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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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new warning message #412

Closed fazeliniah closed 3 years ago

fazeliniah commented 4 years ago

Hello Peptideshaker team, I have encountered a new warning message and subsequent search cancellation. I have attached the report for your review. I'd greatly appreciate any help to fix this. Thanks report.txt

WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/C:/PeptideShaker/PeptideShaker-1.16.45/PeptideShaker-1.16.45/lib/gson-2.4.jar) to field java.awt.Color.value WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release

hbarsnes commented 4 years ago

The "illegal reflective access" messages are just internal Java warnings and can be ignored. However, it does seem like PeptideShaker is having issues opening the search results. Can you also share the PeptideShaker log file?

fazeliniah commented 4 years ago

Thank you very much for your help. I attached the peptideshkaer bug report. PeptideShaker 1.16.45 log.txt

hbarsnes commented 4 years ago

This looks like an issue with the use of multiple threads that we have for some time been trying to fix by redesigning this part of our code. An updated beta version should soon be available for testing. I will keep you posted.

hbarsnes commented 3 years ago

This issue should hopefully be fixed in the new release that is available now. If not, please let us know by opening a new issue.