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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
                aloraine Ann Loraine created issue -
                aloraine Ann Loraine made changes -
                Field Original Value New Value
                Rank Ranked higher
                aloraine 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 :-)
                aloraine Ann Loraine made changes -
                Story Points 0.5 0.25
                aloraine 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.
                aloraine Ann Loraine made changes -
                Assignee Kiran Korey [ kkorey ]
                aloraine Ann Loraine made changes -
                Sprint Spring 2019 Sprint 3 [ 61 ] Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ]
                aloraine 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 ]
                Hide
                Permalink
                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.
                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 ]
                aloraine 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 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                srishteeM Srishtee Marotkar (Inactive) made changes -
                Status In Progress [ 3 ] Open [ 1 ]
                aloraine 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 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Assignee Srishtee Marotkar [ srishteem ]
                aloraine Ann Loraine made changes -
                Link This issue relates to IGBF-1699 [ IGBF-1699 ]
                aloraine Ann Loraine made changes -
                Epic Link IGBF-1531 [ 17617 ]
                aloraine 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 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine 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 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine Ann Loraine made changes -
                Summary Investigate and fix bundle resolution error involving htsjdk-igb Investigate bundle resolution error involving htsjdk-igb
                aloraine Ann Loraine made changes -
                Link This issue blocks IGBF-1767 [ IGBF-1767 ]
                aloraine 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 ]
                aloraine Ann Loraine made changes -
                Rank Ranked higher
                aloraine 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 ]
                Hide
                Permalink
                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Regarding lifecycle of OSGi bundle:
                https://osgi.org/javadoc/r4v43/core/org/osgi/framework/Bundle.html

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Regarding lifecycle of OSGi bundle: https://osgi.org/javadoc/r4v43/core/org/osgi/framework/Bundle.html
                aloraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18348 ] Fall 2019 Workflow Update [ 20077 ]
                aloraine 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:
                    aloraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: