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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:Statial.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings Statial_1.9.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Statial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Statial’ version ‘1.9.0’
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
kontextCurve      317.323 67.852 236.974
plotStateChanges   70.348 27.127  97.498
calcContamination  70.892  0.650  41.761
kontextPlot        44.747 18.661  35.844
relabelKontextual  19.660 11.493  22.803
getMarkerMeans     15.265  0.567  15.422
getAbundances       5.270  0.171   5.442
getDistances        5.038  0.235   5.274
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/Statial.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Statial
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘Statial’ ...
** 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)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  9.949   1.095  11.032