Details
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Type: Bug
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Status: Closed (View Workflow)
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Priority: Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:0.25
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Epic Link:
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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
Activity
Field | Original Value | New Value |
---|---|---|
Rank | Ranked higher |
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 :-) |
Story Points | 0.5 | 0.25 |
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. |
Assignee | Kiran Korey [ kkorey ] |
Sprint | Spring 2019 Sprint 3 [ 61 ] | Spring 2019 Sprint 3, Spring 2019 Sprint 4 [ 61, 62 ] |
Rank | Ranked higher |
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Status | Open [ 1 ] | In Progress [ 3 ] |
Status | In Progress [ 3 ] | Open [ 1 ] |
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] | Srishtee Marotkar [ srishteem ] |
Status | Open [ 1 ] | In Progress [ 3 ] |
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 ] |
Rank | Ranked higher |
Status | In Progress [ 3 ] | Open [ 1 ] |
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 ] |
Rank | Ranked higher |
Assignee | Srishtee Marotkar [ srishteem ] |
Epic Link | IGBF-1531 [ 17617 ] |
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 ] |
Rank | Ranked higher |
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 ] |
Rank | Ranked higher |
Summary | Investigate and fix bundle resolution error involving htsjdk-igb | Investigate bundle resolution error involving htsjdk-igb |
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 ] |
Rank | Ranked higher |
Resolution | Done [ 10000 ] | |
Status | Open [ 1 ] | Closed [ 6 ] |
Assignee | Sai Charan Reddy Vallapureddy [ svallapu ] |
Workflow | Loraine Lab Workflow [ 18348 ] | Fall 2019 Workflow Update [ 20077 ] |
Workflow | Fall 2019 Workflow Update [ 20077 ] | Revised Fall 2019 Workflow Update [ 22211 ] |