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This page was generated on 2025-09-06 12:07 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 2047/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialFDA 1.1.16  (landing page)
Martin Emons
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/spatialFDA
git_branch: devel
git_last_commit: d89d20e
git_last_commit_date: 2025-09-04 10:46:09 -0400 (Thu, 04 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for spatialFDA on kjohnson3

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: 1.1.16
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_1.1.16.tar.gz
StartedAt: 2025-09-05 21:53:39 -0400 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 21:57:48 -0400 (Fri, 05 Sep 2025)
EllapsedTime: 248.8 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialFDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.1.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spatialFDA/DESCRIPTION’ ... OK
* this is package ‘spatialFDA’ version ‘1.1.16’
* 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
crossSpatialInference     7.636  0.468   8.474
plotCrossHeatmap          7.565  0.472   8.200
extractCrossInferenceData 7.572  0.445   8.418
calcCrossMetricPerFov     7.453  0.434   8.394
plotCrossMetricPerFov     6.707  0.276   7.253
* 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-arm64/Resources/library’
* installing *source* package ‘spatialFDA’ ...
** this is package ‘spatialFDA’ version ‘1.1.16’
** 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 (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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")
[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 0.989755562666551"
[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 0.989755562666551"
[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 0.882550254491114"
[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 0.827812664339213"
[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 0.998932745137641"
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 0.82317681350734"
[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 0.836697817694827"
[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 0.81767928566161"
[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 0.778212685014441"
[1] "Calculating Gcross from alpha to Tc"
[1] "Creating design matrix with Onset as reference"
[1] "The adjusted R-squared of the model is 0.778169684435464"
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 52 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 52 ]
> 
> proc.time()
   user  system elapsed 
 60.129   4.504  66.688 

Example timings

spatialFDA.Rcheck/spatialFDA-Ex.timings

nameusersystemelapsed
calcCrossMetricPerFov7.4530.4348.394
calcMetricPerFov3.1250.1463.500
crossSpatialInference7.6360.4688.474
dot-dfToppp2.9610.1733.375
dot-extractMetric2.8780.1313.222
dot-loadExample2.5490.1392.911
dot-speToDf2.8490.1553.198
extractCrossInferenceData7.5720.4458.418
functionalGam4.2390.3164.815
functionalPCA3.3620.1923.745
plotCrossHeatmap7.5650.4728.200
plotCrossMetricPerFov6.7070.2767.253
plotFbPlot2.8350.1413.177
plotFpca2.9570.1763.285
plotMdl4.2000.2814.687
plotMetricPerFov3.4150.1943.792
prepData2.7860.1543.082
print.fpca3.1770.1983.553
spatialInference4.0560.2974.594