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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialFDA_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘spatialFDA/DESCRIPTION’ ... OK
* this is package ‘spatialFDA’ version ‘1.2.1’
* 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 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 ... 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     22.194  0.962  23.515
crossSpatialInference     22.431  0.517  23.257
plotCrossHeatmap          22.044  0.298  22.626
extractCrossInferenceData 21.969  0.244  22.494
plotCrossMetricPerFov     21.582  0.326  22.183
spatialInference          11.225  0.294  11.808
functionalGam             11.190  0.326  11.838
plotMdl                   10.579  0.286  11.151
plotFpca                   8.811  0.322   9.410
plotMetricPerFov           8.845  0.279   9.410
plotFbPlot                 8.575  0.303   9.156
functionalPCA              8.637  0.220   9.133
calcMetricPerFov           8.391  0.321   8.993
print.fpca                 8.463  0.230   8.987
prepData                   8.451  0.222   8.983
rMaxHeuristic              6.996  0.230   7.553
dot-dfToppp                6.813  0.408   7.501
dot-extractMetric          6.519  0.342   7.148
dot-speToDf                6.256  0.360   6.892
dot-loadExample            5.746  0.183   6.209
* 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: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL spatialFDA
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘spatialFDA’ ...
** this is package ‘spatialFDA’ version ‘1.2.1’
** 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 version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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/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
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.989431977684907
Calculating Gcross from alpha to alpha
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.989431977684907
Calculating Gcross from Tc to alpha
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.69794011497926
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.823176814285881
Calculating Gcross from Tc to Tc
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.828441691986767
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.823176814285881
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
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
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
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.823176814285881
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
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.836697818050408
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.81767928694415
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.778212669866928
Calculating Gcross from alpha to Tc
Creating design matrix with Onset as reference
Note: pffr() now defaults to sandwich = "cluster" (cluster-robust covariance). Set sandwich = "none" for the previous default behavior. See ?pffr for details.
The adjusted R-squared of the model is 0.77816970322643
[ FAIL 0 | WARN 153 | SKIP 0 | PASS 55 ]

[ FAIL 0 | WARN 153 | SKIP 0 | PASS 55 ]
> 
> proc.time()
   user  system elapsed 
191.765   3.518 196.863