Running examples in 'sctransform-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: correct
> ### Title: Correct data by setting all latent factors to their median
> ###   values and reversing the regression model
> ### Aliases: correct
> 
> ### ** Examples
> 
> vst_out <- vst(pbmc, return_cell_attr = TRUE)
Calculating cell attributes for input UMI matrix
Variance stabilizing transformation of count matrix of size 910 by 283
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 910 genes, 283 cells

  |                                                                            
  |                                                                      |   0%Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

  |                                                                            
  |==================                                                    |  25%Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

  |                                                                            
  |===================================                                   |  50%Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

  |                                                                            
  |====================================================                  |  75%Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached

  |                                                                            
  |======================================================================| 100%
Found 1 outliers - those will be ignored in fitting/regularization step

Second step: Get residuals using fitted parameters for 910 genes

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |==================                                                    |  25%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |====================================================                  |  75%
  |                                                                            
  |======================================================================| 100%
Calculating gene attributes
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
sctransform
 --- call from context --- 
row_var(rv$y)
 --- call from argument --- 
if (class(x) == "matrix") {
    ret <- row_var_dense(x)
    names(ret) <- rownames(x)
    return(ret)
}
 --- R stacktrace ---
where 1: row_var(rv$y)
where 2: vst(pbmc, return_cell_attr = TRUE)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (x) 
{
    if (class(x) == "matrix") {
        ret <- row_var_dense(x)
        names(ret) <- rownames(x)
        return(ret)
    }
    if (class(x) == "dgCMatrix") {
        ret <- row_var_dgcmatrix(x = x@x, i = x@i, rows = nrow(x), 
            cols = ncol(x))
        names(ret) <- rownames(x)
        return(ret)
    }
    stop("matrix x needs to be of class matrix or dgCMatrix")
}
<bytecode: 0xd07ed20>
<environment: namespace:sctransform>
 --- function search by body ---
Function row_var in namespace sctransform has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "matrix") { : the condition has length > 1
Calls: vst -> row_var
Execution halted