<div dir="ltr">Hi Ian,<div><br></div><div>Glad to hear you figured it out.</div><div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, May 13, 2014 at 1:22 PM, Munro, Ian <span dir="ltr"><<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Curtis
<div><br>
</div>
<div>Thanks. You gave me enough of a clue to solve my problem.</div>
<div>Calling ‘clean & build’ then ‘build with dependencies’ seemed to sort it out.</div>
<div><br>
</div>
<div>In answer to your question I’d rather use an IDE as working from the command line involves knowing what I’m doing & I don’t.</div>
<div><br>
</div>
<div>Regards</div><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Ian</div>
<div><br>
</div>
</font></span><div><br>
<div><div class="">
<div>On 13 May 2014, at 17:34, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>> wrote:</div>
<br>
</div><blockquote type="cite">
<div dir="ltr"><div class="">Hi Ian,
<div><br>
</div>
<div>> <span style="font-family:arial,sans-serif;font-size:13px">For a while now I’ve been building bf with Netbean</span></div>
</div><div><div class="h5"><div><span style="font-family:arial,sans-serif;font-size:13px">...</span></div>
<div>> <span style="font-family:arial,sans-serif;font-size:13px">About 2 weeks ago I started getting the following errors</span></div>
<div><br>
</div>
<div><span style="font-family:arial,sans-serif;font-size:13px">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.</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px">> The import ome.xml.model.Channel cannot be resolved</span><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px">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.</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><font face="arial, sans-serif">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.</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Is there some reason you need to use NB to build the JARs, rather than command line?</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Regards,</font></div>
<div><font face="arial, sans-serif">Curtis</font></div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra">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.</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, May 13, 2014 at 9:49 AM, Munro, Ian <span dir="ltr">
<<a href="mailto:i.munro@imperial.ac.uk" target="_blank">i.munro@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Curtis<br>
<br>
I’d really appreciate any assistance.<br>
<br>
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.<br>
I don’t, however, have a good understanding of the bf structure but the following ‘incantation' seemed to work.<br>
<br>
Edit code e.g. SDTReader.java<br>
<br>
On the ‘Projects’ Window<br>
<br>
Build Bio-Formats library<br>
Build Bio-Formats code generator<br>
Build bioformats-package bundle.<br>
<br>
This generated a bioformats_package 5.0.2 SNAPSHOT which I could then use.<br>
<br>
About 2 weeks ago I started getting the following errors in Step 1 ,the library build.<br>
I’m using open microscopy dev_5_0<br>
<br>
Regards<br>
<br>
ian<br>
<br>
------------------------------------------------------------------------<br>
BUILD FAILURE<br>
------------------------------------------------------------------------<br>
Total time: 8.411s<br>
Finished at: Tue May 13 15:46:08 BST 2014<br>
Final Memory: 17M/310M<br>
------------------------------------------------------------------------<br>
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<br>
org.testng.TestNGException:<br>
Cannot instantiate class loci.formats.utests.xml.Upgrade200909Test<br>
at org.testng.internal.ObjectFactoryImpl.newInstance(ObjectFactoryImpl.java:35)<br>
at org.testng.internal.ClassHelper.createInstance(ClassHelper.java:317)<br>
at org.testng.internal.ClassImpl.getDefaultInstance(ClassImpl.java:71)<br>
at org.testng.internal.ClassImpl.getInstances(ClassImpl.java:90)<br>
at org.testng.internal.TestNGClassFinder.<init>(TestNGClassFinder.java:119)<br>
at org.testng.TestRunner.initMethods(TestRunner.java:379)<br>
at org.testng.TestRunner.init(TestRunner.java:254)<br>
at org.testng.TestRunner.init(TestRunner.java:224)<br>
at org.testng.TestRunner.<init>(TestRunner.java:173)<br>
at org.testng.SuiteRunner$DefaultTestRunnerFactory.newTestRunner(SuiteRunner.java:494)<br>
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:239)<br>
at org.testng.SuiteRunner.run(SuiteRunner.java:193)<br>
at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:910)<br>
at org.testng.TestNG.runSuitesLocally(TestNG.java:879)<br>
at org.testng.TestNG.run(TestNG.java:787)<br>
at org.apache.maven.surefire.testng.TestNGExecutor.run(TestNGExecutor.java:217)<br>
at org.apache.maven.surefire.testng.TestNGXmlTestSuite.execute(TestNGXmlTestSuite.java:84)<br>
at org.apache.maven.surefire.testng.TestNGProvider.invoke(TestNGProvider.java:92)<br>
at org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:200)<br>
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:153)<br>
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:103)<br>
Caused by: java.lang.reflect.InvocationTargetException<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)<br>
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)<br>
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)<br>
at org.testng.internal.ObjectFactoryImpl.newInstance(ObjectFactoryImpl.java:26)<br>
... 20 more<br>
Caused by: java.lang.Error: Unresolved compilation problems:<br>
The import ome.xml.model.Channel cannot be resolved<br>
The import ome.xml.model.Image cannot be resolved<br>
The import ome.xml.model.OME cannot be resolved<br>
The import ome.xml.model.Pixels cannot be resolved<br>
The import ome.xml.model.enums.AcquisitionMode cannot be resolved<br>
OME cannot be resolved to a type<br>
OME cannot be resolved to a type<br>
OME cannot be resolved to a type<br>
The method getRoot() is undefined for the type OMEXMLMetadata<br>
OME cannot be resolved to a type<br>
Image cannot be resolved to a type<br>
OME cannot be resolved to a type<br>
Pixels cannot be resolved to a type<br>
Channel cannot be resolved to a type<br>
AcquisitionMode cannot be resolved to a variable<br>
<br>
at loci.formats.utests.xml.Upgrade200909Test.<init>(Upgrade200909Test.java:38)<br>
... 25 more<br>
-> [Help 1]<br>
<br>
To see the full stack trace of the errors, re-run Maven with the -e switch.<br>
Re-run Maven using the -X switch to enable full debug logging.<br>
<br>
For more information about the errors and possible solutions, please read the following articles:<br>
[Help 1] <a href="http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException" target="_blank">
http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div></div></div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote></div><br></div>