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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:Statial.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Statial_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Statial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Statial’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘cluster’ ‘spatstat.explore’ ‘treekoR’
  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
.Kontext: no visible binding for global variable ‘cellTypeI’
.Kontext: no visible binding for global variable ‘cellTypeJ’
.Kontext: no visible binding for global variable ‘weightParent’
.Kontext: no visible binding for global variable ‘edge’
.Kontext: no visible binding for global variable ‘i’
.Kontext: no visible binding for global variable ‘j’
.Lfunction: no visible binding for global variable ‘cellTypeI’
.Linhomfunction: no visible binding for global variable ‘cellTypeI’
.Linhomfunction: no visible binding for global variable ‘cellTypeJ’
.Linhomfunction: no visible binding for global variable ‘weightParent’
.Linhomfunction: no visible binding for global variable ‘edge’
.Linhomfunction: no visible binding for global variable ‘i’
.Linhomfunction: no visible binding for global variable ‘j’
Kontextual : <anonymous> : <anonymous>: no visible binding for global
  variable ‘d’
Kontextual: no visible binding for global variable ‘test’
Kontextual: no visible binding for global variable ‘parent_name’
KontextualCore: no visible global function definition for ‘.’
KontextualCore: no visible binding for global variable ‘i’
KontextualCore: no visible binding for global variable ‘cellTypeI’
KontextualCore: no visible binding for global variable ‘cellTypeJ’
KontextualCore: no visible binding for global variable ‘Kontext’
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 ‘indx’
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’
getParentPhylo: no visible binding for global variable ‘child’
getParentPhylo: no visible binding for global variable ‘parent’
getParentPhylo: no visible binding for global variable ‘children’
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 child children coef d
  density edge fdr formula from i imageID indx j kontextual
  kontextualSd lm lower marker name original originalSd otherCellType
  parent parent_name predict primaryCellType pt pval r rfMainCellProb
  rfMaxCellProb rfSecondLargestCellProb test to tval type upper value
  weightParent 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 ... WARNING
Undocumented arguments in Rd file 'getParentPhylo.Rd'
  ‘phylo_tree’
Documented arguments not in \usage in Rd file 'getParentPhylo.Rd':
  ‘phlyo_tree’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ...

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Statial
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘Statial’ ...
** this is package ‘Statial’ version ‘1.10.0’
** using staged installation
** R
** data
** 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 (Statial)