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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spicyR_1.21.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spicyR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spicyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘spicyR’ version ‘1.21.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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 ‘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 loading without being on the library search path ... 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’
imageCrossPlot: no visible binding for global variable ‘test’
imageCrossPlot: no visible binding for global variable ‘to’
imageCrossPlot: no visible binding for global variable ‘from’
imageCrossPlot: no visible binding for global variable ‘size_clamped’
imageCrossPlot: 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’
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’
spicy: no visible global function definition for ‘relevel’
spicyBoxPlot: no visible binding for global variable ‘condition’
spicyBoxPlot: no visible binding for global variable ‘pairwiseAssoc’
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 pairwiseAssoc parent pchisq relevel rowname se.coef sig
  size_clamped test to value wt x y
Consider adding
  importFrom("stats", "coef", "density", "pchisq", "relevel")
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 ... ERROR
Running examples in ‘spicyR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convPairs
> ### Title: Converts colPairs object into an abundance matrix based on
> ###   number of nearby interactions for every cell type.
> ### Aliases: convPairs
> 
> ### ** Examples
> 
> data("diabetesData")
> images <- c("A09", "A11", "A16", "A17")
> diabetesData <- diabetesData[
+   , SummarizedExperiment::colData(diabetesData)$imageID %in% images
+ ]
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: [ ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/spicyR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL spicyR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘spicyR’ ...
** this is package ‘spicyR’ version ‘1.21.8’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(spicyR)
> 
> test_check("spicyR")
Dropping unused levels. Using stage = Non-diabetic as base comparison group. If this is not the desired base group, please convert cells$stage into a factor and change the order of levels(cells$stage) so that the base group is at index 1.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 61.123   1.100  77.445