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"	4827
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4600
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4564
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: 2025-11-19 18:57:04 -0500 (Wed, 19 Nov 2025)

EndedAt: 2025-11-19 18:58:01 -0500 (Wed, 19 Nov 2025)

EllapsedTime: 57.7 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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

##############################################################################
##############################################################################
###
### 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 -- Wed Nov 19 18:57:55 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 
  1.287   0.104   1.402

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.000	0.001	0.000
CellMig-class	0.015	0.002	0.017
CellMigPCA	0.717	0.020	0.783
CellMigPCAclust	0.003	0.001	0.005
CellMigPCAclustALL	0.213	0.003	0.223
CellTracker	0.007	0.001	0.008
CellTrackerMainLoop	0.003	0.005	0.009
CentroidArray	0.007	0.001	0.009
CentroidValidation	0.163	0.007	0.183
ComputeTracksStats	0.010	0.001	0.011
DetectRadii	0.001	0.001	0.001
DiAutoCor	0.450	0.007	0.480
DiRatio	0.007	0.000	0.012
DiRatioPlot	0.015	0.006	0.021
EstimateDiameterRange	0.005	0.001	0.005
FMI	0.163	0.003	0.167
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.001	0.000	0.001
FinRes	0.221	0.005	0.232
ForwardMigration	0.319	0.004	0.339
GenAllCombos	0.001	0.000	0.001
LinearConv2	0.007	0.001	0.006
LoadTiff	0	0	0
MSD	0.512	0.019	0.546
MakeHypercube	0.001	0.001	0.000
MigrationStats	0	0	0
NextOdd	0	0	0
NonParallel4OptimizeParams	0	0	0
NonParallelTrackLoop	0	0	0
OptimizeParams	0.007	0.002	0.008
OptimizeParamsMainLoop	0.001	0.004	0.007
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0.000	0.000	0.001
PerAndSpeed	0.094	0.010	0.115
PlotTracksSeparately	0.004	0.001	0.005
PostProcessTracking	0.000	0.001	0.000
Prep4OptimizeParams	0.029	0.002	0.033
ThreeConditions	0.004	0.002	0.006
TrackCellsDataset	0.006	0.001	0.007
TrajectoryDataset	0.011	0.000	0.012
ValidateTrackingArgs	0.000	0.001	0.000
VeAutoCor	0.378	0.006	0.393
VisualizeCntr	0.001	0.000	0.001
VisualizeImg	0.002	0.001	0.001
VisualizeStackCentroids	0.020	0.003	0.025
WSADataset	0.003	0.001	0.004
aggregateFR	0.216	0.007	0.227
aggregateTrackedCells	0.009	0.002	0.011
bpass	0.027	0.001	0.029
circshift	0.001	0.001	0.000
cntrd	0.384	0.005	0.399
fixDA	0	0	0
fixExpName	0	0	0
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0.001	0.000	0.000
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.309	0.004	0.317
getCellImages	0.083	0.328	0.417
getCellMigSlot	0.125	0.245	0.374
getCellTrackMeta	0.007	0.001	0.008
getCellTrackStats	0.010	0.001	0.011
getCellTracks	0.008	0.001	0.009
getCellsMeta	0.007	0.001	0.008
getCellsStats	0.007	0.002	0.008
getDACtable	0.648	0.009	0.659
getDiRatio	0.008	0.001	0.009
getFMItable	0.149	0.003	0.153
getForMigtable	0.187	0.002	0.189
getImageCentroids	0.009	0.002	0.011
getImageStacks	0.023	0.004	0.029
getMSDtable	1.182	0.023	1.239
getOptimizedParameters	0.007	0.000	0.007
getOptimizedParams	0.009	0.001	0.010
getPerAndSpeed	0.094	0.009	0.103
getPopulationStats	0.007	0.000	0.008
getProcessedImages	0.080	0.365	0.454
getProcessingStatus	0.007	0.001	0.007
getResults	0.225	0.006	0.231
getTracks	0.008	0.002	0.010
getVACtable	0.369	0.005	0.376
initializeTrackParams	0	0	0
innerBondRaster	0.000	0.000	0.001
internalPermutation	0.001	0.000	0.000
matfix	0	0	0
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.244	0.007	0.252
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.007	0.001	0.009
plotSampleTracks	0.006	0.001	0.007
preProcCellMig	0.003	0.001	0.003
rmPreProcessing	0.035	0.001	0.036
runTrackingPermutation	0.001	0.000	0.001
setAnalyticParams	0.006	0.001	0.008
setCellMigSlot	0.010	0.001	0.012
setCellTracks	0.006	0.000	0.007
setCellsMeta	0.007	0.001	0.007
setExpName	0.013	0.001	0.013
setOptimizedParams	0.008	0.001	0.009
setProcessedImages	0.007	0.001	0.008
setProcessingStatus	0.007	0.001	0.008
setTrackedCellsMeta	0.011	0.001	0.013
setTrackedCentroids	0.007	0.000	0.008
setTrackedPositions	0.007	0.001	0.008
setTrackingStats	0.007	0.001	0.008
sinkAway	0	0	0
subNetworkTracking	0.001	0.000	0.000
track	0.003	0.001	0.003
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0	0	0
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.025	0.004	0.030
visualizeTrcks	0.016	0.001	0.017
warnMessage	0	0	0
wsaPreProcessing	0.017	0.001	0.018