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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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build failed and test failed #214

Closed Shingzzz closed 1 year ago

Shingzzz commented 1 year ago

Subject of the issue

hello , I try to build and test some kits , but there are few failed .

The first kind : blastmapannots , mapuniprot , uniprotfilterjs

[ant:java] [ERROR] The markup in the document preceding the root element must be well-formed.
[ant:java]   line 1 of https://www.uniprot.org/docs/uniprot.xsd
[ant:java] 
[ant:java] Failed to parse a schema.

> Task :blastmapannots FAILED
compiling xjc :uniprot
:blastmapannots (Thread[Execution worker for ':',5,main]) completed. Took 5.99 secs.

FAILURE: Build failed with an exception.

* Where:
Build file '/root/zqc/jvarkit/build.gradle' line: 343

* What went wrong:
Execution failed for blastmapannots com.github.lindenb.jvarkit.tools.blastmapannots.BlastMapAnnotations.
> Java returned: 255

The second kind : evs2vcf , evsdumpxml

[ant:java] parsing a schema...
[ant:java] [ERROR] White spaces are required between publicId and systemId.
[ant:java]   line 1 of http://evs.gs.washington.edu/wsEVS/EVSDataQueryService?wsdl
[ant:java] 
[ant:java] Failed to parse a schema.

> Task :evs2vcf FAILED
Starting process 'command 'git''. Working directory: /root/zqc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for evs2vcf com.github.lindenb.jvarkit.tools.evs2bed.EvsToVcf because:
  Build cache is disabled
Evs2vcf com.github.lindenb.jvarkit.tools.evs2bed.EvsToVcf is not up-to-date because:
  Task has not declared any outputs despite executing actions.
compiling xjc :evs
:evs2vcf (Thread[Execution worker for ':',5,main]) completed. Took 1.362 secs.

FAILURE: Build failed with an exception.

* Where:
Build file '/root/zqc/jvarkit/build.gradle' line: 359

* What went wrong:
Execution failed for evs2vcf com.github.lindenb.jvarkit.tools.evs2bed.EvsToVcf.
> Java returned: 255

The third kind : vcfoptimizeped4skat , uniprot2svg

[ant:javac] /root/zqc/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/skat/VcfOptimizePedForSkat.java:257: error: cannot find symbol
[ant:javac]             final VcfBurdenFisherH.CtxWriterFactory fisherhFactory = new VcfBurdenFisherH.CtxWriterFactory();
[ant:javac]                                   ^
[ant:javac]   symbol:   class CtxWriterFactory
[ant:javac]   location: class VcfBurdenFisherH
[ant:javac] /root/zqc/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/skat/VcfOptimizePedForSkat.java:257: error: cannot find symbol
[ant:javac]             final VcfBurdenFisherH.CtxWriterFactory fisherhFactory = new VcfBurdenFisherH.CtxWriterFactory();
[ant:javac]                                                                                          ^
[ant:javac]   symbol:   class CtxWriterFactory
[ant:javac]   location: class VcfBurdenFisherH
[ant:javac] /root/zqc/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/skat/VcfOptimizePedForSkat.java:260: error: cannot find symbol
[ant:javac]             final VcfBurdenMAF.CtxWriterFactory mafFactory = new VcfBurdenMAF.CtxWriterFactory();
[ant:javac]                               ^
[ant:javac]   symbol:   class CtxWriterFactory
[ant:javac]   location: class VcfBurdenMAF
[ant:javac] /root/zqc/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/skat/VcfOptimizePedForSkat.java:260: error: cannot find symbol
[ant:javac]             final VcfBurdenMAF.CtxWriterFactory mafFactory = new VcfBurdenMAF.CtxWriterFactory();
[ant:javac]                                                                              ^
[ant:javac]   symbol:   class CtxWriterFactory
[ant:javac]   location: class VcfBurdenMAF
[ant:javac] 4 errors

> Task :vcfoptimizeped4skat FAILED
Starting process 'command 'git''. Working directory: /root/zqc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for vcfoptimizeped4skat com.github.lindenb.jvarkit.tools.skat.VcfOptimizePedForSkat because:
  Build cache is disabled
Vcfoptimizeped4skat com.github.lindenb.jvarkit.tools.skat.VcfOptimizePedForSkat is not up-to-date because:
  Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/zqc/jvarkit/tmp/META-INF
[ant:mkdir] Created dir: /root/zqc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/skat
Starting process 'command 'which''. Working directory: /root/zqc/jvarkit Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/zqc/jvarkit Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/zqc/jvarkit Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 1 source file to /root/zqc/jvarkit/tmp
:vcfoptimizeped4skat (Thread[Execution worker for ':',5,main]) completed. Took 1.876 secs.

FAILURE: Build failed with an exception.

* Where:
Build file '/root/zqc/jvarkit/build.gradle' line: 680

* What went wrong:
Execution failed for vcfoptimizeped4skat com.github.lindenb.jvarkit.tools.skat.VcfOptimizePedForSkat.
> Compile failed; see the compiler error output for details.
[ant:javac] /root/zqc/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/uniprot/UniprotToSvg.java:69: error: cannot find symbo
[ant:javac] import com.github.lindenb.jvarkit.util.LabelledUrlSupplier;
[ant:javac]                                       ^
[ant:javac]   symbol:   class LabelledUrlSupplier
[ant:javac]   location: package com.github.lindenb.jvarkit.util
[ant:javac] /root/zqc/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/uniprot/UniprotToSvg.java:70: error: package com.github.lindenb.jvarkit.util.LabelledUrlSupplier does not exist
[ant:javac] import com.github.lindenb.jvarkit.util.LabelledUrlSupplier.LabelledUrl;
[ant:javac]                                                           ^

> Task :uniprot2svg
Starting process 'command 'git''. Working directory: /root/zqc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for uniprot2svg com.github.lindenb.jvarkit.tools.uniprot.UniprotToSvg because:
  Build cache is disabled
Uniprot2svg com.github.lindenb.jvarkit.tools.uniprot.UniprotToSvg is not up-to-date because:
  Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/zqc/jvarkit/tmp/META-INF
[ant:mkdir] Created dir: /root/zqc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/uniprot
Starting process 'command 'which''. Working directory: /root/zqc/jvarkit Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/zqc/jvarkit Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/zqc/jvarkit Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 1 source file to /root/zqc/jvarkit/tmp

[ant:javac] 2 errors

> Task :uniprot2svg FAILED
:uniprot2svg (Thread[Execution worker for ':',5,main]) completed. Took 2.086 secs.

FAILURE: Build failed with an exception.

* Where:
Build file '/root/zqc/jvarkit/build.gradle' line: 680

* What went wrong:
Execution failed for uniprot2svg com.github.lindenb.jvarkit.tools.uniprot.UniprotToSvg.
> Compile failed; see the compiler error output for details.

The fourth kind : vcfcomparegt , vcfsetdict , vcfensemblvep

[ant:java] Method public void com.github.lindenb.jvarkit.tools.vcfcmp.VCFCompareGTTest.test01(java.lang.String) throws java.lang.Exception requires a @DataProvider named : all-vcf-files
[ant:java]      at org.testng.internal.Parameters.findDataProvider(Parameters.java:513)
[ant:java]      at org.testng.internal.Parameters.handleParameters(Parameters.java:691)
[ant:java]      at org.testng.internal.ParameterHandler.handleParameters(ParameterHandler.java:49)
[ant:java]      at org.testng.internal.ParameterHandler.createParameters(ParameterHandler.java:37)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:924)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
[ant:java] Method public void com.github.lindenb.jvarkit.tools.ensembl.VcfEnsemblVepRestTest.test02(java.lang.String,int,java.lang.String) throws java.io.IOException requires a @DataProvider named : genomic-segments
[ant:java]      at org.testng.internal.Parameters.findDataProvider(Parameters.java:513)
[ant:java]      at org.testng.internal.Parameters.handleParameters(Parameters.java:691)
[ant:java]      at org.testng.internal.ParameterHandler.handleParameters(ParameterHandler.java:49)
[ant:java]      at org.testng.internal.ParameterHandler.createParameters(ParameterHandler.java:37)
[ant:java]      at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:924)
[ant:java]      at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:125)
[ant:java]      at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:109)
[ant:java]      at org.testng.TestRunner.privateRun(TestRunner.java:648)
[ant:java]      at org.testng.TestRunner.run(TestRunner.java:505)
[ant:java]      at org.testng.SuiteRunner.runTest(SuiteRunner.java:455)
[ant:java]      at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:450)
[ant:java]      at org.testng.SuiteRunner.privateRun(SuiteRunner.java:415)
[ant:java]      at org.testng.SuiteRunner.run(SuiteRunner.java:364)
[ant:java]      at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
[ant:java]      at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:84)
[ant:java]      at org.testng.TestNG.runSuitesSequentially(TestNG.java:1208)
[ant:java]      at org.testng.TestNG.runSuitesLocally(TestNG.java:1137)
[ant:java]      at org.testng.TestNG.runSuites(TestNG.java:1049)
[ant:java]      at org.testng.TestNG.run(TestNG.java:1017)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
[ant:java]      at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)

The final kind : prettysam

org.testng.internal.reflect.MethodMatcherException: 
Data provider mismatch
Method: test01([Parameter{index=0, type=java.lang.String, declaredAnnotations=[]}, Parameter{index=1, type=java.lang.String, declaredAnnotations=[]}])
Arguments: [(java.lang.String) ./src/test/resources/FAB23716.nanopore.bam]
    at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
    at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
... Removed 17 stack frames

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