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"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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: 1.18.0

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: 2025-10-30 02:49:08 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 02:51:31 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 143.6 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.5.1 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 ‘1.18.0’
* 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
* 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 ‘1.18.0’
** 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 4.5.1 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 -- Thu Oct 30 02:51:19 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 
  3.530   0.348   3.917

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.001
CellMig-class	0.019	0.002	0.021
CellMigPCA	1.973	0.066	2.044
CellMigPCAclust	0.006	0.002	0.007
CellMigPCAclustALL	0.630	0.011	0.641
CellTracker	0.014	0.003	0.017
CellTrackerMainLoop	0.005	0.007	0.024
CentroidArray	0.013	0.001	0.015
CentroidValidation	0.435	0.017	0.453
ComputeTracksStats	0.027	0.004	0.030
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.317	0.015	1.338
DiRatio	0.011	0.001	0.012
DiRatioPlot	0.036	0.016	0.055
EstimateDiameterRange	0.015	0.002	0.017
FMI	0.426	0.007	0.432
FianlizeOptiParams	0.001	0.000	0.000
FilterTrackedCells	0.002	0.000	0.003
FinRes	0.544	0.013	0.560
ForwardMigration	0.945	0.009	0.954
GenAllCombos	0.003	0.000	0.004
LinearConv2	0.019	0.001	0.021
LoadTiff	0.000	0.000	0.001
MSD	1.684	0.038	1.727
MakeHypercube	0.001	0.001	0.001
MigrationStats	0.000	0.000	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.012	0.002	0.014
OptimizeParamsMainLoop	0.005	0.007	0.023
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.319	0.026	0.356
PlotTracksSeparately	0.008	0.001	0.010
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.095	0.003	0.098
ThreeConditions	0.011	0.003	0.015
TrackCellsDataset	0.009	0.001	0.011
TrajectoryDataset	0.019	0.002	0.022
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.201	0.009	1.213
VisualizeCntr	0.001	0.001	0.003
VisualizeImg	0.005	0.001	0.007
VisualizeStackCentroids	0.051	0.010	0.066
WSADataset	0.004	0.001	0.006
aggregateFR	0.733	0.006	0.740
aggregateTrackedCells	0.020	0.005	0.025
bpass	0.063	0.002	0.067
circshift	0.001	0.000	0.001
cntrd	0.774	0.012	0.787
fixDA	0.000	0.000	0.001
fixExpName	0.001	0.000	0.000
fixFM1	0.001	0.000	0.000
fixFM2	0.000	0.000	0.001
fixFM3	0.000	0.001	0.000
fixFM4	0.000	0.000	0.001
fixFM5	0	0	0
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.000	0.000
fixMSD	0.001	0.001	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0.000	0.001	0.001
fixPER3	0.001	0.000	0.000
getAvailableAggrMetrics	1.033	0.009	1.043
getCellImages	0.274	0.922	1.202
getCellMigSlot	0.369	0.574	0.946
getCellTrackMeta	0.008	0.001	0.009
getCellTrackStats	0.011	0.002	0.013
getCellTracks	0.009	0.002	0.012
getCellsMeta	0.013	0.002	0.016
getCellsStats	0.016	0.003	0.019
getDACtable	1.822	0.014	1.838
getDiRatio	0.017	0.002	0.020
getFMItable	0.440	0.004	0.445
getForMigtable	0.556	0.006	0.563
getImageCentroids	0.018	0.006	0.025
getImageStacks	0.054	0.009	0.064
getMSDtable	4.020	0.036	4.067
getOptimizedParameters	0.009	0.002	0.010
getOptimizedParams	0.011	0.004	0.014
getPerAndSpeed	0.276	0.028	0.315
getPopulationStats	0.009	0.002	0.012
getProcessedImages	0.259	1.605	1.889
getProcessingStatus	0.012	0.002	0.015
getResults	0.666	0.016	0.687
getTracks	0.011	0.002	0.012
getVACtable	1.091	0.008	1.099
initializeTrackParams	0	0	0
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.000	0.002
matfix	0.001	0.001	0.002
nontrivialBondTracking	0.001	0.001	0.001
pkfnd	0.716	0.009	0.726
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0	0	0
plotAllTracks	0.018	0.003	0.022
plotSampleTracks	0.014	0.003	0.018
preProcCellMig	0.006	0.001	0.007
rmPreProcessing	0.077	0.002	0.080
runTrackingPermutation	0.001	0.000	0.001
setAnalyticParams	0.009	0.002	0.010
setCellMigSlot	0.015	0.002	0.016
setCellTracks	0.009	0.002	0.011
setCellsMeta	0.009	0.002	0.010
setExpName	0.018	0.001	0.020
setOptimizedParams	0.011	0.001	0.012
setProcessedImages	0.011	0.001	0.013
setProcessingStatus	0.022	0.006	0.028
setTrackedCellsMeta	0.010	0.002	0.011
setTrackedCentroids	0.012	0.002	0.014
setTrackedPositions	0.012	0.003	0.014
setTrackingStats	0.012	0.002	0.013
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.001	0.001	0.001
track	0.010	0.001	0.010
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.056	0.008	0.065
visualizeTrcks	0.030	0.002	0.033
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.059	0.002	0.061