Multiple platform build/check report for BioC 3.22 - CHECK results for cellmigRation on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4882
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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 kjohnson1

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: 1.18.0

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_1.18.0.tar.gz

StartedAt: 2025-12-12 18:56:35 -0500 (Fri, 12 Dec 2025)

EndedAt: 2025-12-12 19:00:32 -0500 (Fri, 12 Dec 2025)

EllapsedTime: 237.0 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_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.2 Patched (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 ‘1.18.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMSDtable 4.051   0.06   7.028
* 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 ‘1.18.0’
** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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 -- Fri Dec 12 19:00:08 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 
  3.967   0.336   7.410

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.002
CellMig-class	0.038	0.004	0.056
CellMigPCA	2.199	0.077	3.549
CellMigPCAclust	0.012	0.003	0.032
CellMigPCAclustALL	0.671	0.016	1.076
CellTracker	0.023	0.005	0.033
CellTrackerMainLoop	0.006	0.010	0.021
CentroidArray	0.023	0.003	0.034
CentroidValidation	0.489	0.025	0.784
ComputeTracksStats	0.029	0.005	0.114
DetectRadii	0.002	0.001	0.002
DiAutoCor	1.387	0.021	2.129
DiRatio	0.021	0.004	0.035
DiRatioPlot	0.038	0.015	0.076
EstimateDiameterRange	0.013	0.002	0.015
FMI	0.488	0.008	0.729
FianlizeOptiParams	0.001	0.001	0.000
FilterTrackedCells	0.003	0.001	0.004
FinRes	0.662	0.018	1.032
ForwardMigration	1.000	0.015	1.720
GenAllCombos	0.003	0.000	0.002
LinearConv2	0.021	0.002	0.040
LoadTiff	0.001	0.000	0.001
MSD	1.592	0.044	2.459
MakeHypercube	0.001	0.000	0.002
MigrationStats	0.001	0.001	0.002
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.002
NonParallelTrackLoop	0.001	0.000	0.001
OptimizeParams	0.021	0.005	0.040
OptimizeParamsMainLoop	0.006	0.010	0.022
Parallel4OptimizeParams	0.001	0.001	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.325	0.034	0.672
PlotTracksSeparately	0.012	0.004	0.015
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.094	0.004	0.162
ThreeConditions	0.012	0.005	0.023
TrackCellsDataset	0.017	0.004	0.029
TrajectoryDataset	0.031	0.004	0.060
ValidateTrackingArgs	0.001	0.000	0.010
VeAutoCor	1.145	0.019	1.793
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.005	0.001	0.005
VisualizeStackCentroids	0.063	0.010	0.117
WSADataset	0.010	0.002	0.013
aggregateFR	0.683	0.011	1.017
aggregateTrackedCells	0.027	0.008	0.055
bpass	0.086	0.005	0.208
circshift	0.001	0.000	0.001
cntrd	0.747	0.020	1.201
fixDA	0.001	0.000	0.000
fixExpName	0.001	0.001	0.001
fixFM1	0.000	0.000	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0	0	0
fixFM4	0.000	0.000	0.001
fixFM5	0	0	0
fixFM6	0.001	0.001	0.000
fixID1	0.001	0.000	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.001	0.001
fixPER2	0.001	0.001	0.001
fixPER3	0.001	0.000	0.000
getAvailableAggrMetrics	0.993	0.014	1.602
getCellImages	0.249	1.001	1.905
getCellMigSlot	0.401	0.657	1.695
getCellTrackMeta	0.019	0.004	0.039
getCellTrackStats	0.023	0.007	0.037
getCellTracks	0.019	0.005	0.038
getCellsMeta	0.020	0.004	0.030
getCellsStats	0.020	0.005	0.057
getDACtable	2.022	0.026	3.174
getDiRatio	0.023	0.005	0.038
getFMItable	0.494	0.006	0.811
getForMigtable	0.623	0.010	0.976
getImageCentroids	0.027	0.007	0.080
getImageStacks	0.061	0.010	0.120
getMSDtable	4.051	0.060	7.028
getOptimizedParameters	0.016	0.003	0.033
getOptimizedParams	0.019	0.004	0.037
getPerAndSpeed	0.311	0.034	0.599
getPopulationStats	0.020	0.006	0.045
getProcessedImages	0.240	1.046	2.202
getProcessingStatus	0.020	0.004	0.024
getResults	0.673	0.020	1.190
getTracks	0.018	0.003	0.048
getVACtable	1.116	0.017	1.922
initializeTrackParams	0.000	0.001	0.001
innerBondRaster	0.001	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.722	0.015	1.215
plot3DAllTracks	0.000	0.001	0.000
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.022	0.005	0.027
plotSampleTracks	0.021	0.006	0.195
preProcCellMig	0.010	0.003	0.025
rmPreProcessing	0.099	0.004	0.145
runTrackingPermutation	0.002	0.001	0.002
setAnalyticParams	0.019	0.004	0.050
setCellMigSlot	0.030	0.004	0.045
setCellTracks	0.021	0.003	0.024
setCellsMeta	0.019	0.005	0.056
setExpName	0.031	0.005	0.055
setOptimizedParams	0.021	0.005	0.028
setProcessedImages	0.020	0.005	0.034
setProcessingStatus	0.036	0.005	0.072
setTrackedCellsMeta	0.020	0.004	0.024
setTrackedCentroids	0.020	0.004	0.045
setTrackedPositions	0.019	0.005	0.040
setTrackingStats	0.019	0.003	0.032
sinkAway	0.000	0.001	0.002
subNetworkTracking	0.001	0.000	0.001
track	0.009	0.001	0.010
trackHypercubeBuild	0.001	0.001	0.002
trackSlideProcessing	0	0	0
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.000	0.003
trivialBondTracking	0	0	0
visualizeCellTracks	0.067	0.011	0.145
visualizeTrcks	0.047	0.002	0.082
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.057	0.005	0.107