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DESeq2.check #47

Closed Yikun closed 1 year ago

Yikun commented 1 year ago

https://yikun.github.io/bioconductor-0301/report/DESeq2/kunpeng1-checksrc.html

 mix <- unmix(norm.cts, pure, alpha=0.01)
Warning in sqrt(alpha * q) : NaNs produced
Error in optim(par = rep(1, ncol(pure)), fn = sumLossVST, gr = NULL, i,  : 
  L-BFGS-B needs finite values of 'fn'
Calls: unmix -> lapply -> lapply -> FUN -> optim
Execution halted
martin-g commented 1 year ago

The issue seems to be in floating point arithmetic.

martin-g commented 1 year ago

Asked for help at https://support.bioconductor.org/p/9150056/

martin-g commented 1 year ago

Fixed upstream with https://github.com/mikelove/DESeq2/commit/48b80aaac5efd4b9e0d054fc1e4a6e1fa78e782a

martin-g commented 1 year ago

https://bioconductor.org/checkResults/3.18/bioc-LATEST/DESeq2/ is green for Linux ARM64!