-Xmx set but ignored

The heap setting is being silently ignored — check the file's line endings

why

Java desktop tools read -Xmx from a .vmoptions file next to the executable. On Windows that file must use LF-only line endings — Notepad and most Windows editors save CRLF, the launcher fails to parse it, and falls back to the small default heap with no error message at all.

what to do

Re-save with LF endings (VS Code, or Notepad++ → Edit → EOL Conversion → Unix), or write the file on Mac/Linux and copy it over. Then confirm it applied — most tools show the current max heap under Help → About.

traced · confirmed against Cytoscape's launch docs, Sep 2026

This is one entry from BioErrors, a catalogue of bioinformatics error messages that point at the wrong thing. Every entry was traced to its real cause before it was written down.
If your error is not in it, paste it there and it gets traced and added.