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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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build failed，are these packages core packages or important packages and will they affect other toolkits? #220

Closed Shingzzz closed 1 year ago

Shingzzz commented 1 year ago

there are four toolkits : vcfoptimizeped4skat 、evs2vcf 、evs2xml 、gephicmd

I sincerely ask you these questions . Please reply me . Are these packages core packages or important packages and will they affect other toolkits? Thank you very much.

gephicmd

Especially gephicmd，I use ./gradlew gephicmd --info to build it . The result is that:

Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
Removing 0 daemon stop events from registry
Starting a Gradle Daemon (subsequent builds will be faster)
Starting process 'Gradle build daemon'. Working directory: /root/.gradle/daemon/7.4.2 Command: /usr/lib/jvm/java-11-openjdk-11.0.17.0.8-2.el7_9.x86_64/bin/java --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.base/java.nio.charset=ALL-UNNAMED --add-opens java.base/java.net=ALL-UNNAMED --add-opens java.base/java.util.concurrent.atomic=ALL-UNNAMED -XX:MaxMetaspaceSize=256m -XX:+HeapDumpOnOutOfMemoryError -Xms256m -Xmx512m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /root/.gradle/wrapper/dists/gradle-7.4.2-bin/48ivgl02cpt2ed3fh9dbalvx8/gradle-7.4.2/lib/gradle-launcher-7.4.2.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 7.4.2
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 2.497 secs.
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 build in new daemon [memory: 512 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.

FAILURE: Build failed with an exception.

* What went wrong:
Task 'gephicmd' not found in root project 'jvarkit'.

* Try:
> Run gradlew tasks to get a list of available tasks.
> Run with --stacktrace option to get the stack trace.
> Run with --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 8s

vcfoptimizeped4skat

The result is that :

Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
Removing 0 daemon stop events from registry
Starting a Gradle Daemon (subsequent builds will be faster)
Starting process 'Gradle build daemon'. Working directory: /root/.gradle/daemon/7.4.2 Command: /usr/lib/jvm/java-11-openjdk-11.0.17.0.8-2.el7_9.x86_64/bin/java --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.invoke=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.prefs/java.util.prefs=ALL-UNNAMED --add-opens java.base/java.nio.charset=ALL-UNNAMED --add-opens java.base/java.net=ALL-UNNAMED --add-opens java.base/java.util.concurrent.atomic=ALL-UNNAMED -XX:MaxMetaspaceSize=256m -XX:+HeapDumpOnOutOfMemoryError -Xms256m -Xmx512m -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /root/.gradle/wrapper/dists/gradle-7.4.2-bin/48ivgl02cpt2ed3fh9dbalvx8/gradle-7.4.2/lib/gradle-launcher-7.4.2.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 7.4.2
Successfully started process 'Gradle build daemon'
An attempt to start the daemon took 3.314 secs.
The client will now receive all logging from the daemon (pid: 4373). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-4373.out.log
Starting build in new daemon [memory: 512 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 'vcfoptimizeped4skat' from project :
Tasks to be executed: [vcfoptimizeped4skat com.github.lindenb.jvarkit.tools.skat.VcfOptimizePedForSkat]
Tasks that were excluded: []
:vcfoptimizeped4skat (Thread[included builds,5,main]) started.
[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

> Task :vcfoptimizeped4skat
Starting process 'command 'git''. Working directory: /root/hpc/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.
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] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] /root/hpc/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/hpc/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/hpc/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/hpc/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
[ant:javac] 2 warnings

> Task :vcfoptimizeped4skat FAILED
:vcfoptimizeped4skat (Thread[included builds,5,main]) completed. Took 4.893 secs.

FAILURE: Build failed with an exception.

* Where:
Build file '/root/hpc/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.

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 17s
1 actionable task: 1 executed
VCS Checkout Cache (/root/hpc/jvarkit/.gradle/vcs-1) removing files not accessed on or after Wed Nov 02 17:22:36 CST 2022.
VCS Checkout Cache (/root/hpc/jvarkit/.gradle/vcs-1) cleanup deleted 0 files/directories.
VCS Checkout Cache (/root/hpc/jvarkit/.gradle/vcs-1) cleaned up in 0.002 secs.
dependencies-accessors (/root/hpc/jvarkit/.gradle/7.4.2/dependencies-accessors) removing files not accessed on or after Wed Nov 02 17:22:38 CST 2022.
dependencies-accessors (/root/hpc/jvarkit/.gradle/7.4.2/dependencies-accessors) cleanup deleted 0 files/directories.
dependencies-accessors (/root/hpc/jvarkit/.gradle/7.4.2/dependencies-accessors) cleaned up in 0.0 secs.

evs2vcf 、evs2xml

The results are that :

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: 4373). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-4373.out.log
Starting 3rd build in daemon [uptime: 1 hrs 57 mins 51.19 secs, performance: 100%, non-heap usage: 20% of 256 MiB]
Using 2 worker leases.
Watching the file system is configured to be enabled if available
File system watching is inactive
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/checksums/md5-checksums.bin
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/checksums/sha1-checksums.bin
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/checksums/sha256-checksums.bin
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/checksums/sha512-checksums.bin
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/fileHashes/fileHashes.bin
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/fileHashes/resourceHashesCache.bin
Starting Build
Settings evaluated using settings file '/root/hpc/jvarkit/settings.gradle'.
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/dependencies-accessors/executionHistory.bin
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 'evs2vcf' from project :
Tasks to be executed: [evs2vcf com.github.lindenb.jvarkit.tools.evs2bed.EvsToVcf]
Tasks that were excluded: []
:evs2vcf (Thread[included builds,5,main]) started.
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/7.4.2/executionHistory/executionHistory.bin
Invalidating in-memory cache of /root/hpc/jvarkit/.gradle/buildOutputCleanup/outputFiles.bin
[ant:get] ....................................................
[ant:get] ....................................................
[ant:get] .............................
[ant:get] ....
[ant:get] .....
[ant:get] .................

> Task :evs2vcf
Starting process 'command 'git''. Working directory: /root/hpc/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.
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF
[ant:mkdir] Created dir: /root/hpc/jvarkit/dist
Downloading https://repo1.maven.org/maven2/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar to /root/hpc/jvarkit/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/github/samtools/htsjdk/3.0.0
[ant:get] Getting: https://repo1.maven.org/maven2/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar
Downloading https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar to /root/hpc/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/commons-logging/commons-logging/1.1.1
[ant:get] Getting: https://repo1.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
[ant:get] To: /root/hpc/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
Downloading https://repo1.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /root/hpc/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0
[ant:get] Getting: https://repo1.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[ant:get] To: /root/hpc/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
Downloading https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /root/hpc/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1
[ant:get] Getting: https://repo1.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
Downloading https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar to /root/hpc/jvarkit/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/apache/commons/commons-compress/1.19
[ant:get] Getting: https://repo1.maven.org/maven2/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar

[ant:get] ......................................
[ant:get] ........
[ant:get] .....
[ant:get] ....................................................
[ant:get] ....................................................
[ant:get] .................
[ant:get] .....
[ant:get] ....................................................
[ant:get] .
[ant:get] .......
[ant:get] ................
[ant:get] ..........
[ant:get] .....
[ant:get] ....................................................
[ant:get] ................
[ant:get] ....

> Task :evs2vcf
Downloading https://repo1.maven.org/maven2/org/tukaani/xz/1.8/xz-1.8.jar to /root/hpc/jvarkit/lib/org/tukaani/xz/1.8/xz-1.8.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/tukaani/xz/1.8
[ant:get] Getting: https://repo1.maven.org/maven2/org/tukaani/xz/1.8/xz-1.8.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/tukaani/xz/1.8/xz-1.8.jar
Downloading https://repo1.maven.org/maven2/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar to /root/hpc/jvarkit/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/sharegov/mjson/1.4.1
[ant:get] Getting: https://repo1.maven.org/maven2/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar
Downloading https://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar to /root/hpc/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4
[ant:get] Getting: https://repo1.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar
Downloading https://repo1.maven.org/maven2/com/beust/jcommander/1.72/jcommander-1.72.jar to /root/hpc/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/beust/jcommander/1.72
[ant:get] Getting: https://repo1.maven.org/maven2/com/beust/jcommander/1.72/jcommander-1.72.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar
Downloading https://repo1.maven.org/maven2/org/testng/testng/6.14.3/testng-6.14.3.jar to /root/hpc/jvarkit/lib/org/testng/testng/6.14.3/testng-6.14.3.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/testng/testng/6.14.3
[ant:get] Getting: https://repo1.maven.org/maven2/org/testng/testng/6.14.3/testng-6.14.3.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/testng/testng/6.14.3/testng-6.14.3.jar
Downloading https://repo1.maven.org/maven2/javax/xml/bind/jaxb-api/2.2.11/jaxb-api-2.2.11.jar to /root/hpc/jvarkit/lib/javax/xml/bind/jaxb-api/2.2.11/jaxb-api-2.2.11.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/javax/xml/bind/jaxb-api/2.2.11
[ant:get] Getting: https://repo1.maven.org/maven2/javax/xml/bind/jaxb-api/2.2.11/jaxb-api-2.2.11.jar
[ant:get] To: /root/hpc/jvarkit/lib/javax/xml/bind/jaxb-api/2.2.11/jaxb-api-2.2.11.jar
Downloading https://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-core-2.2.11.jar to /root/hpc/jvarkit/lib/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-core-2.2.11.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/sun/xml/bind/jaxb-core/2.2.11
[ant:get] Getting: https://repo1.maven.org/maven2/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-core-2.2.11.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/sun/xml/bind/jaxb-core/2.2.11/jaxb-core-2.2.11.jar
Downloading https://repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-core-2.2.11.jar to /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-core-2.2.11.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11
[ant:get] Getting: https://repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-core-2.2.11.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-core/2.2.11/jaxb-core-2.2.11.jar
Downloading https://repo1.maven.org/maven2/org/glassfish/jaxb/txw2/2.2.11/txw2-2.2.11.jar to /root/hpc/jvarkit/lib/org/glassfish/jaxb/txw2/2.2.11/txw2-2.2.11.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/glassfish/jaxb/txw2/2.2.11
[ant:get] Getting: https://repo1.maven.org/maven2/org/glassfish/jaxb/txw2/2.2.11/txw2-2.2.11.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/glassfish/jaxb/txw2/2.2.11/txw2-2.2.11.jar
Downloading https://repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-runtime-2.4.0-b180830.0438.jar to /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-runtime-2.4.0-b180830.0438.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438
[ant:get] Getting: https://repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-runtime-2.4.0-b180830.0438.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-runtime/2.4.0-b180830.0438/jaxb-runtime-2.4.0-b180830.0438.jar
Downloading https://repo1.maven.org/maven2/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar to /root/hpc/jvarkit/lib/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/javax/activation/javax.activation-api/1.2.0
[ant:get] Getting: https://repo1.maven.org/maven2/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar
[ant:get] To: /root/hpc/jvarkit/lib/javax/activation/javax.activation-api/1.2.0/javax.activation-api-1.2.0.jar
Downloading https://repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-xjc/2.4.0-b180830.0438/jaxb-xjc-2.4.0-b180830.0438.jar to /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-xjc/2.4.0-b180830.0438/jaxb-xjc-2.4.0-b180830.0438.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-xjc/2.4.0-b180830.0438
[ant:get] Getting: https://repo1.maven.org/maven2/org/glassfish/jaxb/jaxb-xjc/2.4.0-b180830.0438/jaxb-xjc-2.4.0-b180830.0438.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/glassfish/jaxb/jaxb-xjc/2.4.0-b180830.0438/jaxb-xjc-2.4.0-b180830.0438.jar

[ant:get] ....................................................
[ant:get] ..........
[ant:get] ..
[ant:get] ..
[ant:get] ....................
[ant:get] .
[ant:get] ....
[ant:get] ...........................
[ant:get] ..........
[ant:java] parsing a schema...

> Task :evs2vcf
Downloading https://repo1.maven.org/maven2/com/sun/istack/istack-commons-tools/3.0.7/istack-commons-tools-3.0.7.jar to /root/hpc/jvarkit/lib/com/sun/istack/istack-commons-tools/3.0.7/istack-commons-tools-3.0.7.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/sun/istack/istack-commons-tools/3.0.7
[ant:get] Getting: https://repo1.maven.org/maven2/com/sun/istack/istack-commons-tools/3.0.7/istack-commons-tools-3.0.7.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/sun/istack/istack-commons-tools/3.0.7/istack-commons-tools-3.0.7.jar
Downloading https://repo1.maven.org/maven2/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7.jar to /root/hpc/jvarkit/lib/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/sun/istack/istack-commons-runtime/3.0.7
[ant:get] Getting: https://repo1.maven.org/maven2/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/sun/istack/istack-commons-runtime/3.0.7/istack-commons-runtime-3.0.7.jar
Downloading https://repo1.maven.org/maven2/com/sun/xml/bind/external/rngom/2.4.0-b180830.0438/rngom-2.4.0-b180830.0438.jar to /root/hpc/jvarkit/lib/com/sun/xml/bind/external/rngom/2.4.0-b180830.0438/rngom-2.4.0-b180830.0438.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/sun/xml/bind/external/rngom/2.4.0-b180830.0438
[ant:get] Getting: https://repo1.maven.org/maven2/com/sun/xml/bind/external/rngom/2.4.0-b180830.0438/rngom-2.4.0-b180830.0438.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/sun/xml/bind/external/rngom/2.4.0-b180830.0438/rngom-2.4.0-b180830.0438.jar
Downloading https://repo1.maven.org/maven2/com/sun/xml/bind/external/relaxng-datatype/2.4.0-b180830.0438/relaxng-datatype-2.4.0-b180830.0438.jar to /root/hpc/jvarkit/lib/com/sun/xml/bind/external/relaxng-datatype/2.4.0-b180830.0438/relaxng-datatype-2.4.0-b180830.0438.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/sun/xml/bind/external/relaxng-datatype/2.4.0-b180830.0438
[ant:get] Getting: https://repo1.maven.org/maven2/com/sun/xml/bind/external/relaxng-datatype/2.4.0-b180830.0438/relaxng-datatype-2.4.0-b180830.0438.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/sun/xml/bind/external/relaxng-datatype/2.4.0-b180830.0438/relaxng-datatype-2.4.0-b180830.0438.jar
Downloading https://repo1.maven.org/maven2/com/sun/xml/dtd-parser/dtd-parser/1.4/dtd-parser-1.4.jar to /root/hpc/jvarkit/lib/com/sun/xml/dtd-parser/dtd-parser/1.4/dtd-parser-1.4.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/com/sun/xml/dtd-parser/dtd-parser/1.4
[ant:get] Getting: https://repo1.maven.org/maven2/com/sun/xml/dtd-parser/dtd-parser/1.4/dtd-parser-1.4.jar
[ant:get] To: /root/hpc/jvarkit/lib/com/sun/xml/dtd-parser/dtd-parser/1.4/dtd-parser-1.4.jar
Downloading https://repo1.maven.org/maven2/org/glassfish/jaxb/xsom/2.4.0-b180830.0438/xsom-2.4.0-b180830.0438.jar to /root/hpc/jvarkit/lib/org/glassfish/jaxb/xsom/2.4.0-b180830.0438/xsom-2.4.0-b180830.0438.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/glassfish/jaxb/xsom/2.4.0-b180830.0438
[ant:get] Getting: https://repo1.maven.org/maven2/org/glassfish/jaxb/xsom/2.4.0-b180830.0438/xsom-2.4.0-b180830.0438.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/glassfish/jaxb/xsom/2.4.0-b180830.0438/xsom-2.4.0-b180830.0438.jar
Downloading https://repo1.maven.org/maven2/org/glassfish/jaxb/codemodel/2.4.0-b180830.0438/codemodel-2.4.0-b180830.0438.jar to /root/hpc/jvarkit/lib/org/glassfish/jaxb/codemodel/2.4.0-b180830.0438/codemodel-2.4.0-b180830.0438.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/lib/org/glassfish/jaxb/codemodel/2.4.0-b180830.0438
[ant:get] Getting: https://repo1.maven.org/maven2/org/glassfish/jaxb/codemodel/2.4.0-b180830.0438/codemodel-2.4.0-b180830.0438.jar
[ant:get] To: /root/hpc/jvarkit/lib/org/glassfish/jaxb/codemodel/2.4.0-b180830.0438/codemodel-2.4.0-b180830.0438.jar
compiling xjc :evs

[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
:evs2vcf (Thread[included builds,5,main]) completed. Took 6.44 secs.

FAILURE: Build failed with an exception.

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

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

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 7s
1 actionable task: 1 executed
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: 4373). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-4373.out.log
Starting 4th build in daemon [uptime: 2 hrs 29 mins 55.29 secs, performance: 100%, non-heap usage: 20% 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 'evs2xml' from project :
Tasks to be executed: [evs2xml com.github.lindenb.jvarkit.tools.evs2bed.EvsDumpXml]
Tasks that were excluded: []
:evs2xml (Thread[included builds,5,main]) started.
[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 :evs2xml FAILED
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for evs2xml com.github.lindenb.jvarkit.tools.evs2bed.EvsDumpXml because:
  Build cache is disabled
Evs2xml com.github.lindenb.jvarkit.tools.evs2bed.EvsDumpXml is not up-to-date because:
  Task has not declared any outputs despite executing actions.
compiling xjc :evs
:evs2xml (Thread[included builds,5,main]) completed. Took 1.05 secs.

FAILURE: Build failed with an exception.

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

* What went wrong:
Execution failed for evs2xml com.github.lindenb.jvarkit.tools.evs2bed.EvsDumpXml.
> Java returned: 255

* Try:
> Run with --stacktrace option to get the stack trace.
> Run with --debug option to get more log output.
> Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 2s
1 actionable task: 1 executed

Thank you for your patience in reading through these questions. Please reply me.

lindenb commented 1 year ago

vcfoptimizeped4skat 、evs2vcf 、evs2xml 、gephicmd

no sorry, they are deprecated , unused, unsupported. You should only compile what you need.

Shingzzz commented 1 year ago

vcfoptimizeped4skat 、evs2vcf 、evs2xml 、gephicmd

no sorry, they are deprecated , unused, unsupported. You should only compile what you need.

thank you very much!