Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3523

Investigate build problem: POM and checksum for com.jidesoft:jide-ultimate-jakarta:jar:3.5.15 is missing, no dependency information available

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          When building main-JDK21 using Docker container, observed these two related warnings:

          [WARNING] The POM for com.jidesoft:jide-ultimate-jakarta:jar:3.5.15 is missing, no dependency information available

          and

          [WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.jar
org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available
    at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63)
    at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414)
    at org.eclipse.aether.util.concurrency.RunnableErrorForwarder.lambda$wrap$0 (RunnableErrorForwarder.java:66)
    at java.util.concurrent.ThreadPoolExecutor.runWorker (ThreadPoolExecutor.java:1144)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run (ThreadPoolExecutor.java:642)
    at java.lang.Thread.run (Thread.java:1583)
    [WARNING] Checksum validation failed, no checksums available from repo2 for https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.jar

          For this task, investigate and fix the source of the above issue.

          IGB and Docker image version info:

          Docker file used to build the container was: https://bitbucket.org/lorainelab/integrated-genome-browser-docker/raw/d26649c086c8c2cc252e8a18b6e2ca3a74413f0b/Dockerfile
          The version of IGB built was: a0860834e (HEAD -> main-JDK21, origin/main-JDK21) removing mac specific code for the right aligned tabs to ensure vertical override is applied

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3525 Investigate build problem: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder"

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3516 Investigate build problem: repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar main-JDK21 warning

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3524 Investigate build problem: Bundle org.lorainelab.igb:flatlaf:bundle:10.0.0 : Classes found in the wrong directory

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3521 Investigate build problem: effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3522 Investigate build problem: unknown parameter ignoreChecksumFailure

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3508 Create Install4J v10 Docker image for JDK21

              • Major - Major loss of function.
              • Closed

                Activity

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                karthik Karthik Raveendran added a comment -

                Checksum and md5 files for jide-ultimate-jakarta-3.5.15.jar has been created and attached to this ticket. The POM issue is potentially due to the fact the modified pom file for jide-ultimate, which is added to repo2, has an extra extension, ".lastUpdated", as in,"jide-ultimate-jakarta-3.5.15.pom.lastUpdated". This could be causing the issue.

                Show
                karthik Karthik Raveendran added a comment - Checksum and md5 files for jide-ultimate-jakarta-3.5.15.jar has been created and attached to this ticket. The POM issue is potentially due to the fact the modified pom file for jide-ultimate, which is added to repo2, has an extra extension, ".lastUpdated", as in,"jide-ultimate-jakarta-3.5.15.pom .lastUpdated ". This could be causing the issue.
                Hide
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                nfreese Nowlan Freese added a comment -

                Comparing repo2 jide-ultimate and jide-ultimate-jakarta repos I agree with Karthik's assessment.

                The jide-ultimate-jakarta-3.5.15.pom.lastUpdated looks strange to me, I'm not even sure it is a pom. I generated a new pom using the command below that more closely matches the pom from jide-ultimate that we had been using. It seems to be working fine on my machine.

                mvn install:install-file \
   -Dfile=/Users/lorainelab/Downloads/jide-ultimate-jakarta-3.5.15.jar \
   -DgroupId=com.jidesoft \
   -DartifactId=jide-ultimate-jakarta \
   -Dversion=3.5.15 \
   -Dpackaging=jar \
   -DgeneratePom=true

                I'm not sure who has write permission to repo2, but I think the next step would be to add the attached md5, sha, and pom to the repo and test the changes.

                Show
                nfreese Nowlan Freese added a comment - Comparing repo2 jide-ultimate and jide-ultimate-jakarta repos I agree with Karthik's assessment. The jide-ultimate-jakarta-3.5.15.pom.lastUpdated looks strange to me, I'm not even sure it is a pom. I generated a new pom using the command below that more closely matches the pom from jide-ultimate that we had been using. It seems to be working fine on my machine. mvn install:install-file \ -Dfile=/Users/lorainelab/Downloads/jide-ultimate-jakarta-3.5.15.jar \ -DgroupId=com.jidesoft \ -DartifactId=jide-ultimate-jakarta \ -Dversion=3.5.15 \ -Dpackaging=jar \ -DgeneratePom= true I'm not sure who has write permission to repo2, but I think the next step would be to add the attached md5, sha, and pom to the repo and test the changes.
                Hide
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                nfreese Nowlan Freese added a comment -

                Testing running mvn clean install locally:
                With no jidesoft in my .m2 -> I see the warning for missing pom and could not validate integrity
                With jidesoft in my .m2 and the pom I created and the md5 and sha that Karthik created -> No warnings regarding pom or integrity
                With jidesoft in my .m2 and the pom I created, no md5 or sha -> No warnings regarding pom or integrity

                It's odd that I don't see the warning regarding the integrity when just the pom is present.

                Show
                nfreese Nowlan Freese added a comment - Testing running mvn clean install locally: With no jidesoft in my .m2 -> I see the warning for missing pom and could not validate integrity With jidesoft in my .m2 and the pom I created and the md5 and sha that Karthik created -> No warnings regarding pom or integrity With jidesoft in my .m2 and the pom I created, no md5 or sha -> No warnings regarding pom or integrity It's odd that I don't see the warning regarding the integrity when just the pom is present.
                Hide
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                ann.loraine Ann Loraine added a comment -

                Please provide the URL/ location for where the attached files need to be deployed to close the ticket.

                Show
                ann.loraine Ann Loraine added a comment - Please provide the URL/ location for where the attached files need to be deployed to close the ticket.
                Hide
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                nfreese Nowlan Freese added a comment -

                Please add the 3 attached files to this location: https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/

                Show
                nfreese Nowlan Freese added a comment - Please add the 3 attached files to this location: https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/
                Hide
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                ann.loraine Ann Loraine added a comment -

                Sorry - a new request for Karthik Raveendran and/or Nowlan Freese:

                Could you please submit the files as a PR to https://bitbucket.org/lorainelab/maven/src/main/htdocs/ ?

                Show
                ann.loraine Ann Loraine added a comment - Sorry - a new request for Karthik Raveendran and/or Nowlan Freese : Could you please submit the files as a PR to https://bitbucket.org/lorainelab/maven/src/main/htdocs/ ?
                Hide
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                nfreese Nowlan Freese added a comment -

                Pull request: https://bitbucket.org/lorainelab/maven/pull-requests/1

                Show
                nfreese Nowlan Freese added a comment - Pull request: https://bitbucket.org/lorainelab/maven/pull-requests/1
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                PR is merged and deployed to the maven.bioviz.org host.

                To test:

                • Check the deployment of the above files. They should now appear in one of the three repos hosted on maven.bioviz.org
                • Remove local .m2 to ensure all the things will get downloaded freshly from the maven repositories hosted on maven.bioviz.org
                • Compile IGB and check to see if the errors mentioned in the ticket re-occur
                Show
                ann.loraine Ann Loraine added a comment - - edited PR is merged and deployed to the maven.bioviz.org host. To test: Check the deployment of the above files. They should now appear in one of the three repos hosted on maven.bioviz.org Remove local .m2 to ensure all the things will get downloaded freshly from the maven repositories hosted on maven.bioviz.org Compile IGB and check to see if the errors mentioned in the ticket re-occur
                Hide
                Permalink
                karthik Karthik Raveendran added a comment -

                The pom error is gone but the checksum error still persists:

                [WARNING] Could not validate integrity of download from https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.pom
org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available
    at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63)
    at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414)
    at org.eclipse.aether.connector.basic.BasicRepositoryConnector.get (BasicRepositoryConnector.java:260)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads (DefaultArtifactResolver.java:536)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve (DefaultArtifactResolver.java:448)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts (DefaultArtifactResolver.java:260)
    at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact (DefaultArtifactResolver.java:242)
    at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom (DefaultArtifactDescriptorReader.java:231)
    at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor (DefaultArtifactDescriptorReader.java:172)
    at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.resolveCachedArtifactDescriptor (DfDependencyCollector.java:382)
    at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.getArtifactDescriptorResult (DfDependencyCollector.java:368)
    at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:218)
    at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:156)
    at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.process (DfDependencyCollector.java:138)
    at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.doCollectDependencies (DfDependencyCollector.java:108)
    at org.eclipse.aether.internal.impl.collect.DependencyCollectorDelegate.collectDependencies (DependencyCollectorDelegate.java:222)
    at org.eclipse.aether.internal.impl.collect.DefaultDependencyCollector.collectDependencies (DefaultDependencyCollector.java:87)
    at org.eclipse.aether.internal.impl.DefaultRepositorySystem.collectDependencies (DefaultRepositorySystem.java:305)
    at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:151)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:224)
    at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:136)
    at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:369)
    at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:327)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:213)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:175)
    at org.apache.maven.lifecycle.internal.MojoExecutor.access$000 (MojoExecutor.java:76)
    at org.apache.maven.lifecycle.internal.MojoExecutor$1.run (MojoExecutor.java:163)
    at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute (DefaultMojosExecutionStrategy.java:39)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:160)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:105)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:73)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:53)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:118)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:261)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:173)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:101)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:910)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:283)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:206)
    at jdk.internal.reflect.DirectMethodHandleAccessor.invoke (DirectMethodHandleAccessor.java:103)
    at java.lang.reflect.Method.invoke (Method.java:580)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:283)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:226)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:407)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:348)
[WARNING] Checksum validation failed, no checksums available from repo2 for https://maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.pom
                Show
                karthik Karthik Raveendran added a comment - The pom error is gone but the checksum error still persists: [WARNING] Could not validate integrity of download from https: //maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.pom org.eclipse.aether.transfer.ChecksumFailureException: Checksum validation failed, no checksums available at org.eclipse.aether.internal.impl.AbstractChecksumPolicy.onNoMoreChecksums (AbstractChecksumPolicy.java:63) at org.eclipse.aether.connector.basic.ChecksumValidator.validate (ChecksumValidator.java:112) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$GetTaskRunner.runTask (BasicRepositoryConnector.java:484) at org.eclipse.aether.connector.basic.BasicRepositoryConnector$TaskRunner.run (BasicRepositoryConnector.java:414) at org.eclipse.aether.connector.basic.BasicRepositoryConnector.get (BasicRepositoryConnector.java:260) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.performDownloads (DefaultArtifactResolver.java:536) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolve (DefaultArtifactResolver.java:448) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifacts (DefaultArtifactResolver.java:260) at org.eclipse.aether.internal.impl.DefaultArtifactResolver.resolveArtifact (DefaultArtifactResolver.java:242) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.loadPom (DefaultArtifactDescriptorReader.java:231) at org.apache.maven.repository.internal.DefaultArtifactDescriptorReader.readArtifactDescriptor (DefaultArtifactDescriptorReader.java:172) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.resolveCachedArtifactDescriptor (DfDependencyCollector.java:382) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.getArtifactDescriptorResult (DfDependencyCollector.java:368) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:218) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.processDependency (DfDependencyCollector.java:156) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.process (DfDependencyCollector.java:138) at org.eclipse.aether.internal.impl.collect.df.DfDependencyCollector.doCollectDependencies (DfDependencyCollector.java:108) at org.eclipse.aether.internal.impl.collect.DependencyCollectorDelegate.collectDependencies (DependencyCollectorDelegate.java:222) at org.eclipse.aether.internal.impl.collect.DefaultDependencyCollector.collectDependencies (DefaultDependencyCollector.java:87) at org.eclipse.aether.internal.impl.DefaultRepositorySystem.collectDependencies (DefaultRepositorySystem.java:305) at org.apache.maven.project.DefaultProjectDependenciesResolver.resolve (DefaultProjectDependenciesResolver.java:151) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.getDependencies (LifecycleDependencyResolver.java:224) at org.apache.maven.lifecycle.internal.LifecycleDependencyResolver.resolveProjectDependencies (LifecycleDependencyResolver.java:136) at org.apache.maven.lifecycle.internal.MojoExecutor.ensureDependenciesAreResolved (MojoExecutor.java:369) at org.apache.maven.lifecycle.internal.MojoExecutor.doExecute (MojoExecutor.java:327) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:213) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:175) at org.apache.maven.lifecycle.internal.MojoExecutor.access$000 (MojoExecutor.java:76) at org.apache.maven.lifecycle.internal.MojoExecutor$1.run (MojoExecutor.java:163) at org.apache.maven.plugin.DefaultMojosExecutionStrategy.execute (DefaultMojosExecutionStrategy.java:39) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:160) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:105) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:73) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:53) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:118) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:261) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:173) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:101) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:910) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:283) at org.apache.maven.cli.MavenCli.main (MavenCli.java:206) at jdk.internal.reflect.DirectMethodHandleAccessor.invoke (DirectMethodHandleAccessor.java:103) at java.lang.reflect.Method.invoke (Method.java:580) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:283) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:226) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:407) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:348) [WARNING] Checksum validation failed, no checksums available from repo2 for https: //maven.bioviz.org/repo2/com/jidesoft/jide-ultimate-jakarta/3.5.15/jide-ultimate-jakarta-3.5.15.pom
                Hide
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                ann.loraine Ann Loraine added a comment -

                Made files:

                • jide-ultimate-jakarta-3.5.15.pom.md5
                • jide-ultimate-jakarta-3.5.15.pom.sha1

                Using utilities "md5" and "shasum".

                Added to the repository bitbucket.org/lorainelab/maven.
                Deployed to bioviz.org.

                Show
                ann.loraine Ann Loraine added a comment - Made files: jide-ultimate-jakarta-3.5.15.pom.md5 jide-ultimate-jakarta-3.5.15.pom.sha1 Using utilities "md5" and "shasum". Added to the repository bitbucket.org/lorainelab/maven. Deployed to bioviz.org.
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                Testing:

                In my local .m2, deleted "jidesoft" from ~/.m2/repository/com.

                Built IGB locally in the usual way with:

                local aloraine$ mvn clean install 2>build.err 1>build.out

                Observed that jidesoft artifacts were downloaded. No errors observed.

                Moving to DONE.

                Show
                ann.loraine Ann Loraine added a comment - - edited Testing: In my local .m2, deleted "jidesoft" from ~/.m2/repository/com. Built IGB locally in the usual way with: local aloraine$ mvn clean install 2>build.err 1>build.out Observed that jidesoft artifacts were downloaded. No errors observed. Moving to DONE.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: