBI install? > > some troubleshooting techniques that may help: > > compare your @INC paths for each environment. > > try a 'use Class::DBI' within your mason component and see if it > croaks -- the errors from a load failure from 'use base' may not be > bubbling up correctly. > > interrogate your class for its methods from each environment: > > use Class::Can; > use Data::Dumper; > print Dumper({ Class::Can->interrogate('ESTdb::Organism') }); > > do a Dumper(\%INC) from each environment, and look for relevant > differences (are Class::DBI and ESTdb::* being loaded from the same > correct lib paths?) > > > > On Aug 6, 2007, at 9:59 AM, Rojas, Fernando (CIAT) wrote: > >> Ok I did it: >> >> This is the perl_code and it runs OK; basically it returns count of >> the tables of database: >> >> [EMAIL PROTECTED] html]# perl scriptotal.pl >> Manihot esculenta >> Manihot esculenta >> 13050 >> 5809 >> 1875 >> 3934 >> >> >> #!/usr/bin/perl >> use ESTdb::Organism; >> use ESTdb::Library; >> #my $root = $m->comp('/root'); >> #my $species = $m->comp('/species'); >> my $species = 'Manihot esculenta'; >> print "$species \n"; >> my $orgn = (ESTdb::Organism->search(name => $species))[0]; print >> $orgn->name(), "\n"; print >> ESTdb::Library->sql_nests_by_species($orgn)->select_val,"\n"; >> 1 ? '' : ESTdb::Est->rel_count({clone => {library => {organism => >> {organism=> $orgn}}}}); print >> ESTdb::Library->sql_ncontig_by_species(1, 999999, $orgn)- >>> select_val,"\n"; >> print ESTdb::Library->sql_ncontig_by_species(2, 99999, $orgn)- >>> select_val,"\n"; >> print ESTdb::Library->sql_ncontig_by_species(1, 1, $orgn)- >>> select_val,"\n"; >> >> I restarted the web server; I can't find mason_data in the system; >> the error running in web persist: >> >> error: Can't locate object method "search" via package >> "ESTdb::Organism" at /usr/local/www/meest/html/index.html line 40. >> >> context: ... >> 36: use ESTdb::Library; >> 37: my $root = $m->comp('/root'); >> 38: my $species = $m->comp('/species'); >> 39: print "$species \n"; >> 40: my $orgn = (ESTdb::Organism->search(name => $species))[0]; >> 41: </%init> >> 42: >> >> code stack: /usr/local/www/meest/html/index.html:40 >> /usr/local/www/meest/html/autohandler:3 >> >> Thank you for more help >> >> >> >> -----Original Message----- >> From: Sherrard Burton [mailto:[EMAIL PROTECTED] >> Sent: Monday, August 06, 2007 9:54 AM >> To: Rojas, Fernando (CIAT) >> Cc: Mason-Users >> Subject: Re: [Mason] Can't locate object method "search" via package >> >> this looks like the stack trace from the earlier error. the latest >> error you mentioned was related to the table method, not search. >> >> error: Error during compilation of /usr/local/www/meest/html/ >> index.html: >>>> Can't locate object method "table" via package "ESTdb::Organism" >>>> at >> /usr/lib/perl5/site_perl/5.8.0/ESTdb/Organism.pm line 3 >>>>>>>> >> >> i would clear out the obj files, which will be a different locations >> depending on your setup. try locate mason_data to see where they >> might >> be. i would also restart the web server to make sure you aren't >> dealing with page caching issues. if that doesn't work, then you >> should expand your script to include all of the method that you are >> calling in the mason page, using the exact same syntax. you basically >> take the code in your mason page and strip out the apache- and >> mason-specific bits. if that doesn't work, then i'm at a loss. >> >> Rojas, Fernando (CIAT) wrote: >>> This is the stack-trace: >>> >>> Trace begun at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ >>> Exceptions.pm >>> line 131 HTML::Mason::Exceptions::rethrow_exception('Can\'t locate >>> object method "search" via package "ESTdb::Organism" at >>> /usr/local/www/meest/html/index.html line 41.^J') called at >>> /usr/local/www/meest/html/index.html line 41 >>> HTML::Mason::Commands::__ANON__ at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Component.pm line 136 >>> HTML::Mason::Component::run('HTML::Mason::Component::FileBased=HASH >>> (0x >>> 924c900)') called at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 1074 eval >>> {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line >>> 1068 HTML::Mason::Request::comp(undef, undef) called at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 760 >>> HTML::Mason::Request::call_next >>> ('HTML::Mason::Request::ApacheHandler=H >>> ASH(0x926642c)') called at /usr/local/www/meest/html/autohandler >>> line >>> 3 HTML::Mason::Commands::__ANON__ at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Component.pm line 136 >>> HTML::Mason::Component::run('HTML::Mason::Component::FileBased=HASH >>> (0x >>> 8b3a9d0)') called at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 1069 eval >>> {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line >>> 1068 HTML::Mason::Request::comp(undef, undef, undef) called at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line 338 eval >>> {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm line >>> 338 >>> eval {...} at /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/Request.pm >>> line 297 >>> HTML::Mason::Request::exec >>> ('HTML::Mason::Request::ApacheHandler=HASH(0 >>> x926642c)') called at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ApacheHandler.pm line 128 >>> eval {...} at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ApacheHandler.pm line 128 >>> HTML::Mason::Request::ApacheHandler::exec >>> ('HTML::Mason::Request::Apach >>> eHandler=HASH(0x926642c)') called at >>> /usr/lib/perl5/site_perl/5.8.0/HTML/Mason/ApacheHandler.pm line 825 >>> HTML::Mason::ApacheHandler::handle_request >>> ('HTML::Mason::ApacheHandler >>> =HASH(0x82ad010)', 'Apache=SCALAR(0x9219438)') called at >>> /usr/local/apache/conf/handler.pl line 32 >>> MyMason::MyApp::handler('Apache=SCALAR(0x9219438)') called at >>> /dev/null line 0 eval {...} at /dev/null line 0 >>> >>> Thanks >>> >>> -----Original Message----- >>> From: Sherrard Burton [mailto:[EMAIL PROTECTED] >>> Sent: Monday, August 06, 2007 9:41 AM >>> To: Rojas, Fernando (CIAT) >>> Cc: Mason-Users >>> Subject: Re: [Mason] Can't locate object method "search" via package >>> >>> but you don't seem to be calling all of the same methods from the >>> script that you are trying to use from the web interface. >>> >>> from the stack trace you should be able to see which line in your >>> mason component called the method that eventually led to this error. >>> >>> ps--you should use reply-all so that these discussions stay on- list >>> where everybody can benefit. >>> >>> Rojas, Fernando (CIAT) wrote: >>>> TY for your help; I have this script that was attached to the >>>> end of >>>> my e-mail and it runs ok: >>>> >>>> #!/usr/bin/perl >>>>>> use strict; >>>>>> use ESTdb::Organism; >>>>>> use ESTdb::Library; >>>>>> my $species = 'Manihot esculenta'; my $orgn = 99; print "$orgn >>>>>>>>> \n"; print "$species :"; my $orgn = >>>>>> (ESTdb::Organism->search(name => $species))[0]; print "$orgn : >>>>>> \n"; >>>>>> my $library = 0; my $name = 'aflp'; print "$name "; my >>>>>> $library = >>>>>> (ESTdb::Library->search(name => $name))[0]; print "$library \n"; >>>> In this case im querying 2 tables of database organism and library >>>> and runs ok: >>>> >>>> Ty for your help again. >>>> >>>> -----Original Message----- >>>> From: Sherrard Burton [mailto:[EMAIL PROTECTED] >>>> Sent: Monday, August 06, 2007 9:32 AM >>>> To: Rojas, Fernando (CIAT) >>>> Subject: Re: [Mason] Can't locate object method "search" via >>>> package >>>> >>>> it sounds like you are having perl problems. are you sure the same >>>> code works from a command-line script? >>>> >>>> that message usually means that you haven't "use"ed the package >>>> that >>>> exports that method, or that that method doesn't exist in the >>>> package. >>>> >>>> maybe you should prototype the code in a perl script or module >>>> called from the command line first so that you can distinguish the >>>> simple perl errors from any that are mason-specific. >>>> >>>> good luck >>>> >>>> >>>> Rojas, Fernando (CIAT) wrote: >>>>> TY for your answer; I tried it; now im getting: >>>>> >>>>> error: Error during compilation of /usr/local/www/meest/html/ >>>>> index.html: >>>>> Can't locate object method "table" via package >>>>> "ESTdb::Organism" at >>>>> /usr/lib/perl5/site_perl/5.8.0/ESTdb/Organism.pm line 3 >>>>> >>>>> TY. >>>>> >>>>> -----Original Message----- >>>>> From: Sherrard Burton [mailto:[EMAIL PROTECTED] >>>>> Sent: Monday, August 06, 2007 7:23 AM >>>>> To: Rojas, Fernando (CIAT) >>>>> Cc: mason-users@lists.sourceforge.net >>>>> Subject: Re: [Mason] Can't locate object method "search" via >>>>> package >>>>> >>>>> i'm not sure, but i'm guessing you should be using >>>>> >>>>> use ESTdb::Organism; >>>>> use ESTdb::Library; >>>>> >>>>> in your mason code instead of >>>>> >>>>> use base 'ESTdb::Organism'; >>>>> use base 'ESTdb::Library'; >>>>> >>>>> >>>>> >>>>> Rojas, Fernando (CIAT) wrote: >>>>>> ______________________________________________ >>>>>> *From: * Rojas, Fernando (CIAT) >>>>>> *Sent: * Friday, August 03, 2007 5:47 PM >>>>>> *To: * 'mason-users@lists.sourceforge.net' >>>>>> *Subject: * >>>>>> >>>>>> HI: I have a web-site running in this environment: >>>>>> >>>>>> Linux (Red Hat 8.0 3-2-7); Apache 1.3.24 Mod-Perl 1.29 Perl >>>>>> 5.8.5; >>>>>> Html-Mason-1.27; MySql 4.1.20; Al CPAN Modules installed >>>>>> >>>>>> Im getting this error running my web aplication: >>>>>> >>>>>> *error:* Can't locate object method "search" via package >>>>>> "ESTdb::Organism" at /usr/local/www/meest/html/index.html line >>>>>> 41. >>>>>> *context:* >>>>>> *...* >>>>>> *37:* use base 'ESTdb::Library'; >>>>>> *38:* my $root = $m->comp('/root'); >>>>>> *39:* my $species = $m->comp('/species'); >>>>>> *40:* print "$species \n"; >>>>>> *41:* my $orgn = (ESTdb::Organism->search(name => $species)) >>>>>> [0]; >>>>>> *42:* </%init> >>>>>> *43:* >>>>>> *code stack:* /usr/local/www/meest/html/index.html:41 >>>>>> /usr/local/www/meest/html/autohandler:3 >>>>>> >>>>>> *The index.html is:* >>>>>> <h1><% $orgn->name() %> ESTs</h1> >>>>>> <p/> >>>>>> <table> >>>>>> <tbody> >>>>>> <tr> <th>ESTs </th> >>>>>> <td> <% >>>>>> ESTdb::Library->sql_nests_by_species($orgn)->select_val >>>>>> %> <% 1 ? '' : ESTdb::Est->rel_count({clone => {library => >>>>>> {organism => {organism=> $orgn}}}})%> </td></tr> >>>>>> <tr> <th>non redondant contigs </th> >>>>>> <td> <% ESTdb::Library->sql_ncontig_by_species(1, 999999, >>>>>> $orgn)->select_val %> <td></tr> >>>>>> <tr> <th>Contigs : </th> >>>>>> <td><% ESTdb::Library->sql_ncontig_by_species(2, 99999, >>>>>> $orgn)->select_val%></td></tr> >>>>>> <tr> <th>Singletons : </th> >>>>>> <td><% ESTdb::Library->sql_ncontig_by_species(1, 1, >>>>>> $orgn)->select_val%></td></tr> </tbody> </table> <hr/> >>>>>> <h2>Search</h2> <ul> <li>search <a >>>>>> href="<%$root%>/byfactor/factor.html">by >>>>>> factor</a></li> <li>search <a >>>>>> href="<%$root%>/bylib/library.html">by >>>>>> lib</a></li> <li>search <a href="<%$root%>/byest/est.html">by >>>>>> est</a></li> <li>search <a href="<%$root%>/bycn/cn.html">by >>>>>> contig</a></li> </ul> <hr/> <h2>Blast</h2> <a >>>>>> href="<%$root%>/blast/blast">blast</a> >>>>>> <!-- >>>>>> <ul> >>>>>> <li>blast on <a href="blast/ests/">ESTs</a></li> <li>blast on <a >>>>>> href="blast/contigs/">Contigs</li> >>>>>> </ul> >>>>>> --> >>>>>> <%init> >>>>>> use strict; >>>>>> use base 'ESTdb::Organism'; >>>>>> use base 'ESTdb::Library'; >>>>>> my $root = $m->comp('/root'); >>>>>> my $species = $m->comp('/species'); print "$species \n"; my $orgn >>>>>> = (ESTdb::Organism->search(name => $species))[0]; </%init> >>>>>> >>>>>> *Organism.pm code is:* >>>>>> package ESTdb::Organism; >>>>>> use base 'ESTdb::DBI'; >>>>>> __PACKAGE__->table('organism'); >>>>>> __PACKAGE__->columns(All => qw/ organism name/); >>>>>> __PACKAGE__->has_many(libs => 'ESTdb::Library'); >>>>>> >>>>>> *DBI.pm is:* >>>>>> package ESTdb::DBI; >>>>>> use strict; >>>>>> use base 'Class::DBI'; >>>>>> use Data::Dumper; >>>>>> my $dsn = 'DBI:mysql:dbname=est;host=localhost;port=3306'; >>>>>> my $user = 'root'; >>>>>> my $password = 'ciatroot'; >>>>>> __PACKAGE__->connection($dsn, $user, $password); >>>>>> #Class::DBI->connection($dsn, $user, $password); >>>>>> #__PACKAGE__->set_db('Main', $dsn, $user, $password); .. >>>>>> >>>>>> *Someone could give me some ideas. What's happening.??* *I have >>>>>> this Perl Script and when I run as root or as another user it >>>>>> runs >>>>>> ok connecting to the database and retrieving information.* >>>>>> >>>>>> #!/usr/bin/perl >>>>>> use strict; >>>>>> use ESTdb::Organism; >>>>>> use ESTdb::Library; >>>>>> my $species = 'Manihot esculenta'; my $orgn = 99; print "$orgn >>>>>>>>> \n"; print "$species :"; my $orgn = >>>>>> (ESTdb::Organism->search(name => $species))[0]; print "$orgn : >>>>>> \n"; >>>>>> my $library = 0; my $name = 'aflp'; print "$name "; my >>>>>> $library = >>>>>> (ESTdb::Library->search(name => $name))[0]; print "$library \n"; >>>>>> >>>>>> >>>>>> Sorry for the long mail;; I hope some help THANKS. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> FERNANDO ROJAS >>>>>> Ingeniero de Sistemas y Computación Unidad de Sistemas de >>>>>> Información Centro Internacional de Agricultura Tropical (CIAT) >>>>>> E-mail: [EMAIL PROTECTED] >>>>>> Phone:(57-2)445-01-00 Ext 3647 >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> - >>>>>> - >>>>>> - >>>>>> - >>>>>> --- >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> - >>>>>> - >>>>>> - >>>>>> - >>>>>> ---- This SF.net email is sponsored by: Splunk Inc. >>>>>> Still grepping through log files to find problems? Stop. >>>>>> Now Search log events and configuration files using AJAX and a >>>>>> browser. >>>>>> Download your FREE copy of Splunk now >> http://get.splunk.com/ >>>>>> >>>>>> >>>>>> ----------------------------------------------------------------- >>>>>> - >>>>>> - >>>>>> - >>>>>> - >>>>>> --- >>>>>> >>>>>> _______________________________________________ >>>>>> Mason-users mailing list >>>>>> Mason-users@lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/mason-users >>> >>> -------------------------------------------------------------------- >>> - >>> - >>> --- This SF.net email is sponsored by: Splunk Inc. >>> Still grepping through log files to find problems? Stop. >>> Now Search log events and configuration files using AJAX and a >>> browser. >>> Download your FREE copy of Splunk now >> http://get.splunk.com/ >>> _______________________________________________ >>> Mason-users mailing list >>> Mason-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/mason-users >> >> --------------------------------------------------------------------- >> - >> --- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a >> browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> _______________________________________________ >> Mason-users mailing list >> Mason-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mason-users > > --- > michael reece :: software engineer :: [EMAIL PROTECTED] > > --- michael reece :: software engineer :: [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Mason-users mailing list Mason-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mason-users
