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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_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/spatialFDA.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 ... ERROR
Running examples in ‘spatialFDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCrossMetricPerFov
> ### Title: Plot a cross type spatial metric per field of view
> ### Aliases: plotCrossMetricPerFov
> 
> ### ** Examples
> 
> # retrieve example data from Damond et al. (2019)
> spe <- .loadExample()
imcdatasets not installed.
  Full functionality, documentation, and loading of data might not be possible without installing
loading from cache
require(“SingleCellExperiment”)
> metricRes <- calcCrossMetricPerFov(spe, c("alpha", "beta"),
+     subsetby = "image_number", fun = "Gcross", marks = "cell_type",
+     rSeq = seq(0, 50, length.out = 50), by = c(
+         "patient_stage", "patient_id",
+         "image_number"
+     ),
+     ncores = 1
+ )
[1] "Calculating Gcross from alpha to alpha"
[1] "Calculating Gcross from beta to alpha"
[1] "Calculating Gcross from alpha to beta"
[1] "Calculating Gcross from beta to beta"
> 
> metricRes$ID <- paste0(
+  metricRes$patient_stage, "|", metricRes$patient_id
+ )
> 
> metricRes <- subset(metricRes, image_number %in% c(138, 139, 140))
> p <- plotCrossMetricPerFov(metricRes,
+     theo = TRUE, correction = "rs",
+     x = "r", imageId = "image_number", ID = "ID"
+ )
Error: Can't find method for generic `&(e1, e2)`:
- e1: <patchwork>
- e2: <theme>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
calcCrossMetricPerFov 22.136  1.529  27.527
functionalGam         16.888  1.135  28.184
functionalPCA          9.655  0.865  17.531
calcMetricPerFov       8.943  0.714  12.507
dot-dfToppp            7.813  0.923  11.566
dot-extractMetric      7.825  0.642  11.246
dot-speToDf            7.360  0.614  10.751
dot-loadExample        5.713  0.506   9.106
* 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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/spatialFDA.Rcheck/00check.log’
for details.

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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-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 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 
143.856   3.397 157.100