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: 10.0.0 Major Release
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Labels:None
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Story Points:0.25
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Epic Link:
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Sprint:Fall 8, Spring 1, Spring 2
Description
IGB tests trigger this warning when building main-JDK21 using Docker image:
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder". SLF4J: Defaulting to no-operation (NOP) logger implementation SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details. Dec 13, 2023 3:56:47 PM com.affymetrix.genometry.parsers.graph.BarParser getSeqGroup WARNING: Did not find genomeVersion Test Group:Test Group. Adding it as new genomeVersion Dec 13, 2023 3:56:48 PM com.affymetrix.genometry.parsers.NibbleResiduesParser parse
For this task, determine the source of the issue and fix it. Also check to see if this is a new error, as it may also occur in main-JDK8. If so, we can probably safely ignore it for now.
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
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- Closed
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- Closed
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IGBF-3508 Create Install4J v10 Docker image for JDK21
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- Closed
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- Closed
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
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| Summary | Investigate build problem: logging | Investigate build problem: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder" |
| Sprint | Fall 8 [ 184 ] | Fall 8, Spring 1 [ 184, 185 ] |
| Rank | Ranked higher |
| Sprint | Fall 8, Spring 1 [ 184, 185 ] | Fall 8, Spring 1, Spring 2 [ 184, 185, 186 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Adding the logback-classic dependency to the poms that were throwing the warning seems to resolve the issue.
Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/f4eca2b7ede557c03faabcca440bc3425365d381
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Tested locally on Mac, no issues.
Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/975
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Merged. New installers built and ready for testing. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Fix Version/s | 10.0.0 Major Release [ 10900 ] |
| Issue Type | Task [ 3 ] | Bug [ 1 ] |
This issue also occurs in main-JDK8 for the following tests:
Running org.lorainelab.igb.synonymlookup.test.SynonymLookupTest
Running com.affymetrix.genometry.NibbleBioSeqTest
Running com.affymetrix.igb.bookmarks.BookMarkTest
It's possible we could fix this issue by adding additional dependencies as discussed in stackoverflow, but this does not seem critical for the JDK-21 release.