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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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Failed to start PeptideShaker #488

Closed fabiocsn closed 1 year ago

fabiocsn commented 2 years ago

Dear,

I a having a problem opening PeptideShaker.

Memory settings read from the user preferences: 4096 args: Range [0, -1) out of bounds for length 10

Could you help me to solve this issue?

All the best, Fábio

hbarsnes commented 2 years ago

Hi Fábio,

Thanks for letting us know. I think I need a bit more information though. Where do you see this error message? Is there more to the message than just what you write above? And are you trying to start PeptideShaker from the command line or by double-clicking the jar file?

Best regards, Harald

hbarsnes commented 2 years ago

Hi again,

Seems like this issue was related to using Java 19. As we assumed that all Java version numbers contained at least one period in them, e.g., 14.0.2.

This has now been corrected and new versions of both tools have been released.

If you still experience problems, please let us know and we'll reopen the issue.

Best regards, Harald

fabiocsn commented 2 years ago

Hi Harald,

Thanks to let me know. Unfortunately, I am facing the same problem after downloading the new version of peptideshaker (2.2.10). Please, see attached the picture of the error. I also included the log files.

Imagem3

PeptideShaker.log startup.log

Best Regards, Fábio

hbarsnes commented 2 years ago

Hi Fábio,

Thanks for the update. However, it seems like you did not update to the most recent version as the latest version is (or rather was, see below) PeptideShaker 2.2.11 (and SearchGUI 4.1.20).

I've now released yet another set of new releases (v2.2.11 and v4.1.20) fixing some additional issues. Can you update to these versions and see if this solves the issue?

Best regards, Harald

fabiocsn commented 2 years ago

Hi Harald,

Thanks again. Appeared now a different message. Can you take a look? I've downloaded version 2.2.12.

All the best, Fábio

Imagem1 startup.log

hbarsnes commented 2 years ago

Hi again,

Aha, I see. The good news is that it should be easy to fix. The bad news is that I won't be able to release new versions until over the weekend.

I'll let you know as soon as the new releases can be downloaded.

Best regards Harald

carolinelennartsson commented 2 years ago

I have the exact same issue with java 19 and peptide-shaker version 2.2.12. Thank you for fixing it, in advance. :)

Best regards, Caroline

hbarsnes commented 2 years ago

PeptideShaker 2.2.13 and SearchGUI 4.1.22 have just been released which should fix the problem. Please give the new versions a go and let me know whether the issue has been resolved.

hbarsnes commented 1 year ago

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.