Missing dependency error
Closed this issue · 5 comments
With newer java (11) versions we get:
LuciphorAdapter_1_input.mzML: Exception in thread "main" java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at umich.ms.fileio.filetypes.mzml.MZMLFile.parseRunInfo(MZMLFile.java:91)
at umich.ms.fileio.filetypes.AbstractLCMSDataSource.fetchRunInfo(AbstractLCMSDataSource.java:74)
at umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource.parseScan(AbstractXMLBasedDataSource.java:640)
at lucxor.globals.read_mzML(globals.java:676)
at lucxor.globals.read_in_spectra(globals.java:646)
at lucxor.LucXor.main(LucXor.java:71)
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:583)
at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:521)
... 6 more
Maybe the Proper long-term solution: (JDK 9 and beyond)
mentioned here https://icetutor.com/question/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-java-9/
is the way to go:
Could you try the mavenized branch of luciphor?
@chhh recently updated the source code to work with Maven.
Download the mavenized branch of luciphor and the build the jar with mvn clean package
.
The working jar should be in targets called lucxor-2.1-SNAPSHOT.one-jar.jar
Thanks for the reply @dfermin . Building and running worked with the mavenized branch.
Q for the conda packaging: do you plan to have releases here on github in the future? Then I could adapat the conda recipe accordingly.
@bernt-matthias @chhh I have a fork with GitHub Actions https://github.com/ypriverol/lucXor and I'm planning to do releases and bug fixing. We can coordinate the efforts to maintain the tool.
Maybe a PR would be an alternative?
I don't know if someone is interested in maintaining and Reviewing PRs? The changes I'm doing big changes in the code for performance and clean some empty functions, variables etc.