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This page was generated on 2025-10-18 12:04 -0400 (Sat, 18 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 2074/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialFDA 1.1.21  (landing page)
Martin Emons
Snapshot Date: 2025-10-17 13:45 -0400 (Fri, 17 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  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialFDA_1.1.21.tar.gz
StartedAt: 2025-10-18 05:04:53 -0400 (Sat, 18 Oct 2025)
EndedAt: 2025-10-18 05:21:39 -0400 (Sat, 18 Oct 2025)
EllapsedTime: 1005.9 seconds
RetCode: 0
Status:   OK  
CheckDir: spatialFDA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings spatialFDA_1.1.21.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.1.21’
* 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 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     21.614  0.859  22.819
extractCrossInferenceData 22.024  0.260  22.615
plotCrossHeatmap          21.817  0.239  22.344
crossSpatialInference     21.354  0.502  22.142
plotCrossMetricPerFov     21.154  0.327  21.763
spatialInference          10.460  0.260  10.995
plotMdl                   10.435  0.284  10.999
functionalGam             10.349  0.270  10.904
plotFpca                   8.537  0.282   9.097
functionalPCA              8.485  0.292   9.102
plotFbPlot                 8.418  0.307   9.005
plotMetricPerFov           8.461  0.241   8.984
prepData                   8.301  0.232   8.812
print.fpca                 8.176  0.279   8.737
calcMetricPerFov           8.136  0.315   8.731
rMaxHeuristic              6.833  0.263   7.423
dot-dfToppp                6.243  0.306   6.832
dot-speToDf                6.158  0.359   6.799
dot-extractMetric          6.190  0.269   6.737
dot-loadExample            5.752  0.246   6.280
* 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


Installation output

spatialFDA.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL spatialFDA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-08-23 r88802) -- "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")
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 0.989755562666548
Calculating Gcross from alpha to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.989755562666548
Calculating Gcross from Tc to alpha
Creating design matrix with Non-diabetic as reference
The adjusted R-squared of the model is 0.697877461129732
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 0.828441693125797
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 0.836697817694868
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 0.778212685014441
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 
179.559   3.693 184.877 

Example timings

spatialFDA.Rcheck/spatialFDA-Ex.timings

nameusersystemelapsed
calcCrossMetricPerFov21.614 0.85922.819
calcMetricPerFov8.1360.3158.731
crossSpatialInference21.354 0.50222.142
dot-dfToppp6.2430.3066.832
dot-extractMetric6.1900.2696.737
dot-loadExample5.7520.2466.280
dot-speToDf6.1580.3596.799
extractCrossInferenceData22.024 0.26022.615
functionalGam10.349 0.27010.904
functionalPCA8.4850.2929.102
plotCrossHeatmap21.817 0.23922.344
plotCrossMetricPerFov21.154 0.32721.763
plotFbPlot8.4180.3079.005
plotFpca8.5370.2829.097
plotMdl10.435 0.28410.999
plotMetricPerFov8.4610.2418.984
prepData8.3010.2328.812
print.fpca8.1760.2798.737
rMaxHeuristic6.8330.2637.423
spatialInference10.460 0.26010.995