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: 2025-11-18 19:05:20 -0500 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 19:06:17 -0500 (Tue, 18 Nov 2025)

EllapsedTime: 57.7 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

##############################################################################
##############################################################################
###
### 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 Nov 18 19:06:12 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 
  1.298   0.119   1.443

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.001
CellMig-class	0.014	0.001	0.016
CellMigPCA	0.689	0.019	0.782
CellMigPCAclust	0.003	0.001	0.004
CellMigPCAclustALL	0.211	0.004	0.232
CellTracker	0.007	0.001	0.008
CellTrackerMainLoop	0.003	0.007	0.010
CentroidArray	0.008	0.002	0.009
CentroidValidation	0.164	0.007	0.181
ComputeTracksStats	0.010	0.002	0.012
DetectRadii	0.001	0.000	0.001
DiAutoCor	0.445	0.007	0.462
DiRatio	0.008	0.001	0.008
DiRatioPlot	0.013	0.004	0.018
EstimateDiameterRange	0.005	0.000	0.006
FMI	0.163	0.003	0.166
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.000	0.000	0.001
FinRes	0.216	0.006	0.228
ForwardMigration	0.321	0.004	0.334
GenAllCombos	0.001	0.000	0.001
LinearConv2	0.007	0.000	0.013
LoadTiff	0.000	0.001	0.001
MSD	0.504	0.023	0.542
MakeHypercube	0.001	0.000	0.001
MigrationStats	0	0	0
NextOdd	0	0	0
NonParallel4OptimizeParams	0	0	0
NonParallelTrackLoop	0	0	0
OptimizeParams	0.009	0.001	0.010
OptimizeParamsMainLoop	0.001	0.004	0.012
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0	0	0
PerAndSpeed	0.095	0.009	0.108
PlotTracksSeparately	0.004	0.000	0.005
PostProcessTracking	0.000	0.001	0.000
Prep4OptimizeParams	0.034	0.001	0.036
ThreeConditions	0.004	0.001	0.007
TrackCellsDataset	0.007	0.002	0.008
TrajectoryDataset	0.011	0.001	0.012
ValidateTrackingArgs	0.001	0.000	0.000
VeAutoCor	0.378	0.006	0.385
VisualizeCntr	0.000	0.000	0.001
VisualizeImg	0.002	0.001	0.003
VisualizeStackCentroids	0.022	0.003	0.024
WSADataset	0.004	0.001	0.005
aggregateFR	0.223	0.004	0.230
aggregateTrackedCells	0.010	0.002	0.014
bpass	0.029	0.001	0.029
circshift	0	0	0
cntrd	0.244	0.006	0.254
fixDA	0.001	0.000	0.000
fixExpName	0.000	0.001	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0.000	0.000	0.001
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0.000	0.000	0.001
fixID1	0	0	0
fixMSD	0.000	0.000	0.001
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.317	0.004	0.330
getCellImages	0.091	0.369	0.486
getCellMigSlot	0.138	0.240	0.383
getCellTrackMeta	0.006	0.001	0.008
getCellTrackStats	0.008	0.001	0.008
getCellTracks	0.007	0.002	0.007
getCellsMeta	0.006	0.001	0.007
getCellsStats	0.007	0.001	0.008
getDACtable	0.669	0.009	0.688
getDiRatio	0.007	0.001	0.008
getFMItable	0.160	0.003	0.168
getForMigtable	0.191	0.004	0.214
getImageCentroids	0.009	0.001	0.010
getImageStacks	0.023	0.003	0.028
getMSDtable	1.326	0.018	1.385
getOptimizedParameters	0.007	0.001	0.008
getOptimizedParams	0.007	0.002	0.009
getPerAndSpeed	0.088	0.009	0.098
getPopulationStats	0.007	0.001	0.008
getProcessedImages	0.080	0.352	0.443
getProcessingStatus	0.007	0.001	0.009
getResults	0.226	0.006	0.235
getTracks	0.008	0.001	0.009
getVACtable	0.367	0.005	0.373
initializeTrackParams	0	0	0
innerBondRaster	0.000	0.000	0.001
internalPermutation	0	0	0
matfix	0	0	0
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.238	0.006	0.248
plot3DAllTracks	0	0	0
plot3DTracks	0.001	0.000	0.000
plotAllTracks	0.007	0.002	0.009
plotSampleTracks	0.006	0.001	0.007
preProcCellMig	0.003	0.001	0.004
rmPreProcessing	0.031	0.001	0.032
runTrackingPermutation	0.000	0.000	0.001
setAnalyticParams	0.008	0.001	0.009
setCellMigSlot	0.013	0.001	0.014
setCellTracks	0.006	0.001	0.009
setCellsMeta	0.007	0.001	0.007
setExpName	0.011	0.001	0.012
setOptimizedParams	0.007	0.001	0.008
setProcessedImages	0.007	0.001	0.008
setProcessingStatus	0.008	0.001	0.009
setTrackedCellsMeta	0.012	0.002	0.014
setTrackedCentroids	0.007	0.001	0.007
setTrackedPositions	0.006	0.001	0.007
setTrackingStats	0.007	0.001	0.007
sinkAway	0.000	0.001	0.001
subNetworkTracking	0.001	0.000	0.001
track	0.003	0.000	0.003
trackHypercubeBuild	0.000	0.000	0.001
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0	0	0
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.022	0.003	0.026
visualizeTrcks	0.018	0.001	0.020
warnMessage	0	0	0
wsaPreProcessing	0.018	0.001	0.020