## ----setup, echo=FALSE, results="hide"------------------------------------------------------------
knitr::opts_chunk$set(
  tidy = FALSE, cache = TRUE,
  dev = "png",
  package.startup.message = FALSE,
  message = FALSE, error = FALSE, warning = TRUE
)
options(width = 100)

## ----error, eval=FALSE----------------------------------------------------------------------------
#  library(variancePartition)
#  data(varPartData)
#  
#  # Redundant formula
#  # This example is an extreme example of redundancy
#  # but more subtle cases often show up in real data
#  form <- ~ Tissue + (1 | Tissue)
#  
#  fit <- dream(geneExpr[1:30, ], form, info)
#  
#  ## Warning in dream(geneExpr[1:30, ], form, info): Model failed for 29 responses.
#  ##   See errors with attr(., 'errors')
#  
#  # Extract gene-level errors
#  attr(fit, "errors")[1:2]
#  
#  ## gene1
#  ## "Error in lmerTest:::as_lmerModLT(model, devfun, tol = tol): (converted from warning)
#  ## Model may not have converged with 1 eigenvalue close to zero: -2.0e-09\n"
#  
#  ## gene2
#  ## "Error: (converted from warning) Model failed to converge
#  ##   with 1 negative eigenvalue: -1.5e-08\n"

## ----eval=FALSE, echo=TRUE------------------------------------------------------------------------
#  library(BiocParallel)
#  
#  # globally specify that all multithreading using bpiterate from BiocParallel
#  # should use 8 cores
#  register(SnowParam(8))

## ----eval=FALSE, echo=TRUE------------------------------------------------------------------------
#  fitExtractVarPartModel(..., BPPARAM = SnowParam(8))
#  
#  fitVarPartModel(..., BPPARAM = SnowParam(8))
#  
#  dream(..., BPPARAM = SnowParam(8))
#  
#  voomWithDreamWeights(..., BPPARAM = SnowParam(8))

## ----session, echo=FALSE--------------------------------------------------------------------------
sessionInfo()