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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_1.1.21.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘spatialFDA/DESCRIPTION’ ... OK
* this is package ‘spatialFDA’ version ‘1.1.21’
* 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     23.899  0.914  25.131
extractCrossInferenceData 22.801  0.293  23.420
plotCrossHeatmap          22.545  0.293  23.239
crossSpatialInference     21.770  0.454  22.518
plotCrossMetricPerFov     21.801  0.218  22.306
functionalGam             11.180  0.268  11.730
plotMdl                   10.926  0.219  11.464
spatialInference          10.435  0.295  11.011
plotMetricPerFov           8.761  0.283   9.403
functionalPCA              8.691  0.217   9.364
calcMetricPerFov           8.581  0.264   9.123
plotFpca                   8.609  0.209   9.136
print.fpca                 8.508  0.270   9.058
plotFbPlot                 8.453  0.248   8.980
prepData                   8.425  0.273   8.980
rMaxHeuristic              6.912  0.261   7.451
dot-dfToppp                6.568  0.380   7.226
dot-speToDf                6.281  0.282   6.924
dot-extractMetric          6.149  0.294   6.729
dot-loadExample            5.820  0.192   6.293
* 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 ‘1.1.21’
** 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 (2025-08-23 r88802) -- "Great Square Root"
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

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
Calculating Gest of alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666548
Calculating Gcross from alpha to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666548
Calculating Gcross from Tc to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.697877461129732
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
Calculating Gcross from alpha to Tc
Creating design matrix with Non-diabetic as reference
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
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
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 0.836697817694868
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 0.778212685014441
Calculating Gcross from alpha to Tc
Creating design matrix with Onset as reference
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 
188.406   5.934 196.218