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  1. IGB
  2. IGBF-1627

Investigate bundle resolution error involving htsjdk-igb

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
    • Story Points:
      0.25
    • Sprint:
      Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6, Summer 2019 Sprint 7, Summer 2019 Sprint 8, Summer 2019 Sprint 9

      Description

      On master, there is an error on startup:

      org.osgi.framework.BundleException: Unable to resolve htsjdk-igb [26](R 26.0): missing requirement [htsjdk-igb [26](R 26.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.commons.jexl2)(version>=2.1.0)(Unable to render embedded object: File ( [[htsjdk-igb [26](R 26.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.commons.jexl2)(version>=2.1.0)() not found.(version>=3.0.0)))]
      at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:4114) ~[igb_exe.jar:na]
      at org.apache.felix.framework.Felix.startBundle(Felix.java:2111) ~[igb_exe.jar:na]
      at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:977) ~[igb_exe.jar:na]
      at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:964) ~[igb_exe.jar:na]
      at com.affymetrix.main.OSGiHandler.loadBundles(OSGiHandler.java:83) [igb_exe.jar:na]
      at com.affymetrix.main.OSGiHandler.startOSGi(OSGiHandler.java:63) [igb_exe.jar:na]
      at com.affymetrix.main.Main.main(Main.java:30) [igb_exe.jar:na]
      15:36:02.340 [main] ERROR com.affymetrix.main.OSGiHandler - Error starting bundle htsjdk-igb:2.16.2

      I have seen the error when running master branch in Netbeans and from command line. Note you will not see the error in the IGB Help menu console because it happens before GUI is started.

      Looks like it could be a quick fix – possibly due import statement missing a package.

      If the missing package is not necessary for anything, I'd prefer to remove it as a dependency from the htsjdk-igb bundle. If this is practical to do, that (of course) requires making changes to our htsjdk-igb branch, which is fine. We can increment the version and deploy onto our nexus repository as usual.

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            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - - edited

            Missing Package : rg.apache.commons.jexl2
            Checked in htsjdk OSGi manifest file. Last import dependency is not loading.

            Show
            svallapu Sai Charan Reddy Vallapureddy (Inactive) added a comment - - edited Missing Package : rg.apache.commons.jexl2 Checked in htsjdk OSGi manifest file. Last import dependency is not loading.
            Hide
            stiwari8 Srishti Tiwari (Inactive) added a comment -
            Show
            stiwari8 Srishti Tiwari (Inactive) added a comment - Regarding lifecycle of OSGi bundle: https://osgi.org/javadoc/r4v43/core/org/osgi/framework/Bundle.html

              People

              • Assignee:
                svallapu Sai Charan Reddy Vallapureddy (Inactive)
                Reporter:
                ann.loraine Ann Loraine
              • Votes:
                0 Vote for this issue
                Watchers:
                3 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: