R Under development (unstable) (2024-01-31 r85845 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(countland)
> 
> test_check("countland")
countland object
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
Performing spectral clustering on dot products...
    done.
countland object
after removing empty cells and genes
the count matrix has 3 genes (rows)
    and 3 cells (columns)
the fraction of entries that are nonzero is 0.6667
Calculating dot products between rows...
    done.
Performing spectral embedding on dot products...
    done.
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1001 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.407
countland object
after removing empty cells and genes
the count matrix has 7 genes (rows)
    and 10 cells (columns)
the fraction of entries that are nonzero is 0.4429
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
subsampling 641 genes to a max total counts of 10
'as(<dgCMatrix>, "dgTMatrix")' is deprecated.
Use 'as(., "TsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
subsampling all cells to a standard sequencing depth of 10
subsampling 641 genes to a max total counts of 10
subsampling all cells to a standard sequencing depth of 10
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
after subsetting and removing empty cells and genes,
after removing empty cells and genes
new number of genes: 25
new number of cells: 100
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
after subsetting and removing empty cells and genes,
after removing empty cells and genes
new number of genes: 805
new number of cells: 25
countland object
after removing empty cells and genes
the count matrix has 1000 genes (rows)
    and 100 cells (columns)
the fraction of entries that are nonzero is 0.4074
new number of genes: 1000
new number of cells: 100
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 66 ]
> 
> proc.time()
   user  system elapsed 
   7.31    0.93    8.20