##############################################################################
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###
### Running command:
###
###   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.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL miloR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'miloR' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'graph' in package 'miloR'
** help
*** installing help indices
  converting help for package 'miloR'
    finding HTML links ... done
    Milo                                    html  
    finding level-2 HTML links ... done

    annotateNhoods                          html  
    buildFromAdjacency                      html  
    buildGraph                              html  
    buildNhoodGraph                         html  
    calcNhoodDistance                       html  
    calcNhoodExpression                     html  
    countCells                              html  
    findNhoodGroupMarkers                   html  
    findNhoodMarkers                        html  
    graphSpatialFDR                         html  
    groupNhoods                             html  
    makeNhoods                              html  
    matrixORMatrix-class                    html  
    methods                                 html  
    miloR-package                           html  
    plotDAbeeswarm                          html  
    plotNhoodExpressionDA                   html  
    plotNhoodGraph                          html  
    plotNhoodGraphDA                        html  
    plotNhoodMA                             html  
    plotNhoodSizeHist                       html  
    sim_discrete                            html  
    sim_trajectory                          html  
    testDiffExp                             html  
    testNhoods                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (miloR)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(miloR)
Loading required package: edgeR
Loading required package: limma
> require(mvtnorm)
Loading required package: mvtnorm
> require(scran)
Loading required package: scran
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'SingleCellExperiment'

The following object is masked from 'package:edgeR':

    cpm

Loading required package: scuttle
> require(scater)
Loading required package: scater
Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:limma':

    plotMDS

> require(MASS)
Loading required package: MASS
> 
> test_check("miloR")
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
Coefficients not estimable: ConditionA 
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]

== Failed tests ================================================================
-- Error (test_buildFromAdjacency.R:56:1): (code run outside of `test_that()`) --
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::buildFromAdjacency(as(sim1.adj, "matrix"), k = 21) at test_buildFromAdjacency.R:56:0
 2.   \-miloR::Milo()
 3.     \-miloR:::.emptyMilo()
 4.       \-methods::new(...)
 5.         +-methods::initialize(value, ...)
 6.         \-methods::initialize(value, ...)
 7.           \-methods::validObject(.Object)
-- 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