第1类错误：AssertionError

错误包：pubmedcodinglang、biostar95652、nozerovariationvcf、pubmeddump、vcfcadd、gtf2xml、pubmedgender、pubmedmap、vcfgnomad、vcf2svg、lowresbam2raster、vcfucsc、bednonoverlappingset、ncbigenedump、vcfstrechofgt、
vcfwindowsplitter

1、pubmedcodinglang

输入以下命令，构建pubmedcodinglang包：

./gradlew pubmedcodinglang --info

输出结果：

Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
The client will now receive all logging from the daemon (pid: 23957). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-23957.out.log
Starting 5th build in daemon [uptime: 1 hrs 48 mins 57.721 secs, performance: 100%, non-heap usage: 18% of 256 MiB]
Using 2 worker leases.
Watching the file system is configured to be enabled if available
File system watching is inactive
Starting Build
Settings evaluated using settings file '/root/hpc/jvarkit/settings.gradle'.
Projects loaded. Root project using build file '/root/hpc/jvarkit/build.gradle'.
Included projects: [root project 'jvarkit']> Configure project :
Evaluating root project 'jvarkit' using build file '/root/hpc/jvarkit/build.gradle'.
All projects evaluated.
Selected primary task 'pubmedcodinglang' from project :
Tasks to be executed: [pubmedcodinglang com.github.lindenb.jvarkit.tools.pubmed.PubmedCodingLanguages]
Tasks that were excluded: []
:pubmedcodinglang (Thread[included builds,5,main]) started.
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8> Task :pubmedcodinglang
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for pubmedcodinglang com.github.lindenb.jvarkit.tools.pubmed.PubmedCodingLanguages because:Build cache is disabled
Pubmedcodinglang com.github.lindenb.jvarkit.tools.pubmed.PubmedCodingLanguages is not up-to-date because:Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/pubmed
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 1 source file to /root/hpc/jvarkit/tmp[ant:javac] 1 warning> Task :pubmedcodinglang
[ant:copy] Copying 1 file to /root/hpc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/pubmed
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF/chromnames
[ant:copy] Copying 1 file to /root/hpc/jvarkit/tmp/META-INF/chromnames
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/tukaani/xz/1.8/xz-1.8.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar into /root/hpc/jvarkit/tmp
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
[ant:jar] Building jar: /root/hpc/jvarkit/dist/pubmedcodinglang.jar
[ant:delete] Deleting directory /root/hpc/jvarkit/tmp
jar file generated :/root/hpc/jvarkit/dist/pubmedcodinglang.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp
Test will be executed in /root/hpc/jvarkit/tests-output/pubmedcodinglang/index.html
[ant:javac] Compiling 2 source files to /root/hpc/jvarkit/tmp[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] 1 warning
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.pubmed.PubmedCodingLanguagesTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.jcommander.LauncherTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.io.IOUtilsTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.LineIteratorsTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.StringUtilsTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.AbstractCharSequenceTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.DelegateCharSequenceTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.vcf.VCFUtilsTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.CharSplitterTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.SequenceDictionaryUtilsTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.fasta.ContigNameConverterTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.util.IntervalParserFactoryTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.util.SimpleIntervalTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.vcf.AFExtractorFactoryTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.vcftrios.DeNovoDetectorTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.CounterTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.bed.BedLineCodecTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.log.ProgressFactoryTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.samtools.ContigDictComparatorTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.SmartComparatorTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.EqualRangeIteratorTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.FilterIteratorTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.MergingIteratorTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.samfilter.SamRecordFilterFactoryTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.reference.TwoBitSequenceFileTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.math.DiscreteMedianTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.primitive.IntArrayTest
[ant:java] Nov 10, 2022 4:33:03 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.primitive.DoubleArrayTest
[ant:java] [WARN][NcbiApiKey]NCBI property file "/root/.ncbi.properties" not found.
[ant:java] [WARN][NcbiApiKey]
[ant:java] *****
[ant:java] *
[ant:java] * NCBI api_key is undefined. see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/.
[ant:java] * 1) can find it in environment variable  `export NCBI_API_KEY=xxxxxxxxx`
[ant:java] * 2) can find it in jvm property java -Dncbi.api.key=xxxxxxxxx ....
[ant:java] * 3) can find it in java property file ( https://en.wikipedia.org/wiki/.properties ) /root/.ncbi.properties with property api_key=xxxxxxxxx
[ant:java] *
[ant:java] *****
[ant:java] [SEVERE][PubmedDump]NCBI API key is not defined
[ant:java] [TEST] end TestSupport
[ant:java] [WARN][NcbiApiKey]NCBI property file "/root/.ncbi.properties" not found.
[ant:java] [WARN][NcbiApiKey]
[ant:java] *****
[ant:java] *
[ant:java] * NCBI api_key is undefined. see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/.
[ant:java] * 1) can find it in environment variable  `export NCBI_API_KEY=xxxxxxxxx`
[ant:java] * 2) can find it in jvm property java -Dncbi.api.key=xxxxxxxxx ....
[ant:java] * 3) can find it in java property file ( https://en.wikipedia.org/wiki/.properties ) /root/.ncbi.properties with property api_key=xxxxxxxxx
[ant:java] *
[ant:java] *****
[ant:java] [SEVERE][PubmedDump]NCBI API key is not defined
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [WARN][AFExtractorFactory]VCF header doesn't contain the INFO field x_AC
[ant:java] [WARN][AFExtractorFactory]VCF header doesn't contain the INFO field x_AC
[ant:java] [INFO][ProgressFactory]. Completed. N=45. That took:2 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=45. That took:1 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=11. That took:5 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=477. That took:6 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:20 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:8 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:10 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:9 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:10 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=12. That took:1 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=12. That took:1 millisecs
[ant:java]
[ant:java] ===============================================
[ant:java] Command line suite
[ant:java] Total tests run: 100, Failures: 2, Skips: 0
[ant:java] ===============================================
[ant:java] > Task :pubmedcodinglang
[ant:java] Java Result: 255
[ant:delete] Deleting directory /root/hpc/jvarkit/tmp
:pubmedcodinglang (Thread[included builds,5,main]) completed. Took 8.821 secs.BUILD SUCCESSFUL in 9s
1 actionable task: 1 executed

从输出结果可以得知，包构建成功，但是100个方法内，有2个测试失败（原为4个，因为有2个url是维基百科，所以有两个连接超时的错误，修改url后解决）。
定位到具体输出页面：

定位到具体代码位置：

protected Path dumpAsXml(final String query ) throws IOException {final Path out = support.createTmpPath(".xml");Assert.assertEquals(new PubmedDump().instanceMain(new String[] {"-o",out.toString(),query}),0);support.assertIsXml(out);return out;}

从代码可得，先创建一个out路径，然后调用Assert.assertEquals将一个PubmedDump()内instanceMain()方法的返回值与0进行比较，由于比较结果不等，所以产生报错。
查看instanceMain()函数：

public int instanceMain(final String args[]) {int ret=RETURN_OK;try {final Status status = parseArgs(args);switch(status){case EXIT_FAILURE: return -1;case EXIT_SUCCESS: return 0;case PRINT_HELP: this.usageBuilder.usage(getJCommander()); return 0;case PRINT_VERSION: System.out.println(getVersion());return 0;case RUN_TESTS: return this.runInternalTests();case OK:break;}try {ret = initialize();if(ret!=RETURN_OK) return ret;}catch(final Throwable err){LOG.severe(err.getMessage());return -1;}try {ret=doWork(getFilenames());if(ret!=RETURN_OK) return ret;}catch(final Throwable err){LOG.severe(err.getMessage());return -1;}}finally{cleanup();}return 0;}

从代码可得知，就是在这个函数里面返回的非0值。
查看parseArgs()函数：

protected Status parseArgs(final String args[]){this.argcargv = Arrays.asList(args);try{getJCommander().parse(args);}catch(final com.beust.jcommander.ParameterException err) {stderr().print("There was an error in the input parameters: ");stderr().println(err.getMessage());return Status.EXIT_FAILURE;}if (this.usageBuilder.shouldPrintUsage()) return Status.PRINT_HELP;if (this.usageBuilder.shouldRunTests()) return Status.RUN_TESTS;if (this.usageBuilder.print_version) return Status.PRINT_VERSION;return Status.OK;}

这里的getJCommander()实际上是返回了一个jcommander对象，所以实际调用的是JCommander.parse()，jcommander.parse()的作用是分析并验证命令行参数，根据后面的catch也可以得知，输入了错误的参数。
回到倒第二层报错：

可知，这个test01()向底层传递了一个String类型的值"Python Bioinformatics 2017 Java"，super.dumpAsXml()接受参数，创建一个out路径，out=“tmp.xml”,所以此时的两个个参数：query=“Python Bioinformatics 2017 Java”、out=“tmp.xml”。将"-o"，out，query做为参数传给instanceMain()，最后则是传入了JCommander.parse，所以是这里的传入参数有错，才会导致报错。

就这个问题，我们联系了开发者，开发者也给出了回复，是因为他更换了工具，但是没有更新测试代码。

2、biostar95652

输入以下命令，构建biostar95652包：

./grawdlew biostar95652 --info

输出结果：

[root@VM-4-5-centos jvarkit]$ ./gradlew biostar95652 --info
Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
The client will now receive all logging from the daemon (pid: 30955). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-30955.out.log
Starting 3rd build in daemon [uptime: 2 hrs 15 mins 10.706 secs, performance: 99%, non-heap usage: 17% of 256 MiB]
Using 2 worker leases.
Watching the file system is configured to be enabled if available
File system watching is inactive
Starting Build
Settings evaluated using settings file '/root/hpc/jvarkit/settings.gradle'.
Projects loaded. Root project using build file '/root/hpc/jvarkit/build.gradle'.
Included projects: [root project 'jvarkit']> Configure project :
Evaluating root project 'jvarkit' using build file '/root/hpc/jvarkit/build.gradle'.
All projects evaluated.
Selected primary task 'biostar95652' from project :
Tasks to be executed: [biostar95652 com.github.lindenb.jvarkit.tools.biostar.Biostar95652]
Tasks that were excluded: []
:biostar95652 (Thread[included builds,5,main]) started.
[ant:java] parsing a schema...> Task :biostar95652
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for biostar95652 com.github.lindenb.jvarkit.tools.biostar.Biostar95652 because:Build cache is disabled
Biostar95652 com.github.lindenb.jvarkit.tools.biostar.Biostar95652 is not up-to-date because:Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF
compiling xjc :gb[ant:java] compiling a schema...
[ant:java] gov/nih/nlm/ncbi/gb/GBAltSeqData.java
[ant:java] gov/nih/nlm/ncbi/gb/GBAltSeqDataItems.java
[ant:java] gov/nih/nlm/ncbi/gb/GBAltSeqItem.java
[ant:java] gov/nih/nlm/ncbi/gb/GBAltSeqItemInterval.java
[ant:java] gov/nih/nlm/ncbi/gb/GBAltSeqItemIsgap.java
[ant:java] gov/nih/nlm/ncbi/gb/GBAuthor.java
[ant:java] gov/nih/nlm/ncbi/gb/GBComment.java
[ant:java] gov/nih/nlm/ncbi/gb/GBCommentParagraph.java
[ant:java] gov/nih/nlm/ncbi/gb/GBCommentParagraphs.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeature.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeatureIntervals.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeaturePartial3.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeaturePartial5.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeatureQuals.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeatureSet.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeatureSetFeatures.java
[ant:java] gov/nih/nlm/ncbi/gb/GBFeatureXrefs.java
[ant:java] gov/nih/nlm/ncbi/gb/GBInterval.java
[ant:java] gov/nih/nlm/ncbi/gb/GBIntervalInterbp.java
[ant:java] gov/nih/nlm/ncbi/gb/GBIntervalIscomp.java
[ant:java] gov/nih/nlm/ncbi/gb/GBKeyword.java
[ant:java] gov/nih/nlm/ncbi/gb/GBQualifier.java
[ant:java] gov/nih/nlm/ncbi/gb/GBReference.java
[ant:java] gov/nih/nlm/ncbi/gb/GBReferenceAuthors.java
[ant:java] gov/nih/nlm/ncbi/gb/GBReferenceXref.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSecondaryAccn.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeq.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqAltSeq.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqCommentSet.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqFeatureSet.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqFeatureTable.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqKeywords.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqOtherSeqids.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqReferences.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqSecondaryAccessions.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqStrucComments.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqXrefs.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSeqid.java
[ant:java] gov/nih/nlm/ncbi/gb/GBSet.java
[ant:java] gov/nih/nlm/ncbi/gb/GBStrucComment.java
[ant:java] gov/nih/nlm/ncbi/gb/GBStrucCommentItem.java
[ant:java] gov/nih/nlm/ncbi/gb/GBStrucCommentItems.java
[ant:java] gov/nih/nlm/ncbi/gb/GBXref.java
[ant:java] gov/nih/nlm/ncbi/gb/ObjectFactory.java
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-api.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-api-2.2.12-b140109.1041.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/txw2-2.2.11.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/istack-commons-runtime-2.21.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-api-2.4.0-b180830.0359.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/txw2-2.4.0-b180830.0438.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/istack-commons-runtime-3.0.7.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/stax-ex-1.8.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/FastInfoset-1.2.15.jar": no such file or directory
[ant:javac] warning: [path] bad path element "/root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/javax.activation-api-1.2.0.jar": no such file or directory
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8> Task :biostar95652
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/biostar
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 2 source files to /root/hpc/jvarkit/tmp[ant:javac] 11 warnings> Task :biostar95652
[ant:copy] Copying 1 file to /root/hpc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/biostar
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF/chromnames
[ant:copy] Copying 1 file to /root/hpc/jvarkit/tmp/META-INF/chromnames
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/tukaani/xz/1.8/xz-1.8.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/javax/xml/bind/jaxb-api/2.2.11/jaxb-api-2.2.11.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-core-2.2.11.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-core-2.2.11.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/glassfish/jaxb/txw2/2.2.11/txw2-2.2.11.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-runtime-2.4.0-b180830.0438.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar into /root/hpc/jvarkit/tm
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
[ant:jar] Building jar: /root/hpc/jvarkit/dist/biostar95652.jar
[ant:delete] Deleting directory /root/hpc/jvarkit/tmp
jar file generated :/root/hpc/jvarkit/dist/biostar95652.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp
Test will be executed in /root/hpc/jvarkit/tests-output/biostar95652/index.html
[ant:javac] Compiling 2 source files to /root/hpc/jvarkit/tmp[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] 1 warning> Task :biostar95652
[ant:mkdir] Created dir: /root/hpc/jvarkit/tests-output/biostar95652[ant:java] Nov 11, 2022 7:27:52 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.biostar.Biostar95652Test
[ant:java] [WARN][NcbiApiKey]NCBI property file "/root/.ncbi.properties" not found.
[ant:java] [WARN][NcbiApiKey]
[ant:java] *****
[ant:java] *
[ant:java] * NCBI api_key is undefined. see https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/.
[ant:java] * 1) can find it in environment variable  `export NCBI_API_KEY=xxxxxxxxx`
[ant:java] * 2) can find it in jvm property java -Dncbi.api.key=xxxxxxxxx ....
[ant:java] * 3) can find it in java property file ( https://en.wikipedia.org/wiki/.properties ) /root/.ncbi.properties with property api_key=xxxxxxxxx
[ant:java] *
[ant:java] *****
[ant:java] [SEVERE][Biostar95652]NCBI API key is not defined
[ant:java] [TEST] end TestSupport
[ant:java]
[ant:java] ===============================================
[ant:java] Command line suite
[ant:java] Total tests run: 1, Failures: 1, Skips: 0
[ant:java] ===============================================
[ant:java] > Task :biostar95652
[ant:java] Java Result: 255
[ant:delete] Deleting directory /root/hpc/jvarkit/tmp#
#
# written for biostar. never used.
#
#:biostar95652 (Thread[included builds,5,main]) completed. Took 10.976 secs.BUILD SUCCESSFUL in 11s
1 actionable task: 1 executed

定位到具体错误位置：

具体代码位置：

发现还是instanceMain()函数有问题。

3、nozerovariationvcf



同意是instanceMain()

4、pubmeddump

5、vcfcadd



14个方法，都是调用instanceMain()

6、gtf2xml


7、pubmedgender


8、pubmedmap


9、vcfgnomad


10、vcf2svg


11、lowresbam2raster


12、bednonoverlappingset


13、ncbigenedump


14、vcfstrechofgt


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