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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miloR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings miloR_1.3.4.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/miloR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'miloR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miloR' version '1.3.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'miloR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::disableValidity'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDAbeeswarm: no visible binding for global variable 'SpatialFDR'
plotDAbeeswarm: no visible binding for global variable 'is_signif'
plotDAbeeswarm: no visible binding for global variable 'logFC'
plotDAbeeswarm: no visible binding for global variable 'Nhood'
plotDAbeeswarm: no visible binding for global variable 'logFC_color'
plotNhoodExpressionDA: no visible binding for global variable 'Nhood'
plotNhoodExpressionDA: no visible binding for global variable 'logFC'
plotNhoodExpressionDA: no visible binding for global variable
  'SpatialFDR'
plotNhoodExpressionDA: no visible binding for global variable
  'logFC_rank'
plotNhoodExpressionDA: no visible binding for global variable '.'
plotNhoodExpressionDA: no visible binding for global variable
  'is_signif'
plotNhoodExpressionDA: no visible binding for global variable 'feature'
plotNhoodExpressionDA: no visible binding for global variable
  'avg_expr'
plotNhoodExpressionDA: no visible binding for global variable 'label'
plotNhoodExpressionGroups: no visible binding for global variable
  'Nhood'
plotNhoodExpressionGroups: no visible binding for global variable
  'NhoodGroup'
plotNhoodExpressionGroups: no visible binding for global variable
  'logFC'
plotNhoodExpressionGroups: no visible binding for global variable
  'feature'
plotNhoodExpressionGroups: no visible binding for global variable
  'logFC_rank'
plotNhoodExpressionGroups: no visible binding for global variable
  'avg_expr'
plotNhoodExpressionGroups: no visible binding for global variable '.'
plotNhoodExpressionGroups: no visible binding for global variable
  'label'
plotNhoodGraph: no visible binding for global variable 'weight'
plotNhoodGraph: no visible binding for global variable 'size'
plotNhoodGraphDA: no visible binding for global variable 'layout'
plotNhoodGroups: no visible binding for global variable 'layout'
plotNhoodMA: no visible binding for global variable 'logCPM'
plotNhoodMA: no visible binding for global variable 'logFC'
plotNhoodMA: no visible binding for global variable 'Sig'
plotNhoodSizeHist: no visible binding for global variable 'nh_size'
Undefined global functions or variables:
  . Nhood NhoodGroup Sig SpatialFDR avg_expr feature is_signif label
  layout logCPM logFC logFC_color logFC_rank nh_size size weight
Consider adding
  importFrom("graphics", "layout")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: findNhoodGroupMarkers.Rd:79-81: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'miloR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildFromAdjacency
> ### Title: Build a graph from an input adjacency matrix
> ### Aliases: buildFromAdjacency
> 
> ### ** Examples
> 
> r <- 1000
> c <- 1000
> k <- 35
> m <- floor(matrix(runif(r*c), r, c))
> for(i in seq_along(1:r)){
+     m[i, sample(1:c, size=k)] <- 1
+ }
> 
> milo <- buildFromAdjacency(m)
Casting to sparse matrix format
Inferring k from matrix
Error in validObject(.Object) : 
  invalid class "Milo" object: 1: invalid object for slot "int_elementMetadata" in class "Milo": got class "S4", should be or extend class "DataFrame"
invalid class "Milo" object: 2: invalid object for slot "int_colData" in class "Milo": got class "S4", should be or extend class "DataFrame"
Calls: buildFromAdjacency ... .emptyMilo -> new -> initialize -> initialize -> validObject
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Error (test_classes.R:86:5): Milo can instantiate an empty object -----------
  Error in `validObject(.Object)`: invalid class "Milo" object: 1: invalid object for slot "int_elementMetadata" in class "Milo": got class "S4", should be or extend class "DataFrame"
  invalid class "Milo" object: 2: invalid object for slot "int_colData" in class "Milo": got class "S4", should be or extend class "DataFrame"
  Backtrace:
      x
   1. \-miloR::Milo() at test_classes.R:86:4
   2.   \-miloR:::.emptyMilo()
   3.     \-methods::new(...)
   4.       +-methods::initialize(value, ...)
   5.       \-methods::initialize(value, ...)
   6.         \-methods::validObject(.Object)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/miloR.Rcheck/00check.log'
for details.