[ome-devel] bio-formats Maven problems

Tue May 13 17:34:38 BST 2014

Hi Ian,

> For a while now I’ve been building bf with Netbeans
...
> About 2 weeks ago I started getting the following errors

Since your goal is to produce a JAR for use with an external project, it
might be simpler to execute either "ant tools" or "mvn package" from the
command line, instead of clicking through an IDE like NetBeans. You can do
this as your last step after making code changes within NetBeans and then
testing them within the IDE, once you are confident the changes are what
you need.

> The import ome.xml.model.Channel cannot be resolved

These errors almost certainly indicate either A) NetBeans is never running
the ome-xml code generation step; or B) NetBeans isn't picking up the
generated sources when compiling the rest of the code.

I tried importing the Bio-Formats dev_5_0 code into a fresh NetBeans 8.0,
then building it at the top level, but I receive an error about genshi not
being installed (even though it is). Probably system Python vs. brewed
Python or similar nonsense. So unfortunately I cannot help troubleshoot the
NB issues much beyond that. However, I do know that NetBeans pretty much
uses the command line Maven to build Maven projects (and you can tell from
the output console), so if the build works on the command line for you, it
is likely to work in NB, as well.

Is there some reason you need to use NB to build the JARs, rather than
command line?

Regards,
Curtis

P.S. In the future it would be nice if the OME-XML code was not required to
be built as part of the Bio-Formats multi-module build. That code does not
change often and would work better as a release versioned dependency. It
would make it much easier to build the rest of Bio-Formats since it would
then all be pure Java again.

On Tue, May 13, 2014 at 9:49 AM, Munro, Ian <i.munro at imperial.ac.uk> wrote:

> Hi Curtis
>
> I’d really appreciate any assistance.
>
> For a while now I’ve been building bf with Netbeans (simply because it was
> the first IDE on the doc page) without a problem.
> I don’t, however, have a good understanding of the bf structure but the
> following ‘incantation' seemed to work.
>
> Edit code e.g. SDTReader.java
>
> On the ‘Projects’ Window
>
> Build Bio-Formats library
> Build Bio-Formats code generator
> Build bioformats-package bundle.
>
> This generated a bioformats_package 5.0.2 SNAPSHOT which I could then use.
>
> About 2 weeks ago I started getting the following errors in Step 1 ,the
> library build.
> I’m using open microscopy dev_5_0
>
> Regards
>
> ian
>
> ------------------------------------------------------------------------
> BUILD FAILURE
> ------------------------------------------------------------------------
> Total time: 8.411s
> Finished at: Tue May 13 15:46:08 BST 2014
> Final Memory: 17M/310M
> ------------------------------------------------------------------------
> Failed to execute goal
> org.apache.maven.plugins:maven-surefire-plugin:2.16:test (default-test) on
> project formats-gpl: Execution default-test of goal
> org.apache.maven.plugins:maven-surefire-plugin:2.16:test failed: There was
> an error in the forked process
> org.testng.TestNGException:
> Cannot instantiate class loci.formats.utests.xml.Upgrade200909Test
> at
> org.testng.internal.ObjectFactoryImpl.newInstance(ObjectFactoryImpl.java:35)
> at org.testng.internal.ClassHelper.createInstance(ClassHelper.java:317)
> at org.testng.internal.ClassImpl.getDefaultInstance(ClassImpl.java:71)
> at org.testng.internal.ClassImpl.getInstances(ClassImpl.java:90)
> at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:119)
> at org.testng.TestRunner.initMethods(TestRunner.java:379)
> at org.testng.TestRunner.init(TestRunner.java:254)
> at org.testng.TestRunner.init(TestRunner.java:224)
> at org.testng.TestRunner.<init>(TestRunner.java:173)
> at
> org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:494)
> at org.testng.SuiteRunner.privateRun(SuiteRunner.java:239)
> at org.testng.SuiteRunner.run(SuiteRunner.java:193)
> at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:910)
> at org.testng.TestNG.runSuitesLocally(TestNG.java:879)
> at org.testng.TestNG.run(TestNG.java:787)
> at
> org.apache.maven.surefire.testng.TestNGExecutor.run(TestNGExecutor.java:217)
> at
> org.apache.maven.surefire.testng.TestNGXmlTestSuite.execute(TestNGXmlTestSuite.java:84)
> at
> org.apache.maven.surefire.testng.TestNGProvider.invoke(TestNGProvider.java:92)
> at
> org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:200)
> at
> org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:153)
> at
> org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:103)
> Caused by: java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
> at
> org.testng.internal.ObjectFactoryImpl.newInstance(ObjectFactoryImpl.java:26)
> ... 20 more
> Caused by: java.lang.Error: Unresolved compilation problems:
> The import ome.xml.model.Channel cannot be resolved
> The import ome.xml.model.Image cannot be resolved
> The import ome.xml.model.OME cannot be resolved
> The import ome.xml.model.Pixels cannot be resolved
> The import ome.xml.model.enums.AcquisitionMode cannot be resolved
> OME cannot be resolved to a type
> OME cannot be resolved to a type
> OME cannot be resolved to a type
> The method getRoot() is undefined for the type OMEXMLMetadata
> OME cannot be resolved to a type
> Image cannot be resolved to a type
> OME cannot be resolved to a type
> Pixels cannot be resolved to a type
> Channel cannot be resolved to a type
> AcquisitionMode cannot be resolved to a variable
>
> at
> loci.formats.utests.xml.Upgrade200909Test.<init>(Upgrade200909Test.java:38)
> ... 25 more
> -> [Help 1]
>
> To see the full stack trace of the errors, re-run Maven with the -e switch.
> Re-run Maven using the -X switch to enable full debug logging.
>
> For more information about the errors and possible solutions, please read
> the following articles:
> [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException
>
>
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