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Nupack error with subsequent pknot refold #786

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luxaritas opened this issue Jul 19, 2024 · 0 comments
Open

Nupack error with subsequent pknot refold #786

luxaritas opened this issue Jul 19, 2024 · 0 comments
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priority: p3/standard Enhancement with nominal value or bug with nominal impact size: md type: bug Something isn't working

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@luxaritas
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Expected Behavior

No error/crash

Current Behavior

Error in backtrack Fg_N5, 10 22 40 56

      at Object.put_char (../node_modules/eternajs-folding-engines/engines/nupack.js:913:5)

  console.error
    FullFoldTemperature error ExitStatus {
      name: 'ExitStatus',
      message: 'Program terminated with exit(1)',
      status: 1
    }

Reproduction Steps

In puzzlemaker:

  • Reset puzzlemaker
  • Switch to nupack
  • Paste structure .((({{..((((.....)))).))).((((((...{{{....)))).........}}}..........}}.))...
  • Paste sequence AGCACGUUUCGAAAAAAUCGAUUGCACCCAGAACACGCAAAAUCUGAAAAAAAAAGCGAAACAAAAAUCGAGGUGC

In unit test:

await nupack = NuPACK.create();
// Works
nupack.foldSequence(Sequence.fromSequenceString("AGCACGUUUCGAAAAAAUCGAUUGCACCCAGAACACGCAAAAUCUGAAAAAAAAAGCGAAACAAAAAUCGAGGUGG"), null, null, true, 37);
// Crash
nupack.foldSequence(Sequence.fromSequenceString("AGCACGUUUCGAAAAAAUCGAUUGCACCCAGAACACGCAAAAUCUGAAAAAAAAAGCGAAACAAAAAUCGAGGUGC"), null, null, true, 37);

Note that if the problem sequence is the first fold to happen when the engine is loaded, all is fine. This only occurs on subsequent folds. I'm guessing there's some nupack global not being reset properly or memory corruption or something.

Environment

No response

Other information

https://forum.eternagame.org/t/error-on-mutation-in-pseudoknot-puzzle/4697/7

@luxaritas luxaritas added type: bug Something isn't working pending triage priority: p3/standard Enhancement with nominal value or bug with nominal impact size: md and removed pending triage labels Jul 19, 2024
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Labels
priority: p3/standard Enhancement with nominal value or bug with nominal impact size: md type: bug Something isn't working
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Status: Todo
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