Fix tests
mvn test
fails because of missing files:
$ mvn test
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------< nl.wur.bif:pantools >-------------------------
[INFO] Building pantools 3.3.2
[INFO] --------------------------------[ jar ]---------------------------------
[INFO]
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ pantools ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/matthijm/projects/etec-big-pangenomics/pantools/src/main/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ pantools ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ pantools ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /Users/matthijm/projects/etec-big-pangenomics/pantools/src/test/resources
[INFO]
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ pantools ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 5 source files to /Users/matthijm/projects/etec-big-pangenomics/pantools/target/test-classes
[INFO]
[INFO] --- maven-surefire-plugin:3.0.0-M5:test (default-test) @ pantools ---
[INFO]
[INFO] -------------------------------------------------------
[INFO] T E S T S
[INFO] -------------------------------------------------------
[INFO] Running nl.wur.bif.pantools.pangenome.GenomeLayerTest
Testing build:
Constructing the pangenome graph database
Failed to read: /Users/matthijm/pantools/example/sample_genomes_path.txt
[INFO]
[INFO] Results:
[INFO]
[INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 7.603 s
[INFO] Finished at: 2021-12-23T11:54:49+01:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:3.0.0-M5:test (default-test) on project pantools: There are test failures.
[ERROR]
[ERROR] Please refer to /Users/matthijm/projects/etec-big-pangenomics/pantools/target/surefire-reports for the individual test results.
[ERROR] Please refer to dump files (if any exist) [date].dump, [date]-jvmRun[N].dump and [date].dumpstream.
[ERROR] The forked VM terminated without properly saying goodbye. VM crash or System.exit called?
[ERROR] Command was /bin/sh -c cd /Users/matthijm/projects/etec-big-pangenomics/pantools && /Users/matthijm/.sdkman/candidates/java/8.0.312-zulu/zulu-8.jdk/Contents/Home/jre/bin/java -jar /Users/matthijm/projects/etec-big-pangenomics/pantools/target/surefire/surefirebooter3365883543667371053.jar /Users/matthijm/projects/etec-big-pangenomics/pantools/target/surefire 2021-12-23T11-54-47_412-jvmRun1 surefire9047863971112943684tmp surefire_07805636002181539321tmp
[ERROR] Error occurred in starting fork, check output in log
[ERROR] Process Exit Code: 1
[ERROR] Crashed tests:
[ERROR] nl.wur.bif.pantools.pangenome.GenomeLayerTest
[ERROR] org.apache.maven.surefire.booter.SurefireBooterForkException: The forked VM terminated without properly saying goodbye. VM crash or System.exit called?
[ERROR] Command was /bin/sh -c cd /Users/matthijm/projects/etec-big-pangenomics/pantools && /Users/matthijm/.sdkman/candidates/java/8.0.312-zulu/zulu-8.jdk/Contents/Home/jre/bin/java -jar /Users/matthijm/projects/etec-big-pangenomics/pantools/target/surefire/surefirebooter3365883543667371053.jar /Users/matthijm/projects/etec-big-pangenomics/pantools/target/surefire 2021-12-23T11-54-47_412-jvmRun1 surefire9047863971112943684tmp surefire_07805636002181539321tmp
[ERROR] Error occurred in starting fork, check output in log
[ERROR] Process Exit Code: 1
[ERROR] Crashed tests:
[ERROR] nl.wur.bif.pantools.pangenome.GenomeLayerTest
[ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:748)
[ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:305)
[ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.run(ForkStarter.java:265)
[ERROR] at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeProvider(AbstractSurefireMojo.java:1314)
[ERROR] at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:1159)
[ERROR] at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:932)
[ERROR] at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:137)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:210)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:156)
[ERROR] at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:148)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:117)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:81)
[ERROR] at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:56)
[ERROR] at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
[ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:305)
[ERROR] at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:192)
[ERROR] at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:105)
[ERROR] at org.apache.maven.cli.MavenCli.execute(MavenCli.java:972)
[ERROR] at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:293)
[ERROR] at org.apache.maven.cli.MavenCli.main(MavenCli.java:196)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
[ERROR] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
[ERROR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
[ERROR] at java.lang.reflect.Method.invoke(Method.java:498)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:282)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:225)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:406)
[ERROR] at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:347)
[ERROR]
[ERROR] -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException