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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
        • Epic Link:
        • 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.

            Attachments

              Issue Links

              blocks

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1767 Fix bundle resolution error involving htsjdk-igb

              • Major - Major loss of function.
              • Closed
              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1699 Remove unneeded dependencies from modules

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                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)(!(version>=3.0.0))) Unresolved requirements: [[htsjdk-igb [26](R 26.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.commons.jexl2)(version>=2.1.0)(!(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.
                		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)(!(version>=3.0.0))) Unresolved requirements: [[htsjdk-igb [26](R 26.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.commons.jexl2)(version>=2.1.0)(!(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 I think it will be a quick fix - looks like a missing package from import.

                If the missing package is not necessary for anything, I'd prefer to remove it as a dependency from the htsjdk-igb itself. If that is the case, we just need to build a new version and re-deploy. and import from the code itself to reduce bloat. But if its already being imported other places, no need to do that. Use your best judgement :-)
                ann.loraine Ann Loraine made changes -
                Story Points 0.5 0.25
                ann.loraine Ann Loraine made changes -
                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)(!(version>=3.0.0))) Unresolved requirements: [[htsjdk-igb [26](R 26.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.commons.jexl2)(version>=2.1.0)(!(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 I think it will be a quick fix - looks like a missing package from import.

                If the missing package is not necessary for anything, I'd prefer to remove it as a dependency from the htsjdk-igb itself. If that is the case, we just need to build a new version and re-deploy. and import from the code itself to reduce bloat. But if its already being imported other places, no need to do that. Use your best judgement :-)
                		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)(!(version>=3.0.0))) Unresolved requirements: [[htsjdk-igb [26](R 26.0)] osgi.wiring.package; (&(osgi.wiring.package=org.apache.commons.jexl2)(version>=2.1.0)(!(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.
                ann.loraine Ann Loraine made changes -
                Assignee Kiran Korey [ kkorey ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ] Srishtee Marotkar [ srishteem ]
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Status Open [ 1 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 61, 62, 63 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5 [ 61, 62, 63 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 61, 62, 63, 64 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Srishtee Marotkar [ srishteem ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-1699 [ IGBF-1699 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1531 [ 17617 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6 [ 61, 62, 63, 64 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6, Summer 2019 Sprint 7 [ 61, 62, 63, 64, 66 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6, Summer 2019 Sprint 7 [ 61, 62, 63, 64, 66 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4, Spring 2019 Sprint 5, Spring 2019 Sprint 6, Summer 2019 Sprint 7, Summer 2019 Sprint 8 [ 61, 62, 63, 64, 66, 67 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Summary Investigate and fix bundle resolution error involving htsjdk-igb Investigate bundle resolution error involving htsjdk-igb
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-1767 [ IGBF-1767 ]
                ann.loraine Ann Loraine made changes -
                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 [ 61, 62, 63, 64, 66, 67 ] 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 [ 61, 62, 63, 64, 66, 67, 68 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Open [ 1 ] Closed [ 6 ]
                svallapu Sai Charan Reddy Vallapureddy (Inactive) made changes -
                Assignee Sai Charan Reddy Vallapureddy [ svallapu ]
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18348 ] Fall 2019 Workflow Update [ 20077 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 20077 ] Revised Fall 2019 Workflow Update [ 22211 ]

                  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: