Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3525

Investigate build problem: SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder"

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          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

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              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3521 Investigate build problem: effective model for org.lorainelab.igb:affymetrix-common:bundle:10.0.0

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3522 Investigate build problem: unknown parameter ignoreChecksumFailure

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3508 Create Install4J v10 Docker image for JDK21

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3516 Investigate build problem: repo1/javax/jlfgr/jlfgr/1.0/jlfgr-1.0.jar main-JDK21 warning

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3523 Investigate build problem: POM and checksum for com.jidesoft:jide-ultimate-jakarta:jar:3.5.15 is missing, no dependency information available

              • Major - Major loss of function.
              • Closed

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                nfreese Nowlan Freese added a comment - - edited

                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.

                Show
                nfreese Nowlan Freese added a comment - - edited 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.
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                nfreese Nowlan Freese added a comment -

                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

                Show
                nfreese Nowlan Freese added a comment - 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
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                nfreese Nowlan Freese added a comment -

                Tested locally on Mac, no issues.

                Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/975

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                nfreese Nowlan Freese added a comment - Tested locally on Mac, no issues. Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/975
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                ann.loraine Ann Loraine added a comment -

                Merged. New installers built and ready for testing. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

                Show
                ann.loraine Ann Loraine added a comment - Merged. New installers built and ready for testing. See: https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: