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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_1.1.17.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialFDA/DESCRIPTION’ ... OK
* this is package ‘spatialFDA’ version ‘1.1.17’
* 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
calcCrossMetricPerFov     27.160  2.354  29.939
plotCrossMetricPerFov     25.540  0.946  26.848
plotCrossHeatmap          24.734  1.470  26.634
extractCrossInferenceData 24.470  1.431  26.275
crossSpatialInference     24.013  1.483  25.830
functionalGam             11.399  0.861  12.576
spatialInference          11.273  0.711  12.276
plotMdl                   10.778  0.742  11.889
plotMetricPerFov           9.542  0.670  10.473
plotFbPlot                 9.360  0.630  10.257
functionalPCA              9.382  0.555  10.177
print.fpca                 9.003  0.608   9.851
calcMetricPerFov           8.784  0.547   9.571
plotFpca                   8.332  0.465   9.147
prepData                   8.110  0.439   8.787
dot-extractMetric          6.773  0.393   7.429
dot-dfToppp                6.707  0.445   7.348
dot-speToDf                6.531  0.347   7.125
rMaxHeuristic              6.144  0.488   6.851
dot-loadExample            5.993  0.382   6.651
* 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: OK

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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/4.5-x86_64/Resources/library’
* installing *source* package ‘spatialFDA’ ...
** this is package ‘spatialFDA’ version ‘1.1.17’
** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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(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")
[1] "Calculating Gest of alpha"
[1] "Calculating markcorr of alpha"
[1] "Calculating Gcross from alpha to Tc"
[1] "Calculating Gest of alpha"
[1] "Calculating Gcross from alpha to beta"
[1] "Calculating Gcross from alpha to alpha"
[1] "Calculating Gcross from beta to alpha"
[1] "Calculating Gcross from delta to alpha"
[1] "Calculating Gcross from alpha to beta"
[1] "Calculating Gcross from beta to beta"
[1] "Calculating Gcross from delta to beta"
[1] "Calculating Gcross from alpha to delta"
[1] "Calculating Gcross from beta to delta"
[1] "Calculating Gcross from delta to delta"
[1] "alpha"
[1] "Calculating Kdot of alpha"
[1] "beta"
[1] "Calculating Kdot of beta"
[1] "delta"
[1] "Calculating Kdot of delta"
[1] "Calculating Lcross from alpha to Tc"
[1] "Calculating Gcross from alpha to Tc"
[1] "Calculating Gcross from alpha to Tc"
[1] "Calculating Gest of beta"

Attaching package: 'tidyr'

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

    expand

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

    matches


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 object is masked from 'package:testthat':

    matches

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
[1] "Calculating Gest of alpha"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.989755562666547"
[1] "Calculating Gcross from alpha to alpha"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.989755562666547"
[1] "Calculating Gcross from Tc to alpha"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.69787746113006"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.82317681350734"
[1] "Calculating Gcross from Tc to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.828441693125798"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.82317681350734"
imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
[1] "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
[1] "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
[1] "Calculating Gcross from alpha to Tc"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.82317681350734"
[1] "Calculating Gest of beta"
[1] "Can not fit a model if one condition has no images with curves"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.836697817694751"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.817679285661609"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.778212685014439"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Onset as reference"
[1] "The adjusted R-squared of the model is 0.778169684435465"
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 55 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 55 ]
> 
> proc.time()
   user  system elapsed 
210.513  17.175 231.143