Multiple platform build/check report for BioC 3.23 - CHECK results for cellmigRation on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4875
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4589
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*

CHECK results for cellmigRation on kjohnson3

To the developers/maintainers of the cellmigRation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellmigRation.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: cellmigRation

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.19.0.tar.gz

StartedAt: 2025-12-16 18:52:04 -0500 (Tue, 16 Dec 2025)

EndedAt: 2025-12-16 18:53:01 -0500 (Tue, 16 Dec 2025)

EllapsedTime: 56.6 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.19.0’
* 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 ‘cellmigRation’ 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 ... NOTE
Documented arguments not in \usage in Rd file 'fixDA.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM1.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM2.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM3.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM4.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM5.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM6.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixID2.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID3.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID4.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixMSD.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixPER1.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'fixPER2.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'innerBondRaster.Rd':
  ‘i’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.23-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.19.0’
** using staged installation
** R
** data
** 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 (cellmigRation)

Tests output

cellmigRation.Rcheck/tests/runTests.Rout


R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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.

> BiocGenerics:::testPackage("cellmigRation")


RUNIT TEST PROTOCOL -- Tue Dec 16 18:52:55 2025 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
cellmigRation RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.314   0.114   1.464

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.000	0.000	0.001
CellMig-class	0.013	0.001	0.014
CellMigPCA	0.718	0.020	0.771
CellMigPCAclust	0.005	0.001	0.005
CellMigPCAclustALL	0.210	0.004	0.226
CellTracker	0.007	0.002	0.008
CellTrackerMainLoop	0.002	0.004	0.009
CentroidArray	0.008	0.001	0.009
CentroidValidation	0.167	0.006	0.179
ComputeTracksStats	0.010	0.002	0.011
DetectRadii	0.001	0.000	0.001
DiAutoCor	0.446	0.007	0.475
DiRatio	0.006	0.001	0.008
DiRatioPlot	0.013	0.006	0.019
EstimateDiameterRange	0.005	0.001	0.005
FMI	0.155	0.003	0.169
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.001	0.000	0.001
FinRes	0.218	0.006	0.229
ForwardMigration	0.313	0.004	0.331
GenAllCombos	0.001	0.000	0.001
LinearConv2	0.006	0.000	0.009
LoadTiff	0.001	0.000	0.001
MSD	0.503	0.026	0.571
MakeHypercube	0.000	0.001	0.000
MigrationStats	0	0	0
NextOdd	0.001	0.000	0.000
NonParallel4OptimizeParams	0	0	0
NonParallelTrackLoop	0	0	0
OptimizeParams	0.007	0.001	0.007
OptimizeParamsMainLoop	0.003	0.005	0.012
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.098	0.011	0.134
PlotTracksSeparately	0.004	0.001	0.005
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.030	0.002	0.038
ThreeConditions	0.004	0.001	0.006
TrackCellsDataset	0.006	0.001	0.007
TrajectoryDataset	0.011	0.000	0.012
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	0.358	0.005	0.378
VisualizeCntr	0.001	0.001	0.001
VisualizeImg	0.002	0.000	0.003
VisualizeStackCentroids	0.021	0.003	0.025
WSADataset	0.003	0.001	0.004
aggregateFR	0.218	0.003	0.232
aggregateTrackedCells	0.008	0.002	0.011
bpass	0.027	0.001	0.029
circshift	0	0	0
cntrd	0.243	0.008	0.275
fixDA	0.001	0.000	0.001
fixExpName	0	0	0
fixFM1	0.000	0.000	0.001
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0.001	0.000	0.000
fixPER2	0	0	0
fixPER3	0.000	0.000	0.001
getAvailableAggrMetrics	0.317	0.003	0.332
getCellImages	0.092	0.371	0.477
getCellMigSlot	0.140	0.230	0.372
getCellTrackMeta	0.008	0.001	0.009
getCellTrackStats	0.010	0.002	0.012
getCellTracks	0.009	0.002	0.010
getCellsMeta	0.007	0.001	0.007
getCellsStats	0.007	0.001	0.008
getDACtable	0.686	0.010	0.699
getDiRatio	0.007	0.001	0.007
getFMItable	0.172	0.002	0.177
getForMigtable	0.191	0.003	0.202
getImageCentroids	0.008	0.002	0.009
getImageStacks	0.021	0.003	0.023
getMSDtable	1.258	0.017	1.314
getOptimizedParameters	0.006	0.001	0.007
getOptimizedParams	0.007	0.001	0.008
getPerAndSpeed	0.088	0.010	0.100
getPopulationStats	0.009	0.001	0.009
getProcessedImages	0.083	0.379	0.477
getProcessingStatus	0.010	0.002	0.011
getResults	0.235	0.007	0.244
getTracks	0.009	0.001	0.010
getVACtable	0.385	0.008	0.398
initializeTrackParams	0	0	0
innerBondRaster	0.001	0.000	0.000
internalPermutation	0.000	0.000	0.001
matfix	0.001	0.001	0.000
nontrivialBondTracking	0	0	0
pkfnd	0.245	0.005	0.268
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.007	0.002	0.009
plotSampleTracks	0.006	0.001	0.009
preProcCellMig	0.004	0.001	0.004
rmPreProcessing	0.035	0.001	0.037
runTrackingPermutation	0.000	0.000	0.001
setAnalyticParams	0.007	0.002	0.008
setCellMigSlot	0.011	0.001	0.014
setCellTracks	0.007	0.001	0.008
setCellsMeta	0.006	0.002	0.008
setExpName	0.012	0.001	0.013
setOptimizedParams	0.008	0.001	0.009
setProcessedImages	0.008	0.001	0.008
setProcessingStatus	0.007	0.001	0.008
setTrackedCellsMeta	0.011	0.003	0.014
setTrackedCentroids	0.006	0.001	0.008
setTrackedPositions	0.007	0.001	0.008
setTrackingStats	0.007	0.002	0.008
sinkAway	0	0	0
subNetworkTracking	0.001	0.000	0.001
track	0.003	0.001	0.003
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0.001	0.000	0.000
trivialBondRaster	0.000	0.001	0.001
trivialBondTracking	0	0	0
visualizeCellTracks	0.020	0.003	0.024
visualizeTrcks	0.015	0.000	0.017
warnMessage	0	0	0
wsaPreProcessing	0.018	0.001	0.020