Error(s) in re-building vignettes:
--- re-building ‘VAM_PBMC3K_Hallmark_LogNormalization.Rnw’ using Sweave
--- finished re-building ‘VAM_PBMC3K_Hallmark_LogNormalization.Rnw’

--- re-building ‘VAM_PBMC3K_LogNormalization.Rnw’ using Sweave
--- finished re-building ‘VAM_PBMC3K_LogNormalization.Rnw’

--- re-building ‘VAM_PBMC3K_SCTransform.Rnw’ using Sweave
--- finished re-building ‘VAM_PBMC3K_SCTransform.Rnw’

--- re-building ‘VAM_pbmc_small.Rnw’ using Sweave
Loading required package: MASS
Loading required package: Matrix
gene.weights not specified, defaulting all weights to 1
Computing VAM distances for 1 gene sets, 80 cells and 230 genes.
Min set size: 5, median size: 5

Error: processing vignette 'VAM_pbmc_small.Rnw' failed with diagnostics:
 chunk 5 
Error in methods::slot(object = object, name = layer) : 
  invalid type or length for slot name

--- failed re-building ‘VAM_pbmc_small.Rnw’

--- re-building ‘VAM_pbmc_small_sctransform.Rnw’ using Sweave
Loading required package: MASS
Loading required package: Matrix
`vst.flavor` is set to 'v2' but could not find glmGamPoi installed.
Please install the glmGamPoi package for much faster estimation.
--------------------------------------------
install.packages('BiocManager')
BiocManager::install('glmGamPoi')
--------------------------------------------
Falling back to native (slower) implementation.

Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in glm.nb(formula = as.formula(new_formula), data = data) :
  alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
  alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
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Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
  alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
  alternation limit reached
Warning: glm.fit: algorithm did not converge
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
  alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in glm.nb(formula = as.formula(new_formula), data = data) :
  alternation limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in sqrt(1/i) : NaNs produced
PC_ 1 
Positive:  CST3, LYZ, HLA-DRA, S100A9, LST1, HLA-DPA1, HLA-DPB1, SAT1, AIF1, HLA-DRB1 
	   IFITM3, S100A8, COTL1, TYROBP, TYMP, CTSS, LGALS1, HLA-DRB5, S100A11, FCN1 
	   SERPINA1, FCER1G, CFD, LGALS2, IFI30, HLA-DQA1, HLA-DQB1, GRN, CFP, CD68 
Negative:  NKG7, CST7, CCL5, GZMA, IL32, CD3D, CTSW, PRF1, HNRNPF, GZMM 
	   GNLY, FGFBP2, CD7, LCK, RARRES3, GZMB, CD3E, CRBN, CD247, EIF4A2 
	   LAMP1, XBP1, LTB, SPON2, IL7R, GYPC, GZMH, LDHB, SSR2, LYAR 
PC_ 2 
Positive:  PPBP, GPX1, SDPR, PF4, GNG11, CLU, SPARC, CD9, GP9, HIST1H2AC 
	   TUBB1, NCOA4, NRGN, CCL5, CA2, TPM4, TREML1, NGFRAP1, PGRMC1, ITGA2B 
	   RUFY1, PTCRA, FERMT3, MYL9, TMEM40, ODC1, ACRBP, PARVB, TSC22D1, TALDO1 
Negative:  IFITM2, HLA-DRA, HLA-DPB1, HNRNPF, HLA-DPA1, HLA-DRB1, TYROBP, LTB, LGALS1, CXCR4 
	   LYZ, LST1, NKG7, EIF4A2, HLA-DRB5, AIF1, S100A11, CTSS, FCER1G, SRSF7 
	   CD3D, CST3, FCGR3A, IL32, HSP90AA1, SSR2, CD79B, HLA-DQB1, LDHB, IFITM3 
PC_ 3 
Positive:  LTB, HLA-DRA, HLA-DRB1, HLA-DQB1, MS4A1, CD79A, HLA-DPB1, CD79B, CXCR4, HLA-DRB5 
	   HLA-DQA1, TCL1A, HLA-DPA1, HLA-DMB, SP100, HVCN1, TMEM123, SNHG7, LY86, NT5C 
	   FCER2, LINC00926, BANK1, FCRLA, PPAPDC1B, NCF1, HLA-DQA2, PIK3IP1, LDHB, TNFAIP8 
Negative:  TYROBP, FCER1G, LGALS1, NKG7, FCGR3A, PRF1, GZMB, GNLY, FGFBP2, CST3 
	   GZMA, CST7, LST1, S100A9, S100A8, AIF1, CTSW, SAT1, GZMM, IFITM3 
	   CCL5, GZMH, CCL4, IGFBP7, S100A11, RHOC, FCN1, SPON2, PSAP, KLRD1 
PC_ 4 
Positive:  CD3D, LDHB, IL7R, LTB, CD3E, NOSIP, TMEM123, MPHOSPH6, THYN1, TAGAP 
	   COTL1, CD2, EIF4A2, AIF1, TAF7, ACAP1, DNAJB1, MAL, SAT1, CTSS 
	   SAFB2, SRSF7, GYPC, ASNSD1, IFITM2, LST1, PIK3IP1, EPC1, TMUB1, TNFAIP8 
Negative:  HLA-DPB1, HLA-DRB1, HLA-DRA, FGFBP2, NKG7, HLA-DPA1, GZMB, GNLY, PRF1, CST7 
	   HLA-DQB1, CTSW, HLA-DQA1, HLA-DRB5, GZMA, GZMH, MS4A1, CD79A, CCL4, HLA-DMB 
	   CLIC3, AKR1C3, NT5C, ALOX5AP, C12orf75, SPON2, IGFBP7, KLRD1, CD79B, TTC38 
PC_ 5 
Positive:  FCGR3A, CD79B, SAT1, IFITM2, AIF1, LST1, RHOC, RP11-290F20.3, FCER1G, EPC1 
	   CTSS, IFITM3, TNFRSF1B, MS4A7, SERPINA1, MS4A1, CD68, RGS2, HNRNPF, HCK 
	   PSAP, C5AR1, HVCN1, CD79A, S100A11, COTL1, WARS, IFI30, ADAR, CARD16 
Negative:  LYZ, S100A9, LGALS2, FCER1A, S100A8, GSTP1, CLEC10A, CD3D, CST3, GPX1 
	   MS4A6A, IL1B, LDHB, HLA-DMA, LGALS3, RPL7L1, IL32, CD14, SRSF7, LCK 
	   CD3E, IL7R, TYMP, RGS1, FCGRT, CFP, GRN, ASGR1, HLA-DQA1, SSR2 
Warning: Number of dimensions changing from 19 to 10
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
07:22:40 UMAP embedding parameters a = 0.9922 b = 1.112
07:22:40 Read 80 rows and found 10 numeric columns
07:22:40 Using Annoy for neighbor search, n_neighbors = 30
07:22:40 Building Annoy index with metric = cosine, n_trees = 50
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:22:40 Writing NN index file to temp file /tmp/RtmpLASoiN/working_dir/RtmpSgQ6Iz/file93e3a50c26e83
07:22:40 Searching Annoy index using 1 thread, search_k = 3000
07:22:40 Annoy recall = 100%
07:22:42 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
07:22:45 Initializing from normalized Laplacian + noise (using RSpectra)
07:22:45 Commencing optimization for 500 epochs, with 1608 positive edges
Using method 'umap'
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
07:22:47 Optimization finished
gene.weights not specified, defaulting all weights to 1
Computing VAM distances for 1 gene sets, 80 cells and 220 genes.
Min set size: 5, median size: 5

Error: processing vignette 'VAM_pbmc_small_sctransform.Rnw' failed with diagnostics:
 chunk 6 
Error in methods::slot(object = object, name = layer) : 
  invalid type or length for slot name

--- failed re-building ‘VAM_pbmc_small_sctransform.Rnw’

SUMMARY: processing the following files failed:
  ‘VAM_pbmc_small.Rnw’ ‘VAM_pbmc_small_sctransform.Rnw’

Error: Vignette re-building failed.
Execution halted