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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spatialFDA_1.1.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialFDA/DESCRIPTION’ ... OK
* this is package ‘spatialFDA’ version ‘1.1.13’
* 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
crossSpatialInference     38.972  0.858  57.401
extractCrossInferenceData 38.066  0.997  52.859
plotCrossHeatmap          38.174  0.825  58.567
plotCrossMetricPerFov     22.025  0.868  43.852
calcCrossMetricPerFov     20.132  1.346  33.787
plotMdl                   17.351  0.624  27.975
functionalGam             17.174  0.562  22.806
spatialInference          13.174  0.471  25.179
functionalPCA              8.867  0.507  15.163
plotFpca                   8.595  0.594  16.828
calcMetricPerFov           8.549  0.594  15.508
print.fpca                 8.561  0.543  13.686
plotMetricPerFov           8.172  0.367  13.423
plotFbPlot                 8.054  0.478  14.750
prepData                   7.906  0.500  14.569
dot-extractMetric          6.862  0.407  15.622
dot-dfToppp                6.923  0.342  11.993
dot-speToDf                6.690  0.332  12.162
dot-loadExample            5.946  0.464  10.254
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL spatialFDA
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘spatialFDA’ ...
** this is package ‘spatialFDA’ version ‘1.1.13’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
[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 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 0.989755559097488"
[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 0.989755559097488"
[1] "Calculating Gcross from acinar to alpha"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.882556049710155"
[1] "Calculating Gcross from alpha to acinar"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.827823624177584"
[1] "Calculating Gcross from acinar to acinar"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "The adjusted R-squared of the model is 0.998932742831901"
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 0.823182128822705"
[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 0.836699233704545"
[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 0.817685932200378"
[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 0.778217165250467"
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 50 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 50 ]
> 
> proc.time()
   user  system elapsed 
259.710   6.739 376.064