##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Statial.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Statial_1.4.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Statial.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Statial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Statial’ version ‘1.4.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Statial’ 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
Namespaces in Imports field not imported from:
  ‘data.table’ ‘spatstat.explore’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.generateBPParam’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Kontextual: no visible binding for global variable ‘test’
Kontextual: no visible binding for global variable ‘parent_name’
calcContamination: no visible global function definition for ‘predict’
calcContamination: no visible binding for global variable ‘.’
calcContamination: no visible binding for global variable ‘cellID’
calcKontextual: no visible binding for global variable ‘d’
calcKontextual: no visible binding for global variable ‘i’
calcKontextual: no visible binding for global variable ‘cellTypeI’
calcKontextual: no visible binding for global variable ‘cellTypeJ’
calcKontextual: no visible binding for global variable ‘Kontext’
calcStateChanges: no visible binding for global variable ‘cellID’
calcStateChanges: no visible binding for global variable
  ‘rfMaxCellProb’
calcStateChanges: no visible binding for global variable
  ‘rfSecondLargestCellProb’
calcStateChanges: no visible binding for global variable
  ‘rfMainCellProb’
calcStateChanges: no visible binding for global variable
  ‘primaryCellType’
calcStateChanges: no visible binding for global variable
  ‘otherCellType’
calcStateChanges: no visible binding for global variable ‘coef’
calcStateChanges: no visible binding for global variable ‘tval’
calcStateChanges: no visible binding for global variable ‘pval’
calcStateChanges: no visible binding for global variable ‘fdr’
calculateChangesMarker : <anonymous>: no visible global function
  definition for ‘pt’
distanceCalculator: no visible binding for global variable ‘cellType’
distanceCalculator: no visible binding for global variable ‘d’
getMarkerMeans: no visible binding for global variable ‘value’
kontextCurve: no visible binding for global variable ‘type’
kontextCurve: no visible binding for global variable ‘r’
kontextCurve: no visible binding for global variable ‘original’
kontextCurve: no visible binding for global variable ‘kontextual’
kontextPlot: no visible binding for global variable ‘r’
kontextPlot: no visible binding for global variable ‘kontextualSd’
kontextPlot: no visible binding for global variable ‘originalSd’
kontextPlot: no visible binding for global variable ‘value’
kontextPlot: no visible binding for global variable ‘name’
kontextPlot: no visible binding for global variable ‘lower’
kontextPlot: no visible binding for global variable ‘upper’
parentCombinations: no visible binding for global variable ‘from’
parentCombinations: no visible binding for global variable ‘to’
plotStateChanges: no visible global function definition for ‘lm’
plotStateChanges: no visible global function definition for ‘formula’
plotStateChanges: no visible global function definition for ‘predict’
plotStateChanges: no visible binding for global variable ‘x’
plotStateChanges: no visible binding for global variable ‘y’
plotStateChanges: no visible binding for global variable ‘density’
plotStateChanges: no visible binding for global variable ‘lm’
prepMatrix: no visible binding for global variable ‘imageID’
prepMatrix: no visible binding for global variable ‘kontextual’
prepMatrix: no visible binding for global variable ‘primaryCellType’
prepMatrix: no visible binding for global variable ‘otherCellType’
prepMatrix: no visible binding for global variable ‘marker’
prepMatrix: no visible binding for global variable ‘type’
relabel: no visible binding for global variable ‘cellType’
Undefined global functions or variables:
  . Kontext cellID cellType cellTypeI cellTypeJ coef d density fdr
  formula from i imageID kontextual kontextualSd lm lower marker name
  original originalSd otherCellType parent_name predict primaryCellType
  pt pval r rfMainCellProb rfMaxCellProb rfSecondLargestCellProb test
  to tval type upper value x y
Consider adding
  importFrom("stats", "coef", "density", "formula", "lm", "predict",
             "pt")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
calcContamination 197.165  4.017  19.878
kontextCurve      157.171 22.691 139.461
kontextPlot       118.068 11.266   6.624
plotStateChanges   87.735 15.183 103.535
relabelKontextual  31.833  8.109  17.715
getMarkerMeans      8.745  0.409   9.212
getAbundances       5.247  0.519   5.811
getDistances        5.042  0.509   5.578
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/Statial.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Statial
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Statial’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (Statial)

R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(Statial)
> 
> test_check("Statial")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 11.446   0.597  12.080