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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings spatialFDA_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.0.0’
* 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 16.060  0.954  17.284
plotCrossMetricPerFov 15.831  0.511  16.559
functionalGam         12.082  0.463  12.750
plotMdl               11.926  0.334  12.463
plotMetricPerFov       7.672  0.417   8.292
plotFpca               7.639  0.285   8.138
functionalPCA          7.452  0.444   8.107
print.fpca             7.295  0.437   7.935
prepData               7.246  0.400   7.852
calcMetricPerFov       7.058  0.462   7.766
plotFbPlot             7.087  0.335   7.632
dot-dfToppp            6.473  0.449   7.145
dot-extractMetric      6.514  0.366   7.137
dot-speToDf            6.015  0.400   6.624
dot-loadExample        4.929  0.354   5.488
* 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-3.21-bioc/R/bin/R CMD INSTALL spatialFDA
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘spatialFDA’ ...
** this is package ‘spatialFDA’ version ‘1.0.0’
** using staged installation
** R
** 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 (2025-06-13) -- "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")
[1] "Calculating Gest of alpha"
[1] "Calculating markcorr of alpha"
[1] "Calculating Gcross from alpha to beta"
[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"

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:GenomeInfoDb':

    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 Gcross from alpha to beta"
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 beta"
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 89.020   3.438  93.114