[ome-users] install from cvs (8-18-06)

Bernd Jagla baj2107 at columbia.edu
Mon Aug 21 19:57:33 BST 2006 

I also tried to reinstall (to get the message) and this is what I got.
(by the way the new install is under /home/bernd/allOMEs/06_08_18/OME

Are these values correct ? [y/n]: y
[Mon Aug 21 14:55:30 2006] [warn] The ScriptAlias directive in
/OME/conf/httpd2.omeis-dev.conf at line 2 will probably never match because
it overlaps an earlier ScriptAlias.
Testing Apache configuration 
  \__ mod_perl [SUCCESS].
  \__ omeis [SUCCESS].
Dropping umask to "0002".
Installing HTML Templates for Web-UI 
  \__ Verifying structure of
/home/bernd/allOMEs/newOME/OME/src/html/Templates 
[SKIPPING].
  \__ Updating user templates [SKIPPING].
  \__ Updating system templates [SKIPPING].
  \__ Setting owner for templates to [SKIPPING].
  \__ Setting permissions for user templates to [SKIPPING].
  \__ Setting permissions for system templates to [SKIPPING].



Bernd

|-----Original Message-----
|From: Josiah Johnston [mailto:siah at nih.gov]
|Sent: Monday, August 21, 2006 2:15 PM
|To: Bernd Jagla
|Cc: 'OME users'
|Subject: Re: [ome-users] install from cvs (8-18-06)
|
|Is your installation root /home/bernd/allOMEs/newOME/OME/ or /home/
|bernd/allOMEs/06_08_18/OME ?
|
| From your installation root, can you type:
|	cvs status src/perl2/OME/Install/CoreDatabaseTablesTask.pm
|
|Also, can you type
|	ls -ld /home/bernd/allOMEs/newOME/OME/src/html/Templates/System/
|Display/Many//generic_ref_minimalList.tmpl /home/bernd/allOMEs/newOME/
|OME/src/html/Templates /home/bernd/allOMEs/newOME /home/bernd/allOMEs
|
|Thanks,
|Josiah
|
|On Aug 21, 2006, at 11:03 AM, Bernd Jagla wrote:
|
|>
|> I guess I should have tried it out first and not think first....
|>
|> When trying to log in I get now the following error message:
|>
|> Error serving OME::Web::Home: HTML::Template->new() : Cannot open
|> included
|> file
|> /home/bernd/allOMEs/newOME/OME/src/html/Templates/System/Display/
|> Many//gener
|> ic_ref_minimalList.tmpl : file not found. at
|> /usr/lib/perl5/site_perl/5.8.6/HTML/Template.pm line 1632
|> 	HTML::Template::_init_template('HTML::Template=HASH(0xa81d81c)')
|> called at /usr/lib/perl5/site_perl/5.8.6/HTML/Template.pm line 1205
|> 	HTML::Template::_init('HTML::Template=HASH(0xa81d81c)') called at
|> /usr/lib/perl5/site_perl/5.8.6/HTML/Template.pm line 1099
|> 	HTML::Template::new('HTML::Template', 'filename',
|> '/home/bernd/allOMEs/newOME/OME/src/html/Templates/System/Disp...',
|> 'path',
|> '/home/bernd/allOMEs/newOME/OME/src/html/Templates/System/Disp...',
|> 'case_sensitive', 1) called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Web/
|> TemplateManager.pm line
|> 367
|>
|> OME::Web::TemplateManager::getRenderingTemplate
|> ('OME::Web::TemplateManager',
|> 'undef', 'ref_minimalList', 'many') called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Web/DBObjRender.pm
|> line 365
|>
|> OME::Web::DBObjRender::renderArray('OME::Web::DBObjRender=HASH
|> (0xa83e178)',
|> 'ARRAY(0xa841258)', 'ref_minimalList', 'HASH(0xa81f21c)') called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Web/Home.pm line 130
|>
|> OME::Web::Home::__getQuickViewProjectData('OME::Web::Home=HASH
|> (0xa80b95c)',
|> 'undef') called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Web/Home.pm line 235
|> 	OME::Web::Home::getPageBody('OME::Web::Home=HASH(0xa80b95c)',
|> 'HTML::Template=HASH(0xa4e15b4)') called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Web.pm line 557
|> 	OME::Web::createOMEPage('OME::Web::Home=HASH(0xa80b95c)',
|> 'HTML::Template=HASH(0xa4e15b4)') called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Web.pm line 404
|> 	OME::Web::serve('OME::Web::Home=HASH(0xa80b95c)') called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/serve.pl line 88
|> 	eval {...} called at
|> /home/bernd/allOMEs/06_08_18/OME/src/perl2/serve.pl line 76
|>
|> ModPerl::ROOT::ModPerl::Registry::home_bernd_allOMEs_06_08_18_OME_src_
|> perl2_
|> serve_2epl::handler('Apache2::RequestRec=SCALAR(0xa788064)') called at
|> /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/ModPerl/
|> RegistryCoo
|> ker.pm line 203
|> 	eval {...} called at
|> /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/ModPerl/
|> RegistryCoo
|> ker.pm line 203
|> 	ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0xa7aa950)')
|> called at
|> /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/ModPerl/
|> RegistryCoo
|> ker.pm line 169
|>
|> ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH
|> (0xa7aa950)'
|> ) called at
|> /usr/lib/perl5/vendor_perl/5.8.6/i386-linux-thread-multi/ModPerl/
|> Registry.pm
|> line 30
|> 	ModPerl::Registry::handler('ModPerl::Registry',
|> 'Apache2::RequestRec=SCALAR(0xa788064)') called at -e line 0
|> 	eval {...} called at -e line 0
|>
|>
|> I guess this is related to the Apache problem I was reporting on
|> earlier.
|> I also attached the Apachelog, but couldn't find anything in there...
|>
|> Bernd
|>
|>
|> |-----Original Message-----
|> |From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-
|> users-
|> |bounces at lists.openmicroscopy.org.uk] On Behalf Of Bernd Jagla
|> |Sent: Monday, August 21, 2006 11:00 AM
|> |To: 'OME users'
|> |Subject: Re: [ome-users] install from cvs (8-18-06)
|> |
|> |I did a cvs update, and I got it installed.
|> |
|> |During installation I got an error message about a concatenation
|> that did
|> |not create a problem, but I wanted to make you aware of it. See
|> attached
|> |log
|> |file for more information...
|> |
|> |Also, I was surprised to see that the Apache config knew my old
|> Template
|> |directory and was skipping some templates there. Is this the correct
|> |behavior? Unfortunately I cannot find the message because it was
|> already
|> |overwritten on my terminal and there is no sign of it in the
|> Apache Log...
|> |
|> |Thanks for the help,
|> |
|> |Best,
|> |
|> |Bernd
|> |
|> ||-----Original Message-----
|> ||From: ome-users-bounces at lists.openmicroscopy.org.uk [mailto:ome-
|> users-
|> ||bounces at lists.openmicroscopy.org.uk] On Behalf Of Bernd Jagla
|> ||Sent: Friday, August 18, 2006 11:20 AM
|> ||To: 'OME users'
|> ||Subject: [ome-users] install from cvs (8-18-06)
|> ||
|> ||I was just trying to do a completely new CVS install (since I
|> found some
|> ||time to play with the new version.)
|> ||
|> ||And pretty close to end I got the following error:
|> ||
|> ||
|> ||
|> ||
|> ||
|> ||Initial user creation
|> ||
|> ||-----------------------
|> ||
|> ||
|> ||
|> ||This user will be yourself or the person who will administer the OME
|> ||
|> ||environment after installation. It is internal to OME. You will
|> use this
|> ||
|> ||username and password to use OME and add new OME users and
|> groups. The
|> ||
|> ||default data directory option is the path on this machine which
|> contains
|> ||
|> ||(or will contain) the proprietary image files (greyscale TIFF's for
|> ||
|> ||example) you wish to import into OME. An example default data
|> directory
|> ||
|> ||would be "/home/joe/my_ome_images".
|> ||
|> ||
|> ||
|> ||            First name: Bernd
|> ||
|> ||             Last name: Jagla
|> ||
|> ||              Username: bernd
|> ||
|> ||        E-mail address: baj2107 at columbia.edu
|> ||
|> ||Default data directory: /home/bernd
|> ||
|> ||
|> ||
|> ||Are these values correct ? [y/n]:
|> ||
|> ||Odd number of elements in anonymous hash at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/
|> CoreDatabaseTablesT
|> |a
|> ||sk.pm line 553.
|> ||
|> ||
|> ||
|> ||
|> ||
|> ||Errors executing task: Column 066e4a292457a2ad4e6bdeefcb6e9e58
|> does not
|> ||exist at /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/
|> DBObject.pm line
|> ||3150
|> ||
|> ||        OME::DBObject::__makeInsertSQLs('OME::UserState',
|> ||'DBI::db=HASH(0xa3c6224)', 'HASH(0xa3d00b4)') called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/DBObject.pm line 3337
|> ||
|> ||        OME::DBObject::__createNewInstance('OME::UserState',
|> ||'DBI::db=HASH(0xa3c6224)', 'HASH(0xa3d00b4)') called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Factory.pm line 856
|> ||
|> ||        eval {...} called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Factory.pm line 855
|> ||
|> ||        OME::Factory::newObject('OME::Factory=HASH(0xa301f68)',
|> ||'OME::UserState', 'HASH(0xa3d00b4)') called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/
|> CoreDatabaseTablesT
|> |a
|> ||sk.pm line 553
|> ||
|> ||
|> ||OME::Install::CoreDatabaseTablesTask::create_experimenter
|> ('OME::SessionMan
|> |a
|> ||ger=HASH(0xa302e90)') called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/
|> CoreDatabaseTablesT
|> |a
|> ||sk.pm line 1457
|> ||
|> ||        OME::Install::CoreDatabaseTablesTask::execute() called at
|> (eval
|> |220)
|> ||line 1
|> ||
|> ||        eval 'OME::Install::CoreDatabaseTablesTask::execute()
|> ||
|> ||;' called at install.pl line 80
|> ||
|> ||        main::run_tasks() called at install.pl line 265
|> ||
|> || at /home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Factory.pm
|> line 858
|> ||
|> ||        OME::Factory::newObject('OME::Factory=HASH(0xa301f68)',
|> ||'OME::UserState', 'HASH(0xa3d00b4)') called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/
|> CoreDatabaseTablesT
|> |a
|> ||sk.pm line 553
|> ||
|> ||
|> ||OME::Install::CoreDatabaseTablesTask::create_experimenter
|> ('OME::SessionMan
|> |a
|> ||ger=HASH(0xa302e90)') called at
|> ||/home/bernd/allOMEs/06_08_18/OME/src/perl2/OME/Install/
|> CoreDatabaseTablesT
|> |a
|> ||sk.pm line 1457
|> ||
|> ||        OME::Install::CoreDatabaseTablesTask::execute() called at
|> (eval
|> |220)
|> ||line 1
|> ||
|> ||        eval 'OME::Install::CoreDatabaseTablesTask::execute()
|> ||
|> ||;' called at install.pl line 80
|> ||
|> ||        main::run_tasks() called at install.pl line 265
|> ||
|> ||
|> ||
|> || at install.pl line 81
|> ||
|> ||        main::run_tasks() called at install.pl line 265
|> ||
|> ||# Looks like your test died before it could output anything.
|> ||
|> ||
|> ||
|> ||
|> ||
|> ||Does this mean anything to anyone?
|> ||
|> ||
|> ||
|> ||Thanks,
|> ||
|> ||
|> ||
|> ||Bernd
|>
|> <ApacheConfigTask.log>
|> _______________________________________________
|> ome-users mailing list
|> ome-users at lists.openmicroscopy.org.uk
|> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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