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

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 lconway

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: 2025-10-17 20:50:33 -0400 (Fri, 17 Oct 2025)

EndedAt: 2025-10-17 20:53:08 -0400 (Fri, 17 Oct 2025)

EllapsedTime: 154.9 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: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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-x86_64/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: x86_64-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 Oct 17 20:52:55 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 
  3.733   0.388   4.149

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.003
CellMig-class	0.027	0.003	0.029
CellMigPCA	2.060	0.080	2.151
CellMigPCAclust	0.006	0.001	0.007
CellMigPCAclustALL	0.772	0.009	0.784
CellTracker	0.012	0.003	0.015
CellTrackerMainLoop	0.005	0.011	0.032
CentroidArray	0.014	0.004	0.019
CentroidValidation	0.542	0.018	0.563
ComputeTracksStats	0.023	0.002	0.026
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.504	0.017	1.528
DiRatio	0.014	0.001	0.017
DiRatioPlot	0.035	0.015	0.054
EstimateDiameterRange	0.016	0.002	0.020
FMI	0.489	0.007	0.498
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.003	0.001	0.004
FinRes	0.702	0.015	0.724
ForwardMigration	1.060	0.008	1.073
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.023	0.001	0.025
LoadTiff	0.001	0.000	0.001
MSD	1.746	0.022	1.778
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.001	0.001	0.002
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.010	0.001	0.012
OptimizeParamsMainLoop	0.004	0.007	0.022
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.000	0.001	0.001
PerAndSpeed	0.323	0.029	0.364
PlotTracksSeparately	0.006	0.001	0.008
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.113	0.003	0.118
ThreeConditions	0.010	0.002	0.012
TrackCellsDataset	0.010	0.002	0.012
TrajectoryDataset	0.032	0.003	0.035
ValidateTrackingArgs	0	0	0
VeAutoCor	1.315	0.022	1.343
VisualizeCntr	0.002	0.001	0.004
VisualizeImg	0.005	0.001	0.008
VisualizeStackCentroids	0.052	0.008	0.060
WSADataset	0.007	0.001	0.008
aggregateFR	0.758	0.009	0.771
aggregateTrackedCells	0.019	0.005	0.024
bpass	0.082	0.003	0.085
circshift	0.000	0.000	0.001
cntrd	0.826	0.013	0.845
fixDA	0.000	0.001	0.000
fixExpName	0.000	0.000	0.001
fixFM1	0.001	0.001	0.000
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.000	0.001	0.000
fixFM6	0.001	0.000	0.000
fixID1	0.000	0.000	0.001
fixMSD	0.000	0.000	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0	0	0
fixPER3	0.000	0.000	0.001
getAvailableAggrMetrics	1.086	0.009	1.100
getCellImages	0.259	0.816	1.080
getCellMigSlot	0.367	0.539	0.913
getCellTrackMeta	0.011	0.003	0.013
getCellTrackStats	0.015	0.003	0.018
getCellTracks	0.013	0.003	0.015
getCellsMeta	0.010	0.002	0.012
getCellsStats	0.012	0.002	0.015
getDACtable	2.313	0.022	2.348
getDiRatio	0.018	0.002	0.021
getFMItable	0.556	0.006	0.563
getForMigtable	0.683	0.006	0.694
getImageCentroids	0.018	0.003	0.022
getImageStacks	0.045	0.006	0.052
getMSDtable	4.449	0.056	4.545
getOptimizedParameters	0.013	0.002	0.015
getOptimizedParams	0.014	0.002	0.016
getPerAndSpeed	0.309	0.030	0.352
getPopulationStats	0.013	0.002	0.016
getProcessedImages	0.259	0.920	1.188
getProcessingStatus	0.010	0.002	0.012
getResults	0.732	0.015	0.754
getTracks	0.014	0.002	0.016
getVACtable	1.091	0.009	1.104
initializeTrackParams	0.001	0.000	0.000
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.001	0.001
nontrivialBondTracking	0.000	0.000	0.001
pkfnd	0.694	0.010	0.709
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0	0	0
plotAllTracks	0.012	0.002	0.016
plotSampleTracks	0.012	0.003	0.015
preProcCellMig	0.006	0.002	0.006
rmPreProcessing	0.109	0.003	0.112
runTrackingPermutation	0.001	0.000	0.002
setAnalyticParams	0.011	0.002	0.013
setCellMigSlot	0.019	0.003	0.022
setCellTracks	0.011	0.003	0.014
setCellsMeta	0.011	0.002	0.013
setExpName	0.018	0.002	0.020
setOptimizedParams	0.010	0.002	0.011
setProcessedImages	0.012	0.003	0.013
setProcessingStatus	0.011	0.003	0.013
setTrackedCellsMeta	0.010	0.002	0.012
setTrackedCentroids	0.011	0.002	0.015
setTrackedPositions	0.011	0.002	0.012
setTrackingStats	0.012	0.002	0.014
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.023	0.004	0.028
track	0.009	0.000	0.009
trackHypercubeBuild	0.000	0.000	0.001
trackSlideProcessing	0.001	0.000	0.000
trackSlideWrapUp	0.001	0.000	0.000
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.000
visualizeCellTracks	0.048	0.006	0.053
visualizeTrcks	0.029	0.002	0.030
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.054	0.002	0.056