Running 'testthat.R' [35s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(Seurat)
  Loading required package: ggplot2
  Loading required package: cowplot
  
  Attaching package: 'cowplot'
  
  The following object is masked from 'package:ggplot2':
  
      ggsave
  
  Loading required package: Matrix
  > 
  > test_check("Seurat")
  Running CCA
  Merging objects
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Rescaling group 1
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Rescaling group 2
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Aligning dimension 1
  Aligning dimension 2
  Aligning dimension 3
  Aligning dimension 4
  Aligning dimension 5
  Calculating for group1 
  	 Separating group1 cells
  	 Running Dimensional Reduction 
  Calculating for group2 
  	 Separating group2 cells
  	 Running Dimensional Reduction 
  Computing nearest neighbor graph
  Computing SNN
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  -- 1. Error: (unknown) (@test_preprocessing.R#128)  ----------------------------
  attempt to set an attribute on NULL
  1: ScaleData(object, vars.to.regress = "nUMI", genes.use = rownames(object@data)[1:10], 
         display.progress = F, model.use = "linear") at testthat/test_preprocessing.R:128
  2: RegressOutResid(object = object, vars.to.regress = vars.to.regress, genes.regress = genes.use, 
         use.umi = use.umi, model.use = model.use, display.progress = display.progress, 
         do.par = do.par, num.cores = num.cores)
  3: foreach(i = 1:max.bin, .combine = "rbind", .options.snow = opts) %dopar% {
         genes.bin.regress <- rownames(x = data.use)[bin.ind == i]
         gene.expr <- as.matrix(x = data.use[genes.bin.regress, , drop = FALSE])
         new.data <- do.call(rbind, lapply(X = genes.bin.regress, FUN = function(x) {
             regression.mat <- cbind(latent.data, gene.expr[x, ])
             colnames(x = regression.mat) <- c(colnames(x = latent.data), "GENE")
             fmla <- as.formula(object = paste0("GENE ", " ~ ", paste(vars.to.regress, 
                 collapse = "+")))
             if (model.use == "linear") {
                 return(lm(formula = fmla, data = regression.mat)$residuals)
             }
             if (model.use == "poisson") {
                 return(residuals(object = glm(formula = fmla, data = regression.mat, 
                     family = "poisson"), type = "pearson"))
             }
             if (model.use == "negbinom") {
                 return(NBResiduals(fmla = fmla, regression.mat = regression.mat, gene = x))
             }
         }))
         new.data
     }
  4: e$fun(obj, substitute(ex), parent.frame(), e$data)
  5: comp(expr, env = envir, options = list(suppressUndefined = TRUE))
  6: genCode(e, cntxt)
  7: cmp(e, cb, cntxt)
  8: cmpCall(e, cb, cntxt)
  9: tryInline(call, cb, cntxt)
  10: h(e, cb, cntxt)
  ...
  34: cmpCall(e, cb, cntxt)
  35: tryInline(call, cb, cntxt)
  36: h(e, cb, cntxt)
  37: cmp(e[[i]], cb, ncntxt)
  38: cmpCall(e, cb, cntxt)
  39: tryInline(call, cb, cntxt)
  40: h(e, cb, cntxt)
  41: cmpComplexAssign(symbol, lhs, value, superAssign, cb, cntxt)
  42: cmpSetterCall(flatPlace[[1]], value, cb, ncntxt)
  43: cmpCallArgs(place[-c(1, 2)], cb, ncntxt)
  
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  NormalizeData has not been run, therefore ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
  ScaleData is running on non-normalized values. Recommended workflow is to run NormalizeData first.
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Calculating gene means
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating gene variance to mean ratios
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Running CCA
  Merging objects
  Performing log-normalization
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Running CCA
  Computing nearest neighbor graph
  Computing SNN
  == testthat results  ===========================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_preprocessing.R#128) 
  
  Error: testthat unit tests failed
  Execution halted