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This page was generated on 2025-07-29 12:09 -0400 (Tue, 29 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4516
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 2038/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
spatialFDA 1.1.3  (landing page)
Martin Emons
Snapshot Date: 2025-07-28 13:25 -0400 (Mon, 28 Jul 2025)
git_url: https://git.bioconductor.org/packages/spatialFDA
git_branch: devel
git_last_commit: 5e8d7ce
git_last_commit_date: 2025-07-25 09:18:13 -0400 (Fri, 25 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 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 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: 1.1.3
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_1.1.3.tar.gz
StartedAt: 2025-07-29 00:03:05 -0400 (Tue, 29 Jul 2025)
EndedAt: 2025-07-29 00:14:54 -0400 (Tue, 29 Jul 2025)
EllapsedTime: 709.2 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_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.1.3’
* 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 ... NOTE
crossSpatialInference : <anonymous>: no visible binding for global
  variable ‘continous’
spatialInference: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID continous
* 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 44.145  2.539  47.171
calcCrossMetricPerFov 19.134  1.657  23.238
plotCrossMetricPerFov 16.532  0.617  17.412
plotMdl               14.700  0.732  15.719
spatialInference      14.505  0.739  15.511
functionalGam         14.339  0.769  15.358
plotMetricPerFov       8.171  0.429   8.852
plotFbPlot             8.049  0.409   8.690
print.fpca             8.057  0.380   8.655
plotFpca               8.062  0.368   8.652
functionalPCA          7.845  0.415   8.653
calcMetricPerFov       7.695  0.489   8.399
prepData               7.654  0.393   8.310
dot-dfToppp            6.875  0.384   7.480
dot-extractMetric      6.537  0.367   7.106
dot-speToDf            6.569  0.320   7.102
dot-loadExample        6.167  0.369   6.748
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck/00check.log’
for details.


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 ‘1.1.3’
** 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)

Tests output

spatialFDA.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "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")
[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: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] "Calculating Gcross from alpha to alpha"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "Calculating Gcross from acinar to alpha"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "Calculating Gcross from alpha to acinar"
[1] "Creating design matrix with Non-diabetic as reference"
[1] "Calculating Gcross from acinar to acinar"
[1] "Creating design matrix with Non-diabetic as reference"
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"
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"
[1] "Calculating Gcross from alpha to beta"
[1] "Creating design matrix with Non-diabetic as reference"
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 5 | SKIP 0 | PASS 44 ]
> 
> proc.time()
   user  system elapsed 
223.953  17.689 244.460 

Example timings

spatialFDA.Rcheck/spatialFDA-Ex.timings

nameusersystemelapsed
calcCrossMetricPerFov19.134 1.65723.238
calcMetricPerFov7.6950.4898.399
crossSpatialInference44.145 2.53947.171
dot-dfToppp6.8750.3847.480
dot-extractMetric6.5370.3677.106
dot-loadExample6.1670.3696.748
dot-speToDf6.5690.3207.102
functionalGam14.339 0.76915.358
functionalPCA7.8450.4158.653
plotCrossMetricPerFov16.532 0.61717.412
plotFbPlot8.0490.4098.690
plotFpca8.0620.3688.652
plotMdl14.700 0.73215.719
plotMetricPerFov8.1710.4298.852
prepData7.6540.3938.310
print.fpca8.0570.3808.655
spatialInference14.505 0.73915.511