Multiple platform build/check report for BioC 3.23 - CHECK results for cellmigRation on lconway

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 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: 1.19.0

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 20:01:17 -0500 (Thu, 20 Nov 2025)

EndedAt: 2025-11-20 20:03:50 -0500 (Thu, 20 Nov 2025)

EllapsedTime: 153.6 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 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-x86_64/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) (2025-10-21 r88958) -- "Unsuffered Consequences"
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 Nov 20 20:03:38 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 
  3.622   0.408   4.061

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.001
CellMig-class	0.022	0.003	0.026
CellMigPCA	2.087	0.084	2.183
CellMigPCAclust	0.006	0.002	0.009
CellMigPCAclustALL	0.688	0.014	0.705
CellTracker	0.012	0.003	0.015
CellTrackerMainLoop	0.005	0.010	0.026
CentroidArray	0.013	0.002	0.016
CentroidValidation	0.456	0.021	0.480
ComputeTracksStats	0.022	0.004	0.026
DetectRadii	0.003	0.001	0.003
DiAutoCor	1.486	0.019	1.517
DiRatio	0.012	0.002	0.014
DiRatioPlot	0.038	0.017	0.060
EstimateDiameterRange	0.018	0.003	0.021
FMI	0.570	0.010	0.584
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.002	0.001	0.002
FinRes	0.675	0.016	0.696
ForwardMigration	1.007	0.011	1.021
GenAllCombos	0.003	0.001	0.003
LinearConv2	0.021	0.001	0.023
LoadTiff	0.001	0.000	0.002
MSD	1.670	0.034	1.713
MakeHypercube	0.001	0.001	0.001
MigrationStats	0.001	0.001	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.012	0.003	0.015
OptimizeParamsMainLoop	0.005	0.010	0.027
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.313	0.026	0.350
PlotTracksSeparately	0.007	0.003	0.009
PostProcessTracking	0.001	0.000	0.000
Prep4OptimizeParams	0.105	0.004	0.109
ThreeConditions	0.011	0.002	0.013
TrackCellsDataset	0.011	0.002	0.013
TrajectoryDataset	0.019	0.002	0.021
ValidateTrackingArgs	0.001	0.001	0.001
VeAutoCor	1.235	0.015	1.257
VisualizeCntr	0.003	0.000	0.003
VisualizeImg	0.006	0.001	0.006
VisualizeStackCentroids	0.043	0.007	0.050
WSADataset	0.006	0.002	0.008
aggregateFR	0.729	0.009	0.740
aggregateTrackedCells	0.016	0.005	0.020
bpass	0.059	0.003	0.063
circshift	0.001	0.000	0.000
cntrd	0.807	0.016	0.829
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.001	0.000
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.001	0.000	0.001
fixFM5	0	0	0
fixFM6	0.000	0.000	0.001
fixID1	0.000	0.000	0.001
fixMSD	0.000	0.000	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0.000	0.000	0.001
fixPER3	0	0	0
getAvailableAggrMetrics	1.079	0.009	1.093
getCellImages	0.276	0.754	1.039
getCellMigSlot	0.381	0.493	0.880
getCellTrackMeta	0.013	0.002	0.016
getCellTrackStats	0.014	0.003	0.017
getCellTracks	0.010	0.004	0.013
getCellsMeta	0.010	0.003	0.013
getCellsStats	0.014	0.003	0.016
getDACtable	2.045	0.018	2.069
getDiRatio	0.016	0.003	0.019
getFMItable	0.463	0.006	0.470
getForMigtable	0.608	0.006	0.617
getImageCentroids	0.017	0.004	0.021
getImageStacks	0.045	0.006	0.053
getMSDtable	4.139	0.043	4.204
getOptimizedParameters	0.011	0.003	0.014
getOptimizedParams	0.010	0.002	0.012
getPerAndSpeed	0.274	0.026	0.308
getPopulationStats	0.013	0.004	0.017
getProcessedImages	0.293	1.232	1.538
getProcessingStatus	0.010	0.002	0.011
getResults	0.635	0.016	0.658
getTracks	0.010	0.002	0.014
getVACtable	1.065	0.010	1.077
initializeTrackParams	0	0	0
innerBondRaster	0.001	0.000	0.002
internalPermutation	0.001	0.000	0.002
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.686	0.010	0.699
plot3DAllTracks	0	0	0
plot3DTracks	0.001	0.001	0.001
plotAllTracks	0.018	0.004	0.022
plotSampleTracks	0.011	0.004	0.015
preProcCellMig	0.004	0.002	0.006
rmPreProcessing	0.080	0.003	0.082
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.012	0.002	0.015
setCellMigSlot	0.018	0.002	0.020
setCellTracks	0.010	0.001	0.011
setCellsMeta	0.013	0.002	0.015
setExpName	0.018	0.002	0.020
setOptimizedParams	0.010	0.002	0.013
setProcessedImages	0.010	0.002	0.012
setProcessingStatus	0.011	0.002	0.013
setTrackedCellsMeta	0.023	0.004	0.026
setTrackedCentroids	0.012	0.003	0.016
setTrackedPositions	0.010	0.003	0.013
setTrackingStats	0.010	0.002	0.013
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.001	0.001	0.002
track	0.009	0.001	0.010
trackHypercubeBuild	0.001	0.001	0.001
trackSlideProcessing	0.000	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.001	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.050	0.007	0.058
visualizeTrcks	0.024	0.002	0.026
warnMessage	0	0	0
wsaPreProcessing	0.047	0.003	0.051