##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Statial.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Statial_1.2.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/Statial.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Statial/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Statial' version '1.2.4'
* 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 '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 ... OK
* 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 binding for global variable 'cellType'
calcContamination: no visible global function definition for 'predict'
calcContamination: no visible binding for global variable '.'
calcContamination: no visible binding for global variable 'cellID'
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 global function definition for 'p.adjust'
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'
inhomL: no visible binding for global variable 'j'
inhomL: no visible binding for global variable 'value'
inhomL: no visible binding for global variable 'i'
inhomL: no visible binding for global variable 'd'
inhomL: no visible binding for global variable 'cellTypeI'
inhomL: no visible binding for global variable 'cellTypeJ'
inhomL: no visible global function definition for '.'
inhomL: no visible binding for global variable 'wt'
inhomLParent: no visible binding for global variable 'd'
inhomLParent: no visible binding for global variable 'i'
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:
  . cellID cellType cellTypeI cellTypeJ coef d density fdr formula from
  i imageID j kontextual kontextualSd lm lower marker name original
  originalSd otherCellType p.adjust parent_name predict primaryCellType
  pt pval r rfMainCellProb rfMaxCellProb rfSecondLargestCellProb test
  to tval type upper value wt x y
Consider adding
  importFrom("stats", "coef", "density", "formula", "lm", "p.adjust",
             "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 145.04   0.72   18.22
plotStateChanges  104.87   7.20  112.10
getMarkerMeans     10.88   1.30   10.97
relabelKontextual   7.71   0.53   23.96
kontextPlot         3.43   0.05   12.08
kontextCurve        3.36   0.01  103.31
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/Statial.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Statial
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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.

> # 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 
   8.93    0.70    9.64