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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialFDA_1.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/spatialFDA.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialFDA/DESCRIPTION’ ... OK
* this is package ‘spatialFDA’ version ‘1.3.1’
* 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 ‘spatialFDA’ 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
extractCrossInferenceData 9.986  0.935  11.746
plotCrossHeatmap          9.743  1.010  12.186
crossSpatialInference     9.519  0.958  11.369
calcCrossMetricPerFov     9.394  0.495  10.591
plotCrossMetricPerFov     8.917  0.532  10.312
spatialInference          4.865  0.429   6.204
functionalGam             4.729  0.502   5.946
plotMdl                   4.682  0.500   5.930
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-spatialInference.R:65:3'): wrapper function gives same result as manual computation ──
  Expected `identical(mdl1$coefficients, mdl2$coefficients)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 4 | WARN 165 | SKIP 0 | PASS 52 ]
  Error:
  ! Test failures.
  Execution halted
* 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
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/spatialFDA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialFDA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘spatialFDA’ ...
** this is package ‘spatialFDA’ version ‘1.3.1’
** using staged installation
** R
** 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 (spatialFDA)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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(spatialFDA)
> 
> test_check("spatialFDA")
imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
require("SingleCellExperiment")
Calculating Gest of alpha
Calculating markcorr of alpha
Calculating Gcross from alpha to Tc
Calculating Gest of alpha
Calculating Gcross from alpha to beta
Calculating Gcross from alpha to alpha
Calculating Gcross from beta to alpha
Calculating Gcross from delta to alpha
Calculating Gcross from alpha to beta
Calculating Gcross from beta to beta
Calculating Gcross from delta to beta
Calculating Gcross from alpha to delta
Calculating Gcross from beta to delta
Calculating Gcross from delta to delta
alpha
Calculating Kdot of alpha
beta
Calculating Kdot of beta
delta
Calculating Kdot of delta
Calculating Lcross from alpha to Tc
Calculating Gcross from alpha to Tc
Calculating Gcross from alpha to Tc
Calculating Gest of beta

Attaching package: 'tidyr'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'dplyr'

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:GenomicRanges':

    intersect, setdiff, union

The following object is masked from 'package:Seqinfo':

    intersect

The following objects are masked from 'package:IRanges':

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, setequal, union

The following object is masked from 'package:generics':

    explain

The following object is masked from 'package:matrixStats':

    count

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Calculating Gest of alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666552
Calculating Gcross from alpha to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666551
Calculating Gcross from Tc to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.697877461130412
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.82317681350734
Calculating Gcross from Tc to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.828441693125797
Saving _problems/test-crossSpatialInference-36.R
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.82317681350734
Saving _problems/test-crossSpatialInference-54.R
Saving _problems/test-crossSpatialInference-59.R
imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Calculating Gcross from alpha to Tc
imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Calculating Gcross from alpha to Tc
imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
Calculating Gcross from alpha to Tc
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.82317681350734
Saving _problems/test-spatialInference-65.R
Calculating Gest of beta
Can not fit a model if one condition has no images with curves
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.836697817694493
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.817679285661611
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.778212685014435
Calculating Gcross from alpha to Tc
Creating design matrix with Onset as reference
The adjusted R-squared of the model is 0.778169684435463
Calculating Gcross from alpha to Tc
Creating design matrix with Onset as reference
The adjusted R-squared of the model is 0.778407753116236
[ FAIL 4 | WARN 165 | SKIP 0 | PASS 52 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-crossSpatialInference.R:36:3'): cross function with one element is identical to the single
          function call ──
Expected `identical(mdl1$coefficients, mdl2$coefficients)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

── Failure ('test-crossSpatialInference.R:54:13'): cross function with one element is identical to the single
          function call ──
Expected `identical(mdl3$coefficients, mdl4$coefficients)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

── Failure ('test-crossSpatialInference.R:59:13'): cross function with one element is identical to the single
          function call in the residuals ──
Expected `identical(mdl3$residuals, mdl4$residuals)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

── Failure ('test-spatialInference.R:65:3'): wrapper function gives same result as manual computation ──
Expected `identical(mdl1$coefficients, mdl2$coefficients)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 


[ FAIL 4 | WARN 165 | SKIP 0 | PASS 52 ]
Error:
! Test failures.
Execution halted