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"	4829
lconway	macOS 12.7.6 Monterey	x86_64	R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"	4602
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"	4566
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: 2025-11-20 18:57:04 -0500 (Thu, 20 Nov 2025)

EndedAt: 2025-11-20 18:58:01 -0500 (Thu, 20 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 -- Thu Nov 20 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 
  1.296   0.108   1.410

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.000
CellMig-class	0.012	0.001	0.015
CellMigPCA	0.707	0.020	0.777
CellMigPCAclust	0.004	0.001	0.005
CellMigPCAclustALL	0.208	0.006	0.240
CellTracker	0.008	0.002	0.009
CellTrackerMainLoop	0.003	0.007	0.013
CentroidArray	0.007	0.001	0.008
CentroidValidation	0.160	0.008	0.182
ComputeTracksStats	0.010	0.001	0.011
DetectRadii	0.000	0.000	0.001
DiAutoCor	0.453	0.006	0.492
DiRatio	0.007	0.001	0.012
DiRatioPlot	0.011	0.004	0.016
EstimateDiameterRange	0.005	0.001	0.010
FMI	0.155	0.003	0.159
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.001	0.000	0.001
FinRes	0.210	0.005	0.225
ForwardMigration	0.308	0.003	0.327
GenAllCombos	0.001	0.000	0.001
LinearConv2	0.006	0.000	0.007
LoadTiff	0	0	0
MSD	0.496	0.028	0.562
MakeHypercube	0.000	0.000	0.001
MigrationStats	0.000	0.001	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.000	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.007	0.001	0.008
OptimizeParamsMainLoop	0.003	0.006	0.010
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0.000	0.000	0.001
PerAndSpeed	0.092	0.011	0.108
PlotTracksSeparately	0.005	0.001	0.005
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.030	0.002	0.034
ThreeConditions	0.004	0.001	0.006
TrackCellsDataset	0.007	0.001	0.007
TrajectoryDataset	0.011	0.001	0.011
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	0.361	0.006	0.397
VisualizeCntr	0.001	0.000	0.001
VisualizeImg	0.002	0.000	0.002
VisualizeStackCentroids	0.021	0.004	0.026
WSADataset	0.003	0.001	0.004
aggregateFR	0.215	0.003	0.242
aggregateTrackedCells	0.009	0.002	0.010
bpass	0.026	0.001	0.030
circshift	0	0	0
cntrd	0.251	0.006	0.261
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	0.000	0.000	0.001
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.323	0.005	0.346
getCellImages	0.087	0.357	0.451
getCellMigSlot	0.130	0.245	0.378
getCellTrackMeta	0.009	0.002	0.009
getCellTrackStats	0.008	0.002	0.010
getCellTracks	0.007	0.002	0.009
getCellsMeta	0.006	0.001	0.007
getCellsStats	0.007	0.001	0.008
getDACtable	0.674	0.009	0.689
getDiRatio	0.008	0.001	0.009
getFMItable	0.159	0.001	0.163
getForMigtable	0.193	0.002	0.195
getImageCentroids	0.010	0.002	0.012
getImageStacks	0.023	0.003	0.030
getMSDtable	1.282	0.018	1.314
getOptimizedParameters	0.006	0.001	0.008
getOptimizedParams	0.007	0.001	0.008
getPerAndSpeed	0.089	0.008	0.097
getPopulationStats	0.008	0.002	0.010
getProcessedImages	0.083	0.385	0.483
getProcessingStatus	0.007	0.002	0.008
getResults	0.217	0.006	0.223
getTracks	0.007	0.001	0.008
getVACtable	0.370	0.004	0.376
initializeTrackParams	0	0	0
innerBondRaster	0.001	0.000	0.001
internalPermutation	0.000	0.001	0.000
matfix	0.001	0.000	0.001
nontrivialBondTracking	0	0	0
pkfnd	0.244	0.008	0.253
plot3DAllTracks	0	0	0
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.008	0.002	0.009
plotSampleTracks	0.006	0.001	0.007
preProcCellMig	0.003	0.001	0.004
rmPreProcessing	0.031	0.002	0.032
runTrackingPermutation	0.001	0.000	0.001
setAnalyticParams	0.007	0.001	0.008
setCellMigSlot	0.013	0.001	0.014
setCellTracks	0.007	0.001	0.009
setCellsMeta	0.007	0.001	0.008
setExpName	0.011	0.001	0.013
setOptimizedParams	0.008	0.001	0.009
setProcessedImages	0.007	0.001	0.007
setProcessingStatus	0.006	0.002	0.007
setTrackedCellsMeta	0.012	0.001	0.013
setTrackedCentroids	0.006	0.001	0.008
setTrackedPositions	0.007	0.001	0.008
setTrackingStats	0.007	0.001	0.007
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	0.001
trivialBondRaster	0	0	0
trivialBondTracking	0	0	0
visualizeCellTracks	0.021	0.002	0.023
visualizeTrcks	0.018	0.001	0.018
warnMessage	0.000	0.001	0.001
wsaPreProcessing	0.017	0.001	0.018