[ome-devel] OME install woes

Jason Swedlow jason at lifesci.dundee.ac.uk
Thu Apr 6 02:15:02 BST 2006 

August-

Obviously, we appreciate your input and help.

We haven't yet released install notes for Ubuntu and don't officially  
support it.  We'd love to include a write-up on our web site-- http:// 
www.openmicroscopy.org/howto/, if you're willing.  We'll help with  
the rogue install-- glad to hear that at least one worked!  We don't  
get too many emails saying ""it worked!".

Thanks much.

Cheers,

Jason

On 5 Apr 2006, at 18:41, august wrote:

> Some install woes.
>
> I have two machines that are identicle in hardware and are running the
> same Ubuntu Linux OS version.   One machine has installed  
> successfully.
> The other machine is having more problems, and I don't know what it is
> exactly.
>
> The install script stopped the first time at:
>
> ERROR LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/OMEIS/ 
> Experiment.ome" -- OUTPUT:
> "500 EOF when chunk header expected
>
> I drop the ome database and run the install sript again, but get a
> Success in loading the Experiment.ome file.  The next one after that,
> Plate.ome, fails however.  And so on.  The next run through.   
> Plate.ome
> is successfully uploaded, but the one after it fails.
>
> any I deas why this is?
>
> Seems the problem is in OME::Image::Server::__callOMEIS
>
> below is the tailend of the insall script output and of the
> CoreDatabase.log file
>
>
> thanks -august.
>
>
>
> ------------------------------------------------------------
> [SUCCESS].
>   \__ /home/swaroop/OME/src/xml/OME/Core/Experimenter.ome [SUCCESS].
>   \__ /home/swaroop/OME/src/xml/OME/Core/Group.ome [SUCCESS].
>   \__ /home/swaroop/OME/src/xml/OME/Core/Instrument.ome NOTICE:   
> CREATE
> TABLE / PRIMARY KEY will create implicit index "instruments_pkey"  
> for table
> "instruments"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "light_sources_pkey" for table "light_sources"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index  
> "lasers_pkey"
> for table "lasers"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "filaments_pkey" for table "filaments"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index  
> "arcs_pkey"
> for table "arcs"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "detectors_pkey" for table "detectors"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "objectives_pkey" for table "objectives"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index  
> "filter_pkey"
> for table "filter"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "excitation_filters_pkey" for table "excitation_filters"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "dichroics_pkey" for table "dichroics"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "emission_filters_pkey" for table "emission_filters"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "filter_sets_pkey" for table "filter_sets"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index  
> "otfs_pkey"
> for table "otfs"
> [SUCCESS].
>   \__ /home/swaroop/OME/src/xml/OME/Core/Image.ome NOTICE:  CREATE  
> TABLE /
> PRIMARY KEY will create implicit index "image_info_pkey" for table
> "image_info"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "imaging_environments_pkey" for table "imaging_environments"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "thumbnails_pkey" for table "thumbnails"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "logical_channels_pkey" for table "logical_channels"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "channel_components_pkey" for table "channel_components"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "display_channels_pkey" for table "display_channels"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "display_options_pkey" for table "display_options"NOTICE:  CREATE  
> TABLE /
> PRIMARY KEY will create implicit index "display_roi_pkey" for table
> "display_roi"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "stage_labels_pkey" for table "stage_labels"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "image_plates_pkey" for table "image_plates"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "image_pixels_pkey" for table "image_pixels"
> NOTICE:  CREATE TABLE / PRIMARY KEY will create implicit index
> "image_dimensions_pkey" for table "image_dimensions"
> [SUCCESS].
>   \__ /home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome  
> [FAILURE].
>
>
> --------------------------------------------------------------------
> Creating OME PostgreSQL SUPERUSER (ome)
> SUCCESS LOADING CLASS "OME::LookupTable"
> SUCCESS LOADING CLASS "OME::LookupTable::Entry"
> SUCCESS LOADING CLASS "OME::DataTable"
> SUCCESS LOADING CLASS "OME::DataTable::Column"
> SUCCESS LOADING CLASS "OME::SemanticType"
> SUCCESS LOADING CLASS "OME::SemanticType::Element"
> SUCCESS LOADING CLASS "OME::SemanticType::BootstrapExperimenter"
> SUCCESS LOADING CLASS "OME::SemanticType::BootstrapGroup"
> SUCCESS LOADING CLASS "OME::SemanticType::BootstrapExperimenterGroup"
> SUCCESS LOADING CLASS "OME::SemanticType::BootstrapRepository"
> SUCCESS LOADING CLASS "OME::Dataset"
> SUCCESS LOADING CLASS "OME::Project"
> SUCCESS LOADING CLASS "OME::Project::DatasetMap"
> SUCCESS LOADING CLASS "OME::Image"
> SUCCESS LOADING CLASS "OME::Image::DatasetMap"
> SUCCESS LOADING CLASS "OME::Feature"
> SUCCESS LOADING CLASS "OME::UserState"
> SUCCESS LOADING CLASS "OME::ViewerPreferences"
> SUCCESS LOADING CLASS "OME::LSID"
> SUCCESS LOADING CLASS "OME::Module::Category"
> SUCCESS LOADING CLASS "OME::Module"
> SUCCESS LOADING CLASS "OME::Module::FormalInput"
> SUCCESS LOADING CLASS "OME::Module::FormalOutput"
> SUCCESS LOADING CLASS "OME::AnalysisChain"
> SUCCESS LOADING CLASS "OME::AnalysisChain::Node"
> SUCCESS LOADING CLASS "OME::AnalysisChain::Link"
> SUCCESS LOADING CLASS "OME::AnalysisPath"
> SUCCESS LOADING CLASS "OME::AnalysisPath::Map"
> SUCCESS LOADING CLASS "OME::ModuleExecution"
> SUCCESS LOADING CLASS "OME::ModuleExecution::ActualInput"
> SUCCESS LOADING CLASS "OME::ModuleExecution::SemanticTypeOutput"
> SUCCESS LOADING CLASS "OME::ModuleExecution::ParentalOutput"
> SUCCESS LOADING CLASS "OME::ModuleExecution::VirtualMEXMap"
> SUCCESS LOADING CLASS "OME::AnalysisChainExecution"
> SUCCESS LOADING CLASS "OME::AnalysisChainExecution::NodeExecution"
> SUCCESS LOADING CLASS "OME::Task"
> SUCCESS LOADING CLASS "OME::Analysis::Engine::Worker"
> SUCCESS LOADING CLASS "OME::Configuration::Variable"
> Checking repository
> Repository URL: http://fiddler/cgi-bin/omeis
> ENVIRONMENT->omeis_url(): http://fiddler/cgi-bin/omeis
> Getting an LWP user agent
> Generating request for http://fiddler/cgi-bin/omeis
> Getting response from http://fiddler/cgi-bin/omeis
> Parsing response from http://fiddler/cgi-bin/omeis
> Repository is configured correctly
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Experiment.ome"
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Plate.ome"
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Screen.ome"
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Experimenter.ome"
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Group.ome"
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Instrument.ome"
> SUCCESS LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/ 
> Image.ome"
> ERROR LOADING XML FILE "/home/swaroop/OME/src/xml/OME/Core/OMEIS/ 
> Repository.ome" -- OUTPUT: "500 EOF when chunk header expected
>  at /home/swaroop/OME/src/perl2/OME/Image/Server.pm line 474
> 	OME::Image::Server::__callOMEIS('OME::Image::Server', 'Method',  
> 'UploadFile', 'File', '/home/swaroop/OME/src/xml/OME/Core/OMEIS/ 
> Repository.ome') called at /home/swaroop/OME/src/perl2/OME/Image/ 
> Server.pm line 1061
> 	OME::Image::Server::uploadFile('OME::Image::Server', '/home/ 
> swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome') called at /home/ 
> swaroop/OME/src/perl2/OME/Image/Server/File.pm line 117
> 	OME::Image::Server::File::upload('OME::Image::Server::File', '/ 
> home/swaroop/OME/src/xml/OME/Core/OMEIS/Repository.ome') called at / 
> home/swaroop/OME/src/perl2/OME/Tasks/OMEImport.pm line 138
> 	OME::Tasks::OMEImport::importFile('OME::Tasks::OMEImport=HASH 
> (0x94ca160)', '/home/swaroop/OME/src/xml/OME/Core/OMEIS/ 
> Repository.ome', 'NoDuplicates', 1, 'IgnoreAlterTableErrors', 1)  
> called at /home/swaroop/OME/src/perl2/OME/Install/ 
> CoreDatabaseTablesTask.pm line 768
> 	eval {...} called at /home/swaroop/OME/src/perl2/OME/Install/ 
> CoreDatabaseTablesTask.pm line 767
> 	OME::Install::CoreDatabaseTablesTask::load_xml_core 
> ('OME::Session=HASH(0x94c164c)', 'GLOB(0x843575c)') called at /home/ 
> swaroop/OME/src/perl2/OME/Install/CoreDatabaseTablesTask.pm line 1113
> 	OME::Install::CoreDatabaseTablesTask::execute() called at (eval  
> 169) line 1
> 	eval 'OME::Install::CoreDatabaseTablesTask::execute()
> ;' called at ./install.pl line 79
> 	main::run_tasks() called at ./install.pl line 249
> "
>
>
>
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> ome-devel at lists.openmicroscopy.org.uk
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