Multiple platform build/check report for BioC 3.22 - CHECK results for cellmigRation on merida1

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"	4883
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 merida1

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: 2025-12-19 01:45:02 -0500 (Fri, 19 Dec 2025)

EndedAt: 2025-12-19 01:50:11 -0500 (Fri, 19 Dec 2025)

EllapsedTime: 309.0 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 4.5.2 (2025-10-31)
* 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getMSDtable        10.460  0.064  10.726
getDACtable         5.977  0.039   6.501
getProcessedImages  0.880  4.031   6.100
getPerAndSpeed      0.627  0.059   5.433
* 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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 Dec 19 01:49:52 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 
  6.677   0.601   7.454

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.004
CellMig-class	0.042	0.006	0.051
CellMigPCA	4.408	0.182	4.746
CellMigPCAclust	0.012	0.006	0.017
CellMigPCAclustALL	1.933	0.037	1.979
CellTracker	0.024	0.008	0.032
CellTrackerMainLoop	0.007	0.011	0.021
CentroidArray	0.026	0.008	0.034
CentroidValidation	1.470	0.046	1.577
ComputeTracksStats	0.043	0.007	0.053
DetectRadii	0.006	0.001	0.007
DiAutoCor	4.071	0.044	4.295
DiRatio	0.034	0.006	0.042
DiRatioPlot	0.059	0.023	0.105
EstimateDiameterRange	0.030	0.003	0.039
FMI	1.425	0.018	1.499
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.007	0.002	0.008
FinRes	1.902	0.030	2.009
ForwardMigration	2.894	0.019	3.060
GenAllCombos	0.006	0.001	0.008
LinearConv2	0.050	0.002	0.056
LoadTiff	0.000	0.001	0.001
MSD	4.365	0.072	4.607
MakeHypercube	0.003	0.002	0.004
MigrationStats	0.002	0.002	0.004
NextOdd	0.000	0.000	0.001
NonParallel4OptimizeParams	0.002	0.001	0.003
NonParallelTrackLoop	0.001	0.001	0.001
OptimizeParams	0.020	0.006	0.027
OptimizeParamsMainLoop	0.006	0.010	0.023
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.002
PerAndSpeed	0.658	0.040	0.735
PlotTracksSeparately	0.013	0.005	0.018
PostProcessTracking	0.001	0.001	0.000
Prep4OptimizeParams	0.213	0.007	0.231
ThreeConditions	0.018	0.007	0.025
TrackCellsDataset	0.019	0.006	0.026
TrajectoryDataset	0.031	0.005	0.037
ValidateTrackingArgs	0.001	0.001	0.002
VeAutoCor	3.297	0.027	3.404
VisualizeCntr	0.004	0.001	0.005
VisualizeImg	0.009	0.002	0.011
VisualizeStackCentroids	0.087	0.015	0.106
WSADataset	0.009	0.004	0.013
aggregateFR	1.933	0.017	1.992
aggregateTrackedCells	0.032	0.013	0.048
bpass	0.153	0.004	0.158
circshift	0.001	0.001	0.002
cntrd	2.306	0.025	2.404
fixDA	0.001	0.000	0.001
fixExpName	0.000	0.001	0.001
fixFM1	0.001	0.001	0.001
fixFM2	0.001	0.000	0.002
fixFM3	0.000	0.000	0.001
fixFM4	0.001	0.000	0.001
fixFM5	0.001	0.001	0.001
fixFM6	0.000	0.001	0.001
fixID1	0.001	0.000	0.002
fixMSD	0.001	0.000	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0.000	0.000	0.001
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	2.801	0.020	2.919
getCellImages	0.840	2.548	3.513
getCellMigSlot	0.860	1.672	2.621
getCellTrackMeta	0.019	0.005	0.025
getCellTrackStats	0.028	0.009	0.038
getCellTracks	0.020	0.008	0.028
getCellsMeta	0.020	0.007	0.027
getCellsStats	0.024	0.007	0.031
getDACtable	5.977	0.039	6.501
getDiRatio	0.039	0.007	0.048
getFMItable	1.417	0.012	1.457
getForMigtable	1.696	0.014	1.737
getImageCentroids	0.035	0.013	0.046
getImageStacks	0.088	0.018	0.107
getMSDtable	10.460	0.064	10.726
getOptimizedParameters	0.020	0.005	0.030
getOptimizedParams	0.022	0.010	0.035
getPerAndSpeed	0.627	0.059	5.433
getPopulationStats	0.021	0.007	0.028
getProcessedImages	0.880	4.031	6.100
getProcessingStatus	0.019	0.005	0.033
getResults	1.865	0.027	2.022
getTracks	0.021	0.007	0.039
getVACtable	3.251	0.040	3.599
initializeTrackParams	0.001	0.001	0.002
innerBondRaster	0.002	0.001	0.004
internalPermutation	0.002	0.000	0.005
matfix	0.002	0.002	0.004
nontrivialBondTracking	0.002	0.001	0.005
pkfnd	2.294	0.035	2.551
plot3DAllTracks	0.000	0.001	0.001
plot3DTracks	0.001	0.001	0.001
plotAllTracks	0.031	0.008	0.045
plotSampleTracks	0.024	0.009	0.092
preProcCellMig	0.009	0.005	0.015
rmPreProcessing	0.228	0.009	0.255
runTrackingPermutation	0.003	0.001	0.006
setAnalyticParams	0.019	0.007	0.030
setCellMigSlot	0.032	0.005	0.038
setCellTracks	0.019	0.005	0.026
setCellsMeta	0.020	0.007	0.029
setExpName	0.032	0.005	0.082
setOptimizedParams	0.020	0.006	0.032
setProcessedImages	0.020	0.006	0.028
setProcessingStatus	0.036	0.007	0.045
setTrackedCellsMeta	0.020	0.006	0.025
setTrackedCentroids	0.019	0.007	0.026
setTrackedPositions	0.019	0.006	0.026
setTrackingStats	0.020	0.008	0.030
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.001	0.002
track	0.018	0.002	0.024
trackHypercubeBuild	0.002	0.001	0.002
trackSlideProcessing	0.001	0.001	0.002
trackSlideWrapUp	0.001	0.001	0.001
trivialBondRaster	0.003	0.000	0.006
trivialBondTracking	0.002	0.001	0.002
visualizeCellTracks	0.093	0.022	0.228
visualizeTrcks	0.045	0.004	0.052
warnMessage	0.001	0.001	0.002
wsaPreProcessing	0.135	0.007	0.178