java.lang.reflect.InvocationTargetException

biostars.org | 4 months ago
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    cramtools without internet access

    biostars.org | 4 months ago
    java.lang.reflect.InvocationTargetException
  2. 0

    LWC: Connection timed out

    GitHub | 5 years ago | Schneidertm
    java.net.ConnectException: Connection timed out
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    {{FilePath.installIfNecessaryFrom}}, used from {{ZipExtractionInstaller}}, is designed to log a warning but continue in case the tool is already unpacked and the server returns an error while it is checking for a newer archive. Yet this stack trace suggests that this logic is not working, because the {{IOException}} comes after {{connect}} in {{getInputStream}}: {code:none} Unpacking <URL> to <TOOLPATH> on <SLAVE> ERROR: Failed to download <URL> from slave; will retry from master java.io.IOException: remote file operation failed: <TOOLPATH> at hudson.remoting.Channel@...:<SLAVE>: java.net.ConnectException: Connection timed out at hudson.FilePath.act(FilePath.java:976) at hudson.FilePath.act(FilePath.java:958) at hudson.FilePath.installIfNecessaryFrom(FilePath.java:797) at hudson.tools.ZipExtractionInstaller.performInstallation(ZipExtractionInstaller.java:79) at hudson.tools.InstallerTranslator.getToolHome(InstallerTranslator.java:68) at hudson.tools.ToolLocationNodeProperty.getToolHome(ToolLocationNodeProperty.java:107) at hudson.tools.ToolInstallation.translateFor(ToolInstallation.java:205) at hudson.model.JDK.forNode(JDK.java:130) at hudson.model.AbstractProject.getEnvironment(AbstractProject.java:350) at hudson.model.AbstractProject.pollWithWorkspace(AbstractProject.java:1444) at hudson.model.AbstractProject._poll(AbstractProject.java:1421) at hudson.model.AbstractProject.poll(AbstractProject.java:1332) at jenkins.triggers.SCMTriggerItem$SCMTriggerItems$Bridge.poll(SCMTriggerItem.java:119) at hudson.triggers.SCMTrigger$Runner.runPolling(SCMTrigger.java:515) at hudson.triggers.SCMTrigger$Runner.run(SCMTrigger.java:544) at hudson.util.SequentialExecutionQueue$QueueEntry.run(SequentialExecutionQueue.java:118) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) Caused by: java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392) at java.net.Socket.connect(Socket.java:579) at java.net.Socket.connect(Socket.java:528) at sun.net.NetworkClient.doConnect(NetworkClient.java:180) at sun.net.www.http.HttpClient.openServer(HttpClient.java:432) at sun.net.www.http.HttpClient.openServer(HttpClient.java:527) at sun.net.www.http.HttpClient.<init>(HttpClient.java:211) at sun.net.www.http.HttpClient.New(HttpClient.java:308) at sun.net.www.http.HttpClient.New(HttpClient.java:326) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:996) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:932) at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:850) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1300) at java.net.URL.openStream(URL.java:1037) at hudson.FilePath$Unpack.invoke(FilePath.java:833) at hudson.FilePath$Unpack.invoke(FilePath.java:827) at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2577) at hudson.remoting.UserRequest.perform(UserRequest.java:121) at hudson.remoting.UserRequest.perform(UserRequest.java:49) at hudson.remoting.Request$2.run(Request.java:324) at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) at ......remote call to <SLAVE>(Native Method) at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1356) at hudson.remoting.UserResponse.retrieve(UserRequest.java:221) at hudson.remoting.Channel.call(Channel.java:752) at hudson.FilePath.act(FilePath.java:969) ... 20 more FATAL: Failed to install <URL> to <TOOLPATH> java.io.IOException: Failed to install <URL> to <TOOLPATH> at hudson.FilePath.installIfNecessaryFrom(FilePath.java:822) at hudson.tools.ZipExtractionInstaller.performInstallation(ZipExtractionInstaller.java:79) at hudson.tools.InstallerTranslator.getToolHome(InstallerTranslator.java:68) at hudson.tools.ToolLocationNodeProperty.getToolHome(ToolLocationNodeProperty.java:107) at hudson.tools.ToolInstallation.translateFor(ToolInstallation.java:205) at hudson.model.JDK.forNode(JDK.java:130) at hudson.model.AbstractProject.getEnvironment(AbstractProject.java:350) at hudson.model.AbstractProject.pollWithWorkspace(AbstractProject.java:1444) at hudson.model.AbstractProject._poll(AbstractProject.java:1421) at hudson.model.AbstractProject.poll(AbstractProject.java:1332) at jenkins.triggers.SCMTriggerItem$SCMTriggerItems$Bridge.poll(SCMTriggerItem.java:119) at hudson.triggers.SCMTrigger$Runner.runPolling(SCMTrigger.java:515) at hudson.triggers.SCMTrigger$Runner.run(SCMTrigger.java:544) at hudson.util.SequentialExecutionQueue$QueueEntry.run(SequentialExecutionQueue.java:118) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745) Caused by: java.io.IOException: Server returned HTTP response code: 504 for URL: <URL> at sun.reflect.GeneratedConstructorAccessor691.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:526) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1675) at sun.net.www.protocol.http.HttpURLConnection$6.run(HttpURLConnection.java:1673) at java.security.AccessController.doPrivileged(Native Method) at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1671) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1244) at org.jvnet.robust_http_client.RetryableHttpStream.getStream(RetryableHttpStream.java:98) at org.jvnet.robust_http_client.RetryableHttpStream.<init>(RetryableHttpStream.java:91) at hudson.ProxyConfiguration.getInputStream(ProxyConfiguration.java:248) at hudson.FilePath.installIfNecessaryFrom(FilePath.java:808) ... 18 more Caused by: java.io.IOException: Server returned HTTP response code: 504 for URL: <URL> at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626) at sun.net.www.protocol.http.HttpURLConnection.getHeaderField(HttpURLConnection.java:2678) at java.net.URLConnection.getHeaderFieldLong(URLConnection.java:639) at java.net.URLConnection.getContentLengthLong(URLConnection.java:511) at java.net.URLConnection.getContentLength(URLConnection.java:495) at org.jvnet.robust_http_client.RetryableHttpStream.<init>(RetryableHttpStream.java:90) ... 20 more {code}

    Jenkins JIRA | 2 years ago | Jesse Glick
    java.io.IOException: remote file operation failed: <TOOLPATH> at hudson.remoting.Channel@...:<SLAVE>: java.net.ConnectException: Connection timed out

  1. eti22 1 times, last 3 weeks ago
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Root Cause Analysis

  1. java.net.ConnectException

    Connection timed out

    at java.net.PlainSocketImpl.socketConnect()
  2. Java RT
    URL.openStream
    1. java.net.PlainSocketImpl.socketConnect(Native Method)
    2. java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:382)
    3. java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:241)
    4. java.net.PlainSocketImpl.connect(PlainSocketImpl.java:228)
    5. java.net.SocksSocketImpl.connect(SocksSocketImpl.java:365)
    6. java.net.Socket.connect(Socket.java:527)
    7. java.net.Socket.connect(Socket.java:476)
    8. sun.net.NetworkClient.doConnect(NetworkClient.java:163)
    9. sun.net.www.http.HttpClient.openServer(HttpClient.java:424)
    10. sun.net.www.http.HttpClient.openServer(HttpClient.java:538)
    11. sun.net.www.http.HttpClient.<init>(HttpClient.java:214)
    12. sun.net.www.http.HttpClient.New(HttpClient.java:300)
    13. sun.net.www.http.HttpClient.New(HttpClient.java:319)
    14. sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:987)
    15. sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:923)
    16. sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:841)
    17. sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1195)
    18. java.net.URL.openStream(URL.java:1010)
    18 frames
  3. net.sf.cram
    Bam2Cram.main
    1. net.sf.cram.ref.ReferenceSource.loadFromPath(ReferenceSource.java:249)
    2. net.sf.cram.ref.ReferenceSource.findBasesByMD5(ReferenceSource.java:283)
    3. net.sf.cram.ref.ReferenceSource.findBases(ReferenceSource.java:179)
    4. net.sf.cram.ref.ReferenceSource.getReferenceBases(ReferenceSource.java:127)
    5. net.sf.cram.Bam2Cram.main(Bam2Cram.java:282)
    5 frames
  4. Java RT
    Method.invoke
    1. sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    2. sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    3. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    4. java.lang.reflect.Method.invoke(Method.java:597)
    4 frames
  5. net.sf.cram
    CramTools.main
    1. net.sf.cram.CramTools.invoke(CramTools.java:93)
    2. net.sf.cram.CramTools.main(CramTools.java:123)
    2 frames