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This page was generated on 2025-10-11 12:05 -0400 (Sat, 11 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4586
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2068/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialFDA 1.1.21  (landing page)
Martin Emons
Snapshot Date: 2025-10-10 13:45 -0400 (Fri, 10 Oct 2025)
git_url: https://git.bioconductor.org/packages/spatialFDA
git_branch: devel
git_last_commit: 93358c0
git_last_commit_date: 2025-10-10 07:08:16 -0400 (Fri, 10 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for spatialFDA on lconway

To the developers/maintainers of the spatialFDA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialFDA.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: spatialFDA
Version: 1.1.21
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialFDA_1.1.21.tar.gz
StartedAt: 2025-10-11 01:17:31 -0400 (Sat, 11 Oct 2025)
EndedAt: 2025-10-11 01:30:31 -0400 (Sat, 11 Oct 2025)
EllapsedTime: 780.2 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialFDA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialFDA_1.1.21.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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     27.161  2.434  30.103
crossSpatialInference     24.817  1.564  26.775
extractCrossInferenceData 24.672  1.377  26.524
plotCrossHeatmap          24.506  1.522  26.449
plotCrossMetricPerFov     24.736  0.990  26.140
spatialInference          12.152  0.740  13.217
plotMdl                   11.974  0.769  13.139
functionalGam             11.524  0.859  12.705
plotMetricPerFov           9.734  0.673  10.818
functionalPCA              9.642  0.641  10.624
plotFpca                   9.532  0.636  10.450
plotFbPlot                 9.369  0.646  10.344
print.fpca                 9.233  0.634  10.176
calcMetricPerFov           8.877  0.597   9.723
prepData                   8.830  0.512   9.614
rMaxHeuristic              7.531  0.639   8.472
dot-dfToppp                7.046  0.421   7.692
dot-extractMetric          6.707  0.418   7.361
dot-speToDf                6.577  0.376   7.202
dot-loadExample            6.149  0.397   6.790
* 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


Installation output

spatialFDA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialFDA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)

Tests output

spatialFDA.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 0.989755562666547
Calculating Gcross from alpha to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666547
Calculating Gcross from Tc to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.69787746113006
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 0.828441693125798
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 0.836697817694751
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 0.778212685014439
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 
212.784  19.685 236.291 

Example timings

spatialFDA.Rcheck/spatialFDA-Ex.timings

nameusersystemelapsed
calcCrossMetricPerFov27.161 2.43430.103
calcMetricPerFov8.8770.5979.723
crossSpatialInference24.817 1.56426.775
dot-dfToppp7.0460.4217.692
dot-extractMetric6.7070.4187.361
dot-loadExample6.1490.3976.790
dot-speToDf6.5770.3767.202
extractCrossInferenceData24.672 1.37726.524
functionalGam11.524 0.85912.705
functionalPCA 9.642 0.64110.624
plotCrossHeatmap24.506 1.52226.449
plotCrossMetricPerFov24.736 0.99026.140
plotFbPlot 9.369 0.64610.344
plotFpca 9.532 0.63610.450
plotMdl11.974 0.76913.139
plotMetricPerFov 9.734 0.67310.818
prepData8.8300.5129.614
print.fpca 9.233 0.63410.176
rMaxHeuristic7.5310.6398.472
spatialInference12.152 0.74013.217