[ome-users] matlab version

Anh Vu anh.q.vu at gmail.com
Wed Jul 27 21:31:29 BST 2005 

I did a fresh CVS checkout. I first delete the OME folder in my home
dir then used the following commands.

$ cvs -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome' login
(Enter "anoncvs" for the password)
$ cvs -z3 -d ':pserver:anoncvs at cvs.openmicroscopy.org.uk:/ome' checkout OME

then i ran the install after su and this is the result I get from the log file.

USING PERL CONFIGURE SCRIPT -- 'perl Makefile.PL '
SUCCESS -- OUTPUT: "You can remove all previous versions of OME with
the following command:
 perl Makefile.PL uninstall
 --------------------------
 Performing `make clean` in directory /home/avu/OME/src/perl2/OME/Matlab
 rm -rf Matlab.c ../blib ./blib Makefile.aperl
blib/arch/auto/OME/Matlab/extralibs.all
blib/arch/auto/OME/Matlab/extralibs.ld perlmain.c tmon.out mon.out
so_locations pm_to_blib *.o *.a perl.exe perl perl Matlab.bs
Matlab.bso Matlab.def libMatlab.def Matlab.exp Matlab.x core
core.*perl.*.? *perl.core core.[0-9] core.[0-9][0-9]
core.[0-9][0-9][0-9] core.[0-9][0-9][0-9][0-9]
core.[0-9][0-9][0-9][0-9][0-9]
 mv Makefile Makefile.old > /dev/null 2>&1
 Checking if your kit is complete...
 Warning: the following files are missing in your kit:
        OME/Image/Pix/Makefile
        OME/ImportExport/Repacker/Makefile
        OME/Web/DBObjRender/__Group.pm
        OME/Web/DBObjRender/__OME_Module.pm
        OME/Web/DBObjRender/__OME_Project.pm
        t/Image-Pix.t
 Please inform the author.
 WARNING:  libtiff must be installed !
 Checking if your kit is complete...
 Looks good
 Writing Makefile for OME::Image::Pix
 Checking if your kit is complete...
 Looks good
 Writing Makefile for Repacker
 Writing Makefile for OME
"

COMPILING MODULE -- 'make'
SUCCESS -- OUTPUT: "cp OME/Install/CoreSystemTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/CoreSystemTask.pm
 cp OME/Web/DefaultHeaderBuilder.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DefaultHeaderBuilder.pm
 cp OME/Web/DBObjRender/__OME_AnalysisChain_Link.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_AnalysisChain_Link.pm
 cp OME/LookupTable/Entry.pm
/home/avu/OME/src/perl2/blib/lib/OME/LookupTable/Entry.pm
 cp OME/Analysis/Engine/UnthreadedPerlExecutor.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/UnthreadedPerlExecutor.pm
 cp OME/ImportEngine/BMPUtils.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/BMPUtils.pm
 cp OME/LSID.pm /home/avu/OME/src/perl2/blib/lib/OME/LSID.pm
 cp OME/ImportExport/ResolveFiles.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/ResolveFiles.pm
 cp OME/Matlab/Matlab.xs /home/avu/OME/src/perl2/blib/lib/OME/Matlab/Matlab.xs
 cp OME/Image/LocalPixels.pm
/home/avu/OME/src/perl2/blib/lib/OME/Image/LocalPixels.pm
 cp OME/Analysis/Engine/Executor.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/Executor.pm
 cp OME/Tests/ForkedImageImport.pl
/home/avu/OME/src/perl2/blib/lib/OME/Tests/ForkedImageImport.pl
 cp OME/AnalysisPath.pm /home/avu/OME/src/perl2/blib/lib/OME/AnalysisPath.pm
 cp OME/SemanticType/Superclass.pm
/home/avu/OME/src/perl2/blib/lib/OME/SemanticType/Superclass.pm
 cp OME/Util/Lint.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Lint.pm
 cp OME/Util/Import.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Import.pm
 cp OME/File.pm /home/avu/OME/src/perl2/blib/lib/OME/File.pm
 cp OME/Remote/Facades/AnnotationFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/AnnotationFacade.pm
 cp OME/ModuleExecution/ParentalOutput.pm
/home/avu/OME/src/perl2/blib/lib/OME/ModuleExecution/ParentalOutput.pm
 cp OME/Web/ImportModules.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/ImportModules.pm
 cp OME/AnalysisChainExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/AnalysisChainExecution.pm
 cp OME/Web/Search/OME_Module.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Search/OME_Module.pm
 cp OME/SetDB.pm /home/avu/OME/src/perl2/blib/lib/OME/SetDB.pm
 cp OME/Image/Pix/t/tinyTest-LE.raw
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/t/tinyTest-LE.raw
 cp OME/Analysis/Engine/Worker.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/Worker.pm
 cp OME/Web/DBObjDetail/__OME_Module.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__OME_Module.pm
 cp OME/Install/t/RegressionSuite.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/t/RegressionSuite.pm
 cp OME/Web/DBObjRender/__OriginalFile.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OriginalFile.pm
 cp OME/Web/Mouse_CG_Annotator.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Mouse_CG_Annotator.pm
 cp OME/Install/InstallationTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/InstallationTask.pm
 cp OME/Remote/Facades/ProjectFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/ProjectFacade.pm
 cp OME/Install/PerlModuleTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/PerlModuleTask.pm
 cp OME/Web/ImportImages.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/ImportImages.pm
 cp OME/Dataset.pm /home/avu/OME/src/perl2/blib/lib/OME/Dataset.pm
 cp OME/Remote/SerializerXMLRPC.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/SerializerXMLRPC.pm
 cp OME/Web/DBObjCreate/OME_Dataset.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjCreate/OME_Dataset.pm
 cp OME/Image/Pixels.pm /home/avu/OME/src/perl2/blib/lib/OME/Image/Pixels.pm
 cp OME/Web/Logout.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/Logout.pm
 cp OME/Tasks/ImageTasks.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ImageTasks.pm
 cp OME/AnalysisChain/Link.pm
/home/avu/OME/src/perl2/blib/lib/OME/AnalysisChain/Link.pm
 cp OME/Analysis/Handlers/EchoHandler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Handlers/EchoHandler.pm
 cp OME/Install/t/Environment_deleteTree_Test.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/t/Environment_deleteTree_Test.pm
 cp OME/Web/FindSpots.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/FindSpots.pm
 cp OME/Analysis/Handlers/MatlabHandler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Handlers/MatlabHandler.pm
 cp OME/Matlab/MatlabInfo.pl
/home/avu/OME/src/perl2/blib/lib/OME/Matlab/MatlabInfo.pl
 cp OME/Install/Util.pm /home/avu/OME/src/perl2/blib/lib/OME/Install/Util.pm
 cp OME/SemanticType/Element.pm
/home/avu/OME/src/perl2/blib/lib/OME/SemanticType/Element.pm
 cp OME/Web/Util/Category.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Util/Category.pm
 cp OME/Remote/DTO/GenericAssembler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/DTO/GenericAssembler.pm
 cp OME/ImportEngine/Params.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/Params.pm
 cp OME/Util/Delete.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Delete.pm
 cp OME/Tasks/AEFacade.pm /home/avu/OME/src/perl2/blib/lib/OME/Tasks/AEFacade.pm
 cp OME/Install/AnalysisConfigTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/AnalysisConfigTask.pm
 cp SVGcatchMsg.pl /home/avu/OME/src/perl2/blib/lib/SVGcatchMsg.pl
 cp OME/Web/DBObjRender/__OME_ModuleExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_ModuleExecution.pm
 cp OME/Web/DBObjRender/__BayesNetClassifier.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__BayesNetClassifier.pm
 cp OME/ImportEngine/LSMreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/LSMreader.pm
 cp OME/Install/PreInstallTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/PreInstallTask.pm
 cp OME/Image/Pix/t/tinyTest-BE.raw
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/t/tinyTest-BE.raw
 cp OME/Util/ExecuteChain.pm
/home/avu/OME/src/perl2/blib/lib/OME/Util/ExecuteChain.pm
 cp OME/Analysis/Modules/Slicers/Pixels.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Slicers/Pixels.pm
 cp OME/Web/DBObjRender/__OME_SemanticType_Element.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_SemanticType_Element.pm
 cp OME/ViewerPreferences.pm
/home/avu/OME/src/perl2/blib/lib/OME/ViewerPreferences.pm
 cp OME/Java/DTOInterface.pm
/home/avu/OME/src/perl2/blib/lib/OME/Java/DTOInterface.pm
 cp OME/Tests/ExportSession.pl
/home/avu/OME/src/perl2/blib/lib/OME/Tests/ExportSession.pl
 cp OME/Web/TaskProgress.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/TaskProgress.pm
 cp OME/ImportEngine/ImportEngine.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/ImportEngine.pm
 cp OME/Analysis/Handlers/DefaultLoopHandler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Handlers/DefaultLoopHandler.pm
 cp OME/Util/Top.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Top.pm
 cp OME/Analysis/Engine/SimpleWorkerExecutor.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/SimpleWorkerExecutor.pm
 cp OME/Module/FormalOutput.pm
/home/avu/OME/src/perl2/blib/lib/OME/Module/FormalOutput.pm
 cp OME/Web/RunClassifier.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/RunClassifier.pm
 cp OME/Web/ExecuteChain.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/ExecuteChain.pm
 cp OME/ImportExport/HierarchyExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/HierarchyExport.pm
 cp OME/UserState.pm /home/avu/OME/src/perl2/blib/lib/OME/UserState.pm
 cp OME/ImportExport/HierarchyImport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/HierarchyImport.pm
 cp OME/Tasks/ClassifierTasks.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ClassifierTasks.pm
 cp OME/Web/XMLFileExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/XMLFileExport.pm
 cp OME/Util/Uninstall.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Uninstall.pm
 cp OME/Util/Export.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Export.pm
 cp OME/Web/DBObjDetail/__OME_Dataset.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__OME_Dataset.pm
 cp OME/Analysis/Modules/Classification/SignatureStitcher.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Classification/SignatureStitcher.pm
 cp OME/ImportExport/Repacker/MANIFEST
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/MANIFEST
 cp OME/ImportExport/DataHistoryImport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/DataHistoryImport.pm
 cp OME/Image/Pix/libpix.c
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/libpix.c
 cp OME/ImportEngine/BMPreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/BMPreader.pm
 cp OME/ImportExport/ModuleImport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/ModuleImport.pm
 cp OME/Web/DBObjRender/__Objective.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__Objective.pm
 cp OME/Web/MouseDisplay.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/MouseDisplay.pm
 cp OME/Analysis/Modules/Tracking/FindSpots.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tracking/FindSpots.pm
 cp OME/Analysis/Modules/Tests/PassThrough.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tests/PassThrough.pm
 cp OME/Util/Commands.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Commands.pm
 cp OME/Web/STdoc.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/STdoc.pm
 cp OME/Web/DBObjRender/__OME_AnalysisChainExecution_NodeExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_AnalysisChainExecution_NodeExecution.pm
 cp OME/Analysis/Modules/PPM/Typecast.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/PPM/Typecast.pm
 cp OME/Feature.pm /home/avu/OME/src/perl2/blib/lib/OME/Feature.pm
 cp OME/Web/GetGraphics.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/GetGraphics.pm
 cp OME/Analysis/Modules/Slicers/Stacks.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Slicers/Stacks.pm
 cp OME/Install/MaintenanceTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/MaintenanceTask.pm
 cp OME/Analysis/Modules/Tracking/TrackSpots.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tracking/TrackSpots.pm
 cp OME/Web/DBObjDetail/__OME_ModuleExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__OME_ModuleExecution.pm
 cp OME/Analysis/Modules/Histogram/PlaneHistogram.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Histogram/PlaneHistogram.pm
 cp OME/Tasks/ChainManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ChainManager.pm
 cp OME/Tasks/AnnotationManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/AnnotationManager.pm
 cp OME/Analysis/Modules/PPM/FourierTransform.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/PPM/FourierTransform.pm
 cp OME/Image/DatasetMap.pm
/home/avu/OME/src/perl2/blib/lib/OME/Image/DatasetMap.pm
 cp OME/Analysis/Handlers/NoopHandler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Handlers/NoopHandler.pm
 cp OME/Fork.pm /home/avu/OME/src/perl2/blib/lib/OME/Fork.pm
 cp OME/ImportExport/DataHistoryExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/DataHistoryExport.pm
 cp OME/Module/Category.pm
/home/avu/OME/src/perl2/blib/lib/OME/Module/Category.pm
 cp OME/Tasks/PixelsManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/PixelsManager.pm
 cp OME/Tasks/CategoryManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/CategoryManager.pm
 cp OME/Analysis/Modules/Tests/FauxSignature.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tests/FauxSignature.pm
 cp OME/Analysis/Modules/Slicers/Timepoints.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Slicers/Timepoints.pm
 cp OME/ImportEngine/GELreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/GELreader.pm
 cp OME/Web.pm /home/avu/OME/src/perl2/blib/lib/OME/Web.pm
 cp OME/ImportEngine/MetamorphHTDFormat.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/MetamorphHTDFormat.pm
 cp OME/Analysis/Engine/FeatureHierarchy.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/FeatureHierarchy.pm
 cp OME/Web/DBObjRender/__OME_AnalysisChainExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_AnalysisChainExecution.pm
 cp OME/Util/Classifier.pm
/home/avu/OME/src/perl2/blib/lib/OME/Util/Classifier.pm
 cp OME/Web/DBObjRender.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender.pm
 cp OME/DBConnection.pm /home/avu/OME/src/perl2/blib/lib/OME/DBConnection.pm
 cp OME/Install/LibraryTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/LibraryTask.pm
 cp OME/Configuration/Variable.pm
/home/avu/OME/src/perl2/blib/lib/OME/Configuration/Variable.pm
 cp OME/Util/GroupAdmin.pm
/home/avu/OME/src/perl2/blib/lib/OME/Util/GroupAdmin.pm
 cp omeapi.pod /home/avu/OME/src/perl2/blib/lib/omeapi.pod
 cp OME/Web/Login.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/Login.pm
 cp OME/Tasks/HistoryManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/HistoryManager.pm
 cp OME/Remote/DTO/ProjectAssembler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/DTO/ProjectAssembler.pm
 cp OME/Tasks/LSIDManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/LSIDManager.pm
 cp OME/Tasks/AttributeManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/AttributeManager.pm
 cp OME/Image/Pix/t/test.t
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/t/test.t
 cp OME/Analysis/Modules/Tests/DatasetSignature.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tests/DatasetSignature.pm
 cp OME/Web/DBObjRender/__OME_AnalysisChain_Node.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_AnalysisChain_Node.pm
 cp OME/Image/Pix/Changes /home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/Changes
 cp OME/SemanticType/BootstrapRepository.pm
/home/avu/OME/src/perl2/blib/lib/OME/SemanticType/BootstrapRepository.pm
 cp OME/Web/DBObjRender/__Pixels.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__Pixels.pm
 cp OME/Web/Util/Dataset.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Util/Dataset.pm
 cp OME/ModuleExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/ModuleExecution.pm
 cp OME/Analysis/Modules/Histogram/StackHistogram.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Histogram/StackHistogram.pm
 cp OME/Web/SaveViewerSettings.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/SaveViewerSettings.pm
 cp OME/Matlab/Matlab.pm /home/avu/OME/src/perl2/blib/lib/OME/Matlab/Matlab.pm
 cp OME/Matlab/Makefile.old
/home/avu/OME/src/perl2/blib/lib/OME/Matlab/Makefile.old
 cp OME/Install/t/Environment_copyTree_Test1.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/t/Environment_copyTree_Test1.pm
 cp OME/Remote/Prototypes.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Prototypes.pm
 cp OME/Analysis/Modules/Tests/FindBounds.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tests/FindBounds.pm
 cp OME/Install/t/Environment_scanDir_Test.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/t/Environment_scanDir_Test.pm
 cp OME/Analysis/Engine/README.DISTRIBUTED
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/README.DISTRIBUTED
 cp OME/Tasks/OMEXMLImportExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/OMEXMLImportExport.pm
 cp OME/Remote/Facades/XMLUtils.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/XMLUtils.pm
 cp OME/Util/dbAdmin.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/dbAdmin.pm
 cp OME/ImportExport/ChainExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/ChainExport.pm
 cp OME/Tests/SOAP-2.pl /home/avu/OME/src/perl2/blib/lib/OME/Tests/SOAP-2.pl
 cp OME/Task.pm /home/avu/OME/src/perl2/blib/lib/OME/Task.pm
 cp OME/ImportEngine/STKreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/STKreader.pm
 cp OME/ImportExport/Repacker/Repacker.xs
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/Repacker.xs
 cp OME/AnalysisChainExecution/NodeExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/AnalysisChainExecution/NodeExecution.pm
 cp OME/Web/DBObjDetail/__OME_Image.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__OME_Image.pm
 cp OME/Web/VisBio.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/VisBio.pm
 cp OME/Remote/XMLRPC.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote/XMLRPC.pm
 cp OME/Web/Search.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/Search.pm
 cp OME/ImportExport/Repacker/README
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/README
 cp OME/Web/DBObjRender/__OME_Image.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_Image.pm
 cp OME/Tasks/ImportManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ImportManager.pm
 cp OME/Analysis/Modules/Statistics/StackStatistics.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Statistics/StackStatistics.pm
 cp OME/Util/OMEAdmin.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/OMEAdmin.pm
 cp OME/Analysis/Modules/Slicers/Channels.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Slicers/Channels.pm
 cp OME/Tasks/ProjectManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ProjectManager.pm
 cp OME/ImportEngine/BioradReader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/BioradReader.pm
 cp OME/Remote/Facades/ConfigFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/ConfigFacade.pm
 cp OME/Web/UploadImage.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/UploadImage.pm
 cp OME/ImportExport/SemanticTypeImport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/SemanticTypeImport.pm
 cp OME/Web/DBObjDetail/__CategoryGroup.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__CategoryGroup.pm
 cp OME/Tasks/ImageManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ImageManager.pm
 cp OME/Web/Search/Experimenter.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Search/Experimenter.pm
 cp OME/Web/DBObjCreate.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjCreate.pm
 cp OME/ImportExport/ChainImport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/ChainImport.pm
 cp OME/Web/TrainClassifier.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/TrainClassifier.pm
 cp OME/Web/DefaultMenuBuilder.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DefaultMenuBuilder.pm
 cp OME/Analysis/Handlers/CLIHandler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Handlers/CLIHandler.pm
 cp OME/ModuleExecution/SemanticTypeOutput.pm
/home/avu/OME/src/perl2/blib/lib/OME/ModuleExecution/SemanticTypeOutput.pm
 cp OME/Image/Pix/typemap /home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/typemap
 cp OME/LookupTable.pm /home/avu/OME/src/perl2/blib/lib/OME/LookupTable.pm
 cp OME/Configuration.pm /home/avu/OME/src/perl2/blib/lib/OME/Configuration.pm
 cp OME/SemanticType/BootstrapGroup.pm
/home/avu/OME/src/perl2/blib/lib/OME/SemanticType/BootstrapGroup.pm
 cp OME/Factory.pm /home/avu/OME/src/perl2/blib/lib/OME/Factory.pm
 cp OME/Matlab/Makefile.PL
/home/avu/OME/src/perl2/blib/lib/OME/Matlab/Makefile.PL
 cp OME/Analysis/Modules/PPM/Gradient.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/PPM/Gradient.pm
 cp OME/ImportExport/SemanticTypeExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/SemanticTypeExport.pm
 cp OME/ImportEngine/AbstractFormat.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/AbstractFormat.pm
 cp OME/SemanticType/BootstrapExperimenterGroup.pm
/home/avu/OME/src/perl2/blib/lib/OME/SemanticType/BootstrapExperimenterGroup.pm
 cp OME/AnalysisChain/Node.pm
/home/avu/OME/src/perl2/blib/lib/OME/AnalysisChain/Node.pm
 cp OME/ImportEngine/DICOM.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/DICOM.pm
 cp OME/Web/DBObjRender/__Instrument.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__Instrument.pm
 cp OME/SemanticType.pm /home/avu/OME/src/perl2/blib/lib/OME/SemanticType.pm
 cp OME/Web/DBObjRender/__OME_Task.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_Task.pm
 cp OME/Remote/Apache2/Transport.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Apache2/Transport.pm
 cp OME/Remote.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote.pm
 cp OME/Tasks/NotificationManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/NotificationManager.pm
 cp OME/Matlab/test.pl /home/avu/OME/src/perl2/blib/lib/OME/Matlab/test.pl
 cp OME/ImportExport/Repacker/Makefile.PL
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/Makefile.PL
 cp OME/Web/CategoryGroup_Annotator.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/CategoryGroup_Annotator.pm
 cp OME/Remote/Apache/HTTPProxy.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Apache/HTTPProxy.pm
 cp OME/Remote/Facades/DatasetFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/DatasetFacade.pm
 cp OME/Java/SemanticTypeInterface.pm
/home/avu/OME/src/perl2/blib/lib/OME/Java/SemanticTypeInterface.pm
 cp OME/Install/ApacheConfigTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/ApacheConfigTask.pm
 cp OME/Analysis/Engine/DataPaths.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/DataPaths.pm
 cp OME/Analysis/Modules/Slicers/Planes.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Slicers/Planes.pm
 cp OME/Web/DBObjRender/__OME_DataTable_Column.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_DataTable_Column.pm
 cp OME/Tasks/DatasetManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/DatasetManager.pm
 cp OME/Install/t/Environment_copyTree_Test2.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/t/Environment_copyTree_Test2.pm
 cp OME/Web/Home.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/Home.pm
 cp OME/Matlab/MANIFEST /home/avu/OME/src/perl2/blib/lib/OME/Matlab/MANIFEST
 cp OME/ImportEngine/XMLreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/XMLreader.pm
 cp OME/Database/Delegate.pm
/home/avu/OME/src/perl2/blib/lib/OME/Database/Delegate.pm
 cp OME/Web/Search/OME_ModuleExecution.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Search/OME_ModuleExecution.pm
 cp OME/DataTable/Column.pm
/home/avu/OME/src/perl2/blib/lib/OME/DataTable/Column.pm
 cp OME/ImportExport/Repacker/Repacker.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/Repacker.pm
 cp OME/ModuleExecution/VirtualMEXMap.pm
/home/avu/OME/src/perl2/blib/lib/OME/ModuleExecution/VirtualMEXMap.pm
 cp OME/Remote/StandaloneServer.pl
/home/avu/OME/src/perl2/blib/lib/OME/Remote/StandaloneServer.pl
 cp OME/Analysis/Modules/Tests/ImageSignature.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tests/ImageSignature.pm
 cp OME/ImportExport/Repacker/Changes
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/Changes
 cp OME/Analysis/Modules/Statistics/PlaneStatistics.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Statistics/PlaneStatistics.pm
 cp OME/ImportExport/Repacker/test.pl
/home/avu/OME/src/perl2/blib/lib/OME/ImportExport/Repacker/test.pl
 cp OME/Remote/Facades/ChainRetrievalFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/ChainRetrievalFacade.pm
 cp OME/Image.pm /home/avu/OME/src/perl2/blib/lib/OME/Image.pm
 cp OME/Tasks/OMEExport.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/OMEExport.pm
 cp OME/Web/ImportFiles.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/ImportFiles.pm
 cp OME/Install/Environment.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/Environment.pm
 cp OME/ImportEngine/DICOMconstants.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/DICOMconstants.pm
 cp OME/Remote/Facades/ImportFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/ImportFacade.pm
 cp OME/Remote/Facades/SessionFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/SessionFacade.pm
 cp OME/Install/t/Environment_copyTree_Test3.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/t/Environment_copyTree_Test3.pm
 cp OME/Module.pm /home/avu/OME/src/perl2/blib/lib/OME/Module.pm
 cp OME/AnalysisChain.pm /home/avu/OME/src/perl2/blib/lib/OME/AnalysisChain.pm
 cp OME/Remote/DTO.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote/DTO.pm
 cp OME/Util/Templates.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/Templates.pm
 cp OME/Web/Search/OME_Project.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Search/OME_Project.pm
 cp OME/Project.pm /home/avu/OME/src/perl2/blib/lib/OME/Project.pm
 cp OME/Install/CoreDatabaseTablesTask.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/CoreDatabaseTablesTask.pm
 cp OME/Image/Pix/libpix.h
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/libpix.h
 cp OME/AnalysisPath/Map.pm
/home/avu/OME/src/perl2/blib/lib/OME/AnalysisPath/Map.pm
 cp OME/Remote/Apache2/HTTPProxy.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Apache2/HTTPProxy.pm
 cp OME/Util/UserAdmin.pm /home/avu/OME/src/perl2/blib/lib/OME/Util/UserAdmin.pm
 cp OME/ImportEngine/TIFFreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/TIFFreader.pm
 cp OME/Image/Pix/MANIFEST
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/MANIFEST
 cp OME/Web/DBObjCreate/Category.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjCreate/Category.pm
 cp OME/Tests/XMLRPC.pl /home/avu/OME/src/perl2/blib/lib/OME/Tests/XMLRPC.pl
 cp OME/Remote/Apache/Transport.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Apache/Transport.pm
 cp OME/Install/Terminal.pm
/home/avu/OME/src/perl2/blib/lib/OME/Install/Terminal.pm
 cp OME/Analysis/Modules/Classification/ML_BayesNet_Trainer.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Classification/ML_BayesNet_Trainer.pm
 cp OME/Analysis/Engine.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine.pm
 cp OME/Web/Search/OME_Dataset.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Search/OME_Dataset.pm
 cp serve.pl /home/avu/OME/src/perl2/blib/lib/serve.pl
 cp OME/Tasks/SemanticTypeManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/SemanticTypeManager.pm
 cp OME/Remote/Facades/AnalysisFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/AnalysisFacade.pm
 cp OME/DataTable.pm /home/avu/OME/src/perl2/blib/lib/OME/DataTable.pm
 cp OME/Project/DatasetMap.pm
/home/avu/OME/src/perl2/blib/lib/OME/Project/DatasetMap.pm
 cp OME/Web/DBObjRender/__Experimenter.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__Experimenter.pm
 cp OME/SessionManager.pm /home/avu/OME/src/perl2/blib/lib/OME/SessionManager.pm
 cp OME/Remote/Apache2.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote/Apache2.pm
 cp OME/Util/OMECommander.pm
/home/avu/OME/src/perl2/blib/lib/OME/Util/OMECommander.pm
 cp OME/Tasks/OMEImport.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/OMEImport.pm
 cp OME/Remote/Facades/HistoryFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/HistoryFacade.pm
 cp OME/ImportEngine/DICOMreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/DICOMreader.pm
 cp OME/Web/DBObjDetail.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail.pm
 cp OME/Analysis/Engine/NonblockingSlaveWorkerCGI.pl
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/NonblockingSlaveWorkerCGI.pl
 cp OME/Web/DBObjRender/__OME_DataTable.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_DataTable.pm
 cp OME/Tests/SOAP.pl /home/avu/OME/src/perl2/blib/lib/OME/Tests/SOAP.pl
 cp OME/Remote/Apache.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote/Apache.pm
 cp OME/Image/Server.pm /home/avu/OME/src/perl2/blib/lib/OME/Image/Server.pm
 cp OME/Analysis/Modules/Tests/FindRatio.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Tests/FindRatio.pm
 cp OME/Web/DBObjTable.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjTable.pm
 cp OME/Image/Pix/Pix.xs /home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/Pix.xs
 cp OME/Analysis/Modules/Classification/ML_BayesNet_Classifier.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Modules/Classification/ML_BayesNet_Classifier.pm
 cp OME/Analysis/Engine/ForkedPerlExecutor.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/ForkedPerlExecutor.pm
 cp OME/Matlab/Changes /home/avu/OME/src/perl2/blib/lib/OME/Matlab/Changes
 cp OME/Java/omejava /home/avu/OME/src/perl2/blib/lib/OME/Java/omejava
 cp OME/Image/Server/Pixels.pm
/home/avu/OME/src/perl2/blib/lib/OME/Image/Server/Pixels.pm
 cp OME/Tests/InteractiveSOAP.pl
/home/avu/OME/src/perl2/blib/lib/OME/Tests/InteractiveSOAP.pl
 cp OME/ModuleExecution/ActualInput.pm
/home/avu/OME/src/perl2/blib/lib/OME/ModuleExecution/ActualInput.pm
 cp OME/Web/DBObjRender/__Category.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__Category.pm
 cp OME/LocalFile.pm /home/avu/OME/src/perl2/blib/lib/OME/LocalFile.pm
 cp OME/Remote/RPC2.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote/RPC2.pm
 cp OME/Tasks/ModuleExecutionManager.pm
/home/avu/OME/src/perl2/blib/lib/OME/Tasks/ModuleExecutionManager.pm
 cp OME/Web/MouseSearch.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/MouseSearch.pm
 cp OME/Matlab/typemap /home/avu/OME/src/perl2/blib/lib/OME/Matlab/typemap
 cp OME/SemanticType/BootstrapExperimenter.pm
/home/avu/OME/src/perl2/blib/lib/OME/SemanticType/BootstrapExperimenter.pm
 cp OME/Remote/Dispatcher.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Dispatcher.pm
 cp OME/Web/DBObjRender/__OME_Dataset.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjRender/__OME_Dataset.pm
 cp OME/ImportEngine/TIFFUtils.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/TIFFUtils.pm
 cp OME/Image/Pix/t/tinyTest.d3d.dv
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/t/tinyTest.d3d.dv
 cp OME/Web/FileTable.pm /home/avu/OME/src/perl2/blib/lib/OME/Web/FileTable.pm
 cp LogService.pl /home/avu/OME/src/perl2/blib/lib/LogService.pl
 cp OME/Remote/Facades/GenericFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/GenericFacade.pm
 cp OME.pm /home/avu/OME/src/perl2/blib/lib/OME.pm
 cp OME/Analysis/Handler.pm
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Handler.pm
 cp OME/Module/FormalInput.pm
/home/avu/OME/src/perl2/blib/lib/OME/Module/FormalInput.pm
 cp OME/Remote/Facades/ModuleExecutionFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/ModuleExecutionFacade.pm
 cp omemodules.pod /home/avu/OME/src/perl2/blib/lib/omemodules.pod
 cp OME/Web/DBObjDetail/__OME_Project.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__OME_Project.pm
 cp OME/Remote/Facade.pm /home/avu/OME/src/perl2/blib/lib/OME/Remote/Facade.pm
 cp OME/Session.pm /home/avu/OME/src/perl2/blib/lib/OME/Session.pm
 cp OME/Database/PostgresDelegate.pm
/home/avu/OME/src/perl2/blib/lib/OME/Database/PostgresDelegate.pm
 cp OME/Remote/DeserializerXMLRPC.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/DeserializerXMLRPC.pm
 cp OME/Image/Pix/Pix.pm /home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/Pix.pm
 cp OME/Web/Search/Group.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/Search/Group.pm
 cp newdevelopers.pod /home/avu/OME/src/perl2/blib/lib/newdevelopers.pod
 cp OME/Remote/Facades/ModuleRetrievalFacade.pm
/home/avu/OME/src/perl2/blib/lib/OME/Remote/Facades/ModuleRetrievalFacade.pm
 cp OME/DBObject.pm /home/avu/OME/src/perl2/blib/lib/OME/DBObject.pm
 cp OME/Web/DBObjCreate/OME_Project.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjCreate/OME_Project.pm
 cp OME/Analysis/Engine/install_worker_node.pl
/home/avu/OME/src/perl2/blib/lib/OME/Analysis/Engine/install_worker_node.pl
 cp OME/Image/Server/File.pm
/home/avu/OME/src/perl2/blib/lib/OME/Image/Server/File.pm
 cp OME/ImportEngine/DVreader.pm
/home/avu/OME/src/perl2/blib/lib/OME/ImportEngine/DVreader.pm
 cp OME/Image/Pix/Makefile.PL
/home/avu/OME/src/perl2/blib/lib/OME/Image/Pix/Makefile.PL
 cp OME/Web/DBObjDetail/__Category.pm
/home/avu/OME/src/perl2/blib/lib/OME/Web/DBObjDetail/__Category.pm
 make[1]: Entering directory `/home/avu/OME/src/perl2/OME/Image/Pix'
 cp Pix.pm /home/avu/OME/src/perl2/blib/lib/OME/Image/Pix.pm
 /usr/bin/perl /usr/lib/perl5/5.8.3/ExtUtils/xsubpp  -typemap
/usr/lib/perl5/5.8.3/ExtUtils/typemap -typemap typemap  Pix.xs >
Pix.xsc && mv Pix.xsc Pix.c
 gcc -c  -I/sw/include -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -march=i386 -mcpu=i686   -DVERSION=\"2.004001\"
-DXS_VERSION=\"2.004001\" -fPIC
"-I/usr/lib/perl5/5.8.3/i386-linux-thread-multi/CORE"   Pix.c
 gcc -c  -I/sw/include -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
-DDEBUGGING -fno-strict-aliasing -I/usr/local/include
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g
-pipe -march=i386 -mcpu=i686   -DVERSION=\"2.004001\"
-DXS_VERSION=\"2.004001\" -fPIC
"-I/usr/lib/perl5/5.8.3/i386-linux-thread-multi/CORE"   libpix.c
 Running Mkbootstrap for OME::Image::Pix ()
 chmod 644 Pix.bs
 rm -f /home/avu/OME/src/perl2/blib/arch/auto/OME/Image/Pix/Pix.so
 gcc  -shared -L/usr/local/lib Pix.o libpix.o  -o
/home/avu/OME/src/perl2/blib/arch/auto/OME/Image/Pix/Pix.so  
-L/usr/local/lib -ltiff
 chmod 755 /home/avu/OME/src/perl2/blib/arch/auto/OME/Image/Pix/Pix.so
 cp Pix.bs /home/avu/OME/src/perl2/blib/arch/auto/OME/Image/Pix/Pix.bs
 chmod 644 /home/avu/OME/src/perl2/blib/arch/auto/OME/Image/Pix/Pix.bs
 Manifying /home/avu/OME/src/perl2/blib/man3/OME::Image::Pix.3pm
 make[1]: Leaving directory `/home/avu/OME/src/perl2/OME/Image/Pix'
 make[1]: Entering directory `/home/avu/OME/src/perl2/OME/ImportExport/Repacker'
 cp Repacker.pm /home/avu/OME/src/perl2/blib/lib/Repacker.pm
 /usr/bin/perl /usr/lib/perl5/5.8.3/ExtUtils/xsubpp  -typemap
/usr/lib/perl5/5.8.3/ExtUtils/typemap  Repacker.xs > Repacker.xsc &&
mv Repacker.xsc Repacker.c
 gcc -c   -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBUGGING
-fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -march=i386
-mcpu=i686   -DVERSION=\"2.004001\" -DXS_VERSION=\"2.004001\" -fPIC
"-I/usr/lib/perl5/5.8.3/i386-linux-thread-multi/CORE"   Repacker.c
 Running Mkbootstrap for Repacker ()
 chmod 644 Repacker.bs
 rm -f /home/avu/OME/src/perl2/blib/arch/auto/Repacker/Repacker.so
 gcc  -shared -L/usr/local/lib Repacker.o  -o
/home/avu/OME/src/perl2/blib/arch/auto/Repacker/Repacker.so
 chmod 755 /home/avu/OME/src/perl2/blib/arch/auto/Repacker/Repacker.so
 cp Repacker.bs /home/avu/OME/src/perl2/blib/arch/auto/Repacker/Repacker.bs
 chmod 644 /home/avu/OME/src/perl2/blib/arch/auto/Repacker/Repacker.bs
 Manifying /home/avu/OME/src/perl2/blib/man3/Repacker.3pm
 make[1]: Leaving directory `/home/avu/OME/src/perl2/OME/ImportExport/Repacker'
 cp OME/Java/omejava /home/avu/OME/src/perl2/blib/script/omejava
 /usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)"
/home/avu/OME/src/perl2/blib/script/omejava
"

INSTALLING MODULE -- 'make install'
SUCCESS -- OUTPUT: "make[1]: Entering directory
`/home/avu/OME/src/perl2/OME/Image/Pix'
 make[1]: Leaving directory `/home/avu/OME/src/perl2/OME/Image/Pix'
 make[1]: Entering directory `/home/avu/OME/src/perl2/OME/ImportExport/Repacker'
 make[1]: Leaving directory `/home/avu/OME/src/perl2/OME/ImportExport/Repacker'
 Writing /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi/auto/OME/.packlist
 Appending installation info to
/usr/lib/perl5/5.8.3/i386-linux-thread-multi/perllocal.pod
"

USING PERL CONFIGURE SCRIPT -- 'perl Makefile.PL avu /usr/local/matlab'
SUCCESS -- OUTPUT: "X connection to localhost:10.0 broken (explicit
kill or server shutdown).
 X connection to localhost:10.0 broken (explicit kill or server shutdown).
 Matlab Vers: glnx86
 Matlab Arch: /usr/local/matlab
 Matlab Home: 7.0.4.352
 Include:  -I/usr/local/matlab/extern/include
 Lib:      -L/usr/local/matlab/bin/glnx86 -lmx -leng -lut -lmat
-licudata -licui18n -licuuc -lustdio -lz
 Lib Path: /usr/local/matlab/bin/glnx86

 Checking if your kit is complete...
 Looks good
 Modifying LD_RUN_PATH...
 Modifying LD_LIBRARY_PATH...
 Adding LD_LIBRARY_PATH to Make Test ...
 Writing Makefile for OME::Matlab
"

COMPILING MODULE -- 'make'
SUCCESS -- OUTPUT: "cp Matlab.pm blib/lib/OME/Matlab.pm
 cp MatlabInfo.pl blib/lib/OME/MatlabInfo.pl
 /usr/bin/perl /usr/lib/perl5/5.8.3/ExtUtils/xsubpp  -typemap
/usr/lib/perl5/5.8.3/ExtUtils/typemap -typemap typemap  Matlab.xs >
Matlab.xsc && mv Matlab.xsc Matlab.c
 Please specify prototyping behavior for Matlab.xs (see perlxs manual)
 gcc -c  -I/usr/local/matlab/extern/include -D_REENTRANT -D_GNU_SOURCE
-DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing
-I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-I/usr/include/gdbm -O2 -g -pipe -march=i386 -mcpu=i686  
-DVERSION=\"2.004001\" -DXS_VERSION=\"2.004001\" -fPIC
"-I/usr/lib/perl5/5.8.3/i386-linux-thread-multi/CORE"   Matlab.c
 In file included from /usr/local/matlab/extern/include/matrix.h:203,
                  from Matlab.xs:41:
 /usr/local/matlab/extern/include/tmwtypes.h:682: warning: useless
keyword or type name in empty declaration
 /usr/local/matlab/extern/include/tmwtypes.h:682: warning: empty declaration
 Matlab.xs: In function `XS_OME__Matlab__Array_getAll':
 Matlab.xs:743: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:746: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:749: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:752: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:755: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:758: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:761: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:764: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:767: warning: use of cast expressions as lvalues is deprecated
 Matlab.xs:770: warning: use of cast expressions as lvalues is deprecated
 Running Mkbootstrap for OME::Matlab ()
 chmod 644 Matlab.bs
 rm -f blib/arch/auto/OME/Matlab/Matlab.so
 gcc  -shared -L/usr/local/lib Matlab.o  -o
blib/arch/auto/OME/Matlab/Matlab.so   -L/usr/local/matlab/bin/glnx86
-lmx -leng -lut -lmat -licudata -licui18n -licuuc -lustdio -lz
-L/usr/local/lib
 chmod 755 blib/arch/auto/OME/Matlab/Matlab.so
 cp Matlab.bs blib/arch/auto/OME/Matlab/Matlab.bs
 chmod 644 blib/arch/auto/OME/Matlab/Matlab.bs
 Manifying blib/man3/OME::Matlab.3pm
"

TESTING MODULE -- su -l avu -c 'make test '
FAILURE -- OUTPUT: "Makefile out-of-date with respect to Makefile.PL
 Cleaning current config before rebuilding Makefile...
 make -f Makefile.old clean > /dev/null 2>&1 || /bin/sh -c true
 /usr/bin/perl Makefile.PL "avu" "/usr/local/matlab"
 You must run the makefile as root to pass it a matlab_user at
MatlabInfo.pl line 58.
 Matlab Vers:
 Matlab Arch:
 Matlab Home:
 Include:
 Lib:
 Lib Path:

 Could not open '../../OME.pm': No such file or directory at
/usr/lib/perl5/5.8.3/ExtUtils/MM_Unix.pm line 3079.
 Checking if your kit is complete...
 Looks good
 make: *** [Makefile] Error 2
"



On 7/23/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> Anh,
> 
> Did you do a fresh CVS checkout or just a CVS update?
> Please try a fresh CVS checkout. If you have more problems with the
> installer, please send me the complete
> /var/tmp/OME/install/PerlModuleTask.log file.
> 
> The error message suggests that you are having conflicts between old
> and new Makefiles:
> "Makefile out-of-date with respect to Makefile.PL
> Cleaning current config before rebuilding Makefile..."
> 
> Tom
> 
> My output was :
> TESTING MODULE -- su -l tmacur1 -c 'make test '
> SUCCESS -- OUTPUT: "Agent pid 13847
>   rm -f blib/arch/auto/OME/Matlab/Matlab.bundle
> 
> LD_RUN_PATH="/Applications/MATLAB701/bin/mac:/Applications/MATLAB701/
> bin/mac" MACOSX_DEPLOYMENT_TARGET=10.3 cc  -bundle -undefined
> dynamic_lookup -L/usr/local/lib Matlab.o  -o
> blib/arch/auto/OME/Matlab/Matlab.bundle
> -L/Applications/MATLAB701/bin/mac -lmx -leng -lut -lmat -licudata
> -licui18n -licuuc -lustdio -lz -L/usr/local/lib -L/sw/lib
>   chmod 755 blib/arch/auto/OME/Matlab/Matlab.bundle
>   cp Matlab.bs blib/arch/auto/OME/Matlab/Matlab.bs
>   chmod 644 blib/arch/auto/OME/Matlab/Matlab.bs
>   PERL_DL_NONLAZY=1 LD_LIBRARY_PATH=/Applications/MATLAB701/bin/mac
> /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
>   Trying to compute 4x8 using MATLAB ...
>   Perl: OME::Matlab::Array=SCALAR(0x18560fc)
>       Class:  double
>       Order:  2
>       Dims:   1x1
>       Values: (32)
>   Test Passed. Perl Matlab API is correctly installed.
> "
> 
> Tom
> 
> On Jul 23, 2005, at 1:57 AM, Anh Vu wrote:
> 
> > Hi! I tried the instructions within the email and downloaded the
> > newest CVS version and make modification to the ld file, but when i
> > tried to install, it gave me an error at the testing stage during
> > Matlab perl api configuration. A standard installation without the
> > optional perl module setup installed and worked just fine.
> >
> > This is the error message from within PerlModuleTask.log
> > ***********************************************************************
> > **********************************
> > ----------------------------
> >  Optional Perl Module Setup
> > ----------------------------
> >
> > (All verbose information logged in
> > /var/tmp/OME/install/PerlModuleTask.log)
> >
> >
> > MATLAB Perl API configuration:
> >  Install MATLAB Perl API?: no
> >    Config MATLAB for dev?: no
> >
> > Are these values correct ? [y/n]: n
> > Install analysis engine interface to MATLAB ? [y/n]: y
> > The user which MATLAB should be run under [avu]:
> > Path to MATLAB installation [/usr/local/matlab]:
> > Path to MATLAB binary [/usr/local/bin/matlab]:
> > Configure MATLAB Perl API for developers? [y/n]: y
> > Path to OME's matlab src files [/home/avu/OME/src/matlab]:
> > "
> >
> > TESTING MODULE -- su -l avu -c 'make test '
> > FAILURE -- OUTPUT: "Makefile out-of-date with respect to Makefile.PL
> >  Cleaning current config before rebuilding Makefile...
> >  make -f Makefile.old clean > /dev/null 2>&1 || /bin/sh -c true
> >  /usr/bin/perl Makefile.PL "avu" "/usr/local/matlab"
> >  You must run the makefile as root to pass it a matlab_user at
> > MatlabInfo.pl line 58.
> >  Matlab Vers:
> >  Matlab Arch:
> >  Matlab Home:
> >  Include:
> >  Lib:
> >  Lib Path:
> >
> >  Could not open '../../OME.pm': No such file or directory at
> > /usr/lib/perl5/5.8.3/ExtUtils/MM_Unix.pm line 3079.
> >  Checking if your kit is complete...
> >  Looks good
> >  make: *** [Makefile] Error 2
> > "
> > ***********************************************************************
> > **********************************
> >
> > Thanks!
> > -Anh
> >
> > On 7/22/05, T. J. Macura <tm289 at cam.ac.uk> wrote:
> >> Hi Anh,
> >>
> >> I looked back to the list archive and saw the message you wrote on Jun
> >> 14th.
> >> Sorry I didn't get back to you sooner, I was very busy then and didn't
> >> have spare time to help users. Your email fell through the cracks.
> >>
> >> In fact, now I am on vacation (for 7 days) in Wyoming USA enjoying
> >> Teton National Forest (near Yellowstone). Hiking, cycling, and
> >> white-water rafting.
> >> I hope I can make it up to you.
> >>
> >> Last week I installed OME from CVS on RH Fedora Core 3.  I was able to
> >> get the MatlabHandler to work, but only after lots of tweeking.
> >> This necessitated some changes to the installer. So please try to get
> >> OME from CVS and let me know how it works with importing the Matlab
> >> Modules.
> >>
> >> One thing I had to do (and you probably will have to do as well) is to
> >> modify ld.so.conf and run /sbin/ldconfig.
> >> Here is the contents of my /etc/ld.so.conf
> >> [tmacur1 at ome2 ~]$ cat /etc/ld.so.conf
> >> include ld.so.conf.d/*.conf
> >> /usr/lib/
> >> /usr/local/lib
> >> /usr/bin/MATLAB7SP2/bin/glnx86
> >> /usr/X11R6/lib
> >>
> >> You probably need to change the MATLAB line. You see /usr/local/* etc?
> >> I added those by hand. Those directories must be put before the MATLAB
> >> directory so default system libraries (and not system libraries that
> >> come with MATLAB) are used during linking.
> >>
> >> If you have problems with the Module Import once more, please send me
> >> the error messages and I will get back to you promptly.
> >>
> >> Tom
> >>
> >>> I'm running OME 2.4.0 on Fedora Core 3 with kernel version 2.6.5. I
> >>> also have matlab R14 running on the server. I have written some
> >>> matlab
> >>> scripts that perform identification for a given input image and
> >>> outputs some statistical data for that image and I am trying to
> >>> intergrate those scripts into OME so that I can run the analysis and
> >>> store the statistical data into the OME database.
> >>>
> >>> -Anh
> >>>
> >>
> >>
> >> On Jul 21, 2005, at 12:07 PM, Anh Vu wrote:
> >>
> >>> I also have problem with the matlabhandler trying to get it to work
> >>> with OME. Whenever I try to import a matlab module it would fail and
> >>> complains about the matlabhandler, so could anyone help me on that?
> >>> Any suggestion as to what I should do to get it working? I'm using
> >>> the
> >>> very early release of OME version 2.3.0 btw. I have some basic
> >>> knowledge in Perl, so I can try to modify the code, but then I can't
> >>> narrow down where the problem is.
> >>>
> >>> Anh
> >>>
> >>
> >>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> 
>

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