##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/spatialFDA.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 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
calcCrossMetricPerFov     33.176  1.881  35.537
extractCrossInferenceData 26.695  1.378  28.407
plotCrossHeatmap          25.675  1.323  27.321
plotCrossMetricPerFov     25.730  1.007  27.082
crossSpatialInference     24.575  1.255  26.188
functionalGam             11.815  0.794  12.881
plotMdl                   11.786  0.718  12.752
spatialInference          11.420  0.601  12.277
plotMetricPerFov           9.901  0.598  10.753
plotFbPlot                 9.883  0.544  10.677
functionalPCA              9.725  0.568  10.531
plotFpca                   9.698  0.581  10.552
print.fpca                 9.553  0.566  10.414
prepData                   9.423  0.563  10.226
calcMetricPerFov           9.309  0.638  10.219
rMaxHeuristic              7.753  0.601   8.579
dot-dfToppp                7.675  0.476   8.402
dot-extractMetric          7.473  0.432   8.185
dot-speToDf                7.033  0.468   7.698
dot-loadExample            5.294  0.333   5.853
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialFDA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
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")
see ?imcdatasets and browseVignettes('imcdatasets') for documentation
loading from cache
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:EBImage':

    combine

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

see ?imcdatasets and browseVignettes('imcdatasets') for documentation
loading from cache
Calculating Gest of alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666547
Calculating Gcross from alpha to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666547
Calculating Gcross from Tc to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.69787746113006
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 0.828441693125798
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.82317681350734
see ?imcdatasets and browseVignettes('imcdatasets') for documentation
loading from cache
Calculating Gcross from alpha to Tc
see ?imcdatasets and browseVignettes('imcdatasets') for documentation
loading from cache
Calculating Gcross from alpha to Tc
see ?imcdatasets and browseVignettes('imcdatasets') for documentation
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
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 0.836697817694751
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.817679285661609
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.778212685014439
Calculating Gcross from alpha to Tc
Creating design matrix with Onset as reference
The adjusted R-squared of the model is 0.778169684435465
Calculating Gcross from alpha to Tc
Creating design matrix with Onset as reference
The adjusted R-squared of the model is 0.778407752943767
[ FAIL 0 | WARN 165 | SKIP 0 | PASS 56 ]

[ FAIL 0 | WARN 165 | SKIP 0 | PASS 56 ]
> 
> proc.time()
   user  system elapsed 
246.362  16.312 265.629