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: 1.17.0

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: 2025-10-28 20:01:21 -0400 (Tue, 28 Oct 2025)

EndedAt: 2025-10-28 20:03:52 -0400 (Tue, 28 Oct 2025)

EllapsedTime: 151.5 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_1.17.0.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 -- Tue Oct 28 20:03:40 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 
  3.599   0.351   3.976

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.002
CellMig-class	0.024	0.003	0.027
CellMigPCA	2.007	0.073	2.093
CellMigPCAclust	0.006	0.002	0.008
CellMigPCAclustALL	0.734	0.010	0.748
CellTracker	0.011	0.002	0.013
CellTrackerMainLoop	0.006	0.007	0.026
CentroidArray	0.013	0.002	0.015
CentroidValidation	0.503	0.018	0.525
ComputeTracksStats	0.020	0.002	0.023
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.394	0.013	1.412
DiRatio	0.019	0.001	0.020
DiRatioPlot	0.037	0.015	0.055
EstimateDiameterRange	0.016	0.002	0.018
FMI	0.516	0.005	0.522
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.002	0.000	0.003
FinRes	0.687	0.014	0.706
ForwardMigration	1.063	0.008	1.076
GenAllCombos	0.002	0.000	0.003
LinearConv2	0.018	0.001	0.020
LoadTiff	0.001	0.001	0.002
MSD	1.597	0.019	1.624
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.000	0.001	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.001	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.011	0.002	0.013
OptimizeParamsMainLoop	0.004	0.008	0.023
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.299	0.027	0.337
PlotTracksSeparately	0.006	0.001	0.008
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.101	0.003	0.105
ThreeConditions	0.009	0.002	0.012
TrackCellsDataset	0.011	0.002	0.013
TrajectoryDataset	0.032	0.003	0.035
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.217	0.022	1.246
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.004	0.001	0.005
VisualizeStackCentroids	0.044	0.008	0.051
WSADataset	0.005	0.002	0.007
aggregateFR	0.661	0.006	0.670
aggregateTrackedCells	0.017	0.004	0.021
bpass	0.078	0.003	0.081
circshift	0	0	0
cntrd	0.711	0.013	0.726
fixDA	0.001	0.001	0.000
fixExpName	0	0	0
fixFM1	0.000	0.001	0.001
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.001	0.001	0.000
fixFM6	0.000	0.000	0.001
fixID1	0.000	0.000	0.001
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0.000	0.000	0.001
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	1.001	0.008	1.012
getCellImages	0.264	0.840	1.119
getCellMigSlot	0.355	0.531	0.893
getCellTrackMeta	0.009	0.002	0.011
getCellTrackStats	0.013	0.003	0.016
getCellTracks	0.012	0.003	0.015
getCellsMeta	0.010	0.002	0.011
getCellsStats	0.014	0.002	0.016
getDACtable	2.164	0.023	2.202
getDiRatio	0.018	0.002	0.020
getFMItable	0.483	0.004	0.488
getForMigtable	0.563	0.005	0.569
getImageCentroids	0.015	0.003	0.019
getImageStacks	0.039	0.006	0.045
getMSDtable	3.911	0.037	3.968
getOptimizedParameters	0.010	0.002	0.012
getOptimizedParams	0.011	0.003	0.014
getPerAndSpeed	0.303	0.029	0.342
getPopulationStats	0.011	0.002	0.014
getProcessedImages	0.258	1.371	1.641
getProcessingStatus	0.011	0.002	0.013
getResults	0.704	0.017	0.727
getTracks	0.014	0.003	0.016
getVACtable	1.178	0.013	1.197
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.001	0.000	0.002
internalPermutation	0.000	0.000	0.001
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.001	0.001	0.001
pkfnd	0.676	0.008	0.688
plot3DAllTracks	0	0	0
plot3DTracks	0.000	0.001	0.000
plotAllTracks	0.015	0.003	0.019
plotSampleTracks	0.013	0.002	0.016
preProcCellMig	0.005	0.001	0.007
rmPreProcessing	0.098	0.003	0.101
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.011	0.002	0.014
setCellMigSlot	0.017	0.002	0.018
setCellTracks	0.011	0.002	0.014
setCellsMeta	0.010	0.001	0.013
setExpName	0.018	0.002	0.019
setOptimizedParams	0.011	0.002	0.012
setProcessedImages	0.009	0.001	0.011
setProcessingStatus	0.011	0.002	0.013
setTrackedCellsMeta	0.010	0.002	0.012
setTrackedCentroids	0.011	0.002	0.014
setTrackedPositions	0.011	0.001	0.014
setTrackingStats	0.009	0.001	0.011
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.023	0.007	0.031
track	0.009	0.000	0.009
trackHypercubeBuild	0.001	0.001	0.002
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.000
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.046	0.007	0.053
visualizeTrcks	0.027	0.002	0.029
warnMessage	0.001	0.001	0.000
wsaPreProcessing	0.042	0.001	0.043