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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spicyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spicyR’ version ‘1.18.1’
* 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 ‘spicyR’ 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 code 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
.format_data: no visible binding for global variable ‘imageID’
.format_data: no visible binding for global variable ‘cellType’
bubblePlot: no visible binding for global variable ‘parent’
bubblePlot: no visible binding for global variable ‘cellTypeB_id’
bubblePlot: no visible binding for global variable ‘cellTypeB_numeric’
bubblePlot: no visible binding for global variable ‘condition’
convPairs: no visible binding for global variable ‘rowname’
convPairs: no visible binding for global variable ‘cellType_from’
convPairs: no visible binding for global variable ‘cellType_to’
convPairs: no visible binding for global variable ‘one’
convPairs: no visible binding for global variable ‘n_close’
convPairs: no visible binding for global variable ‘test’
convPairs: no visible binding for global variable ‘association’
getCellSummary: no visible binding for global variable ‘cellID’
getCellSummary: no visible binding for global variable ‘imageCellID’
getCellSummary: no visible binding for global variable ‘x’
getCellSummary: no visible binding for global variable ‘y’
getCellSummary: no visible binding for global variable ‘cellType’
getCellSummary: no visible binding for global variable ‘.’
getCellType: no visible binding for global variable ‘cellType’
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’
inhomLPair: no visible binding for global variable ‘cellTypeI’
inhomLPair: no visible binding for global variable ‘cellTypeJ’
plotImage: no visible binding for global variable ‘x’
plotImage: no visible binding for global variable ‘y’
plotImage: no visible binding for global variable ‘density’
plotImage: no visible binding for global variable ‘cellTypeNew’
spatialSurv : <anonymous>: no visible global function definition for
  ‘pchisq’
spatialSurv: no visible binding for global variable ‘test’
spatialSurv: no visible binding for global variable ‘coef’
spatialSurv: no visible binding for global variable ‘se.coef’
spatialSurv: no visible binding for global variable ‘p.value’
spicyBoxPlot: no visible binding for global variable ‘condition’
survBubble: no visible binding for global variable ‘test’
survBubble: no visible binding for global variable ‘parent’
survBubble: no visible binding for global variable ‘to’
survBubble: no visible binding for global variable ‘from’
survBubble: no visible binding for global variable ‘p.value’
survBubble: no visible binding for global variable ‘logP’
survBubble: no visible binding for global variable ‘coef’
survBubble: no visible binding for global variable ‘sig’
Undefined global functions or variables:
  . association cellID cellType cellTypeB_id cellTypeB_numeric
  cellTypeI cellTypeJ cellTypeNew cellType_from cellType_to coef
  condition d density from i imageCellID imageID j logP n_close one
  p.value parent pchisq rowname se.coef sig test to value wt x y
Consider adding
  importFrom("stats", "coef", "density", "pchisq")
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 LazyData ... 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
spicy       35.561  0.235  36.011
convPairs   25.273  1.215  26.996
getPairwise 11.487  0.417  12.009
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spicyR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘spicyR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (spicyR)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(spicyR)
> 
> test_check("spicyR")
Skipping argument checks as `getPairwise()` is being called within `spicy()`
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
100.856   3.058 105.355