Multiple platform build/check report for BioC 3.22 - CHECK results for cellmigRation on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4887
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4677
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4622
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4632
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: 1.17.0

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_1.17.0.tar.gz

StartedAt: 2025-10-16 18:52:12 -0400 (Thu, 16 Oct 2025)

EndedAt: 2025-10-16 18:53:00 -0400 (Thu, 16 Oct 2025)

EllapsedTime: 47.6 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.17.0’
* 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-3.22-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/4.5-arm64/Resources/library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.17.0’
** 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 version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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 Oct 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 
  1.202   0.094   1.294

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.001
CellMig-class	0.013	0.001	0.014
CellMigPCA	0.624	0.017	0.642
CellMigPCAclust	0.003	0.001	0.004
CellMigPCAclustALL	0.212	0.003	0.215
CellTracker	0.007	0.001	0.009
CellTrackerMainLoop	0.001	0.003	0.006
CentroidArray	0.007	0.000	0.008
CentroidValidation	0.151	0.005	0.156
ComputeTracksStats	0.009	0.001	0.010
DetectRadii	0.001	0.000	0.001
DiAutoCor	0.422	0.005	0.434
DiRatio	0.006	0.000	0.007
DiRatioPlot	0.012	0.005	0.018
EstimateDiameterRange	0.005	0.001	0.005
FMI	0.153	0.002	0.155
FianlizeOptiParams	0.001	0.001	0.000
FilterTrackedCells	0.001	0.000	0.001
FinRes	0.212	0.005	0.219
ForwardMigration	0.299	0.003	0.302
GenAllCombos	0.001	0.000	0.001
LinearConv2	0.006	0.000	0.007
LoadTiff	0.001	0.000	0.001
MSD	0.454	0.008	0.463
MakeHypercube	0.001	0.000	0.000
MigrationStats	0	0	0
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.001	0.000
NonParallelTrackLoop	0	0	0
OptimizeParams	0.006	0.000	0.008
OptimizeParamsMainLoop	0.001	0.003	0.010
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0	0	0
PerAndSpeed	0.087	0.008	0.096
PlotTracksSeparately	0.004	0.001	0.005
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.029	0.002	0.031
ThreeConditions	0.004	0.001	0.006
TrackCellsDataset	0.006	0.001	0.007
TrajectoryDataset	0.015	0.002	0.017
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	0.364	0.012	0.376
VisualizeCntr	0.001	0.000	0.001
VisualizeImg	0.001	0.000	0.002
VisualizeStackCentroids	0.019	0.002	0.022
WSADataset	0.003	0.001	0.003
aggregateFR	0.203	0.003	0.206
aggregateTrackedCells	0.008	0.001	0.010
bpass	0.030	0.002	0.031
circshift	0	0	0
cntrd	0.228	0.005	0.234
fixDA	0.001	0.000	0.000
fixExpName	0.000	0.000	0.001
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	0.000	0.000	0.001
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.295	0.003	0.298
getCellImages	0.079	0.252	0.334
getCellMigSlot	0.122	0.179	0.301
getCellTrackMeta	0.007	0.001	0.008
getCellTrackStats	0.008	0.002	0.009
getCellTracks	0.006	0.001	0.008
getCellsMeta	0.006	0.001	0.007
getCellsStats	0.007	0.001	0.008
getDACtable	0.637	0.011	0.655
getDiRatio	0.007	0.001	0.007
getFMItable	0.155	0.003	0.162
getForMigtable	0.186	0.002	0.189
getImageCentroids	0.009	0.002	0.009
getImageStacks	0.020	0.003	0.023
getMSDtable	1.188	0.019	1.207
getOptimizedParameters	0.007	0.001	0.008
getOptimizedParams	0.007	0.001	0.008
getPerAndSpeed	0.090	0.011	0.101
getPopulationStats	0.007	0.001	0.008
getProcessedImages	0.076	0.328	0.412
getProcessingStatus	0.007	0.001	0.007
getResults	0.200	0.007	0.207
getTracks	0.007	0.001	0.008
getVACtable	0.339	0.004	0.342
initializeTrackParams	0	0	0
innerBondRaster	0.000	0.000	0.001
internalPermutation	0	0	0
matfix	0.000	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.000
pkfnd	0.220	0.007	0.227
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.007	0.002	0.008
plotSampleTracks	0.006	0.001	0.007
preProcCellMig	0.003	0.001	0.004
rmPreProcessing	0.036	0.002	0.037
runTrackingPermutation	0.000	0.000	0.001
setAnalyticParams	0.006	0.001	0.008
setCellMigSlot	0.011	0.001	0.012
setCellTracks	0.007	0.001	0.008
setCellsMeta	0.007	0.001	0.008
setExpName	0.011	0.001	0.011
setOptimizedParams	0.006	0.001	0.007
setProcessedImages	0.006	0.001	0.007
setProcessingStatus	0.007	0.001	0.008
setTrackedCellsMeta	0.006	0.001	0.008
setTrackedCentroids	0.006	0.001	0.007
setTrackedPositions	0.007	0.001	0.007
setTrackingStats	0.006	0.001	0.007
sinkAway	0	0	0
subNetworkTracking	0.001	0.000	0.001
track	0.013	0.007	0.019
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0	0	0
trivialBondTracking	0.001	0.000	0.000
visualizeCellTracks	0.020	0.003	0.024
visualizeTrcks	0.016	0.001	0.016
warnMessage	0	0	0
wsaPreProcessing	0.018	0.001	0.019