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"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4670
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4604
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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: 2025-12-09 02:16:36 -0500 (Tue, 09 Dec 2025)

EndedAt: 2025-12-09 02:21:47 -0500 (Tue, 09 Dec 2025)

EllapsedTime: 311.5 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_1.18.0.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 10.622  0.071  11.018
getDACtable  6.027  0.035   6.324
* 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 -- Tue Dec  9 02:21:26 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 
  6.797   0.594   7.862

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.005
CellMig-class	0.042	0.008	0.050
CellMigPCA	4.363	0.185	4.809
CellMigPCAclust	0.011	0.005	0.018
CellMigPCAclustALL	1.961	0.033	2.092
CellTracker	0.024	0.008	0.036
CellTrackerMainLoop	0.007	0.008	0.018
CentroidArray	0.026	0.008	0.035
CentroidValidation	1.476	0.045	1.597
ComputeTracksStats	0.042	0.007	0.052
DetectRadii	0.006	0.001	0.007
DiAutoCor	4.092	0.040	4.316
DiRatio	0.034	0.006	0.042
DiRatioPlot	0.057	0.024	0.087
EstimateDiameterRange	0.030	0.003	0.032
FMI	1.418	0.014	1.505
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.006	0.001	0.007
FinRes	1.912	0.031	2.046
ForwardMigration	2.877	0.022	3.039
GenAllCombos	0.005	0.001	0.007
LinearConv2	0.051	0.003	0.055
LoadTiff	0.001	0.001	0.002
MSD	4.352	0.059	4.575
MakeHypercube	0.003	0.001	0.004
MigrationStats	0.001	0.002	0.003
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.002	0.000	0.002
NonParallelTrackLoop	0.001	0.000	0.000
OptimizeParams	0.019	0.007	0.027
OptimizeParamsMainLoop	0.006	0.010	0.018
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.000	0.000	0.002
PerAndSpeed	0.671	0.044	0.758
PlotTracksSeparately	0.013	0.006	0.022
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.217	0.008	0.245
ThreeConditions	0.018	0.010	0.033
TrackCellsDataset	0.019	0.007	0.026
TrajectoryDataset	0.031	0.006	0.038
ValidateTrackingArgs	0.001	0.001	0.001
VeAutoCor	3.300	0.025	3.493
VisualizeCntr	0.004	0.002	0.006
VisualizeImg	0.009	0.002	0.011
VisualizeStackCentroids	0.089	0.018	0.112
WSADataset	0.009	0.006	0.016
aggregateFR	1.962	0.016	2.071
aggregateTrackedCells	0.032	0.016	0.051
bpass	0.154	0.004	0.168
circshift	0.001	0.000	0.002
cntrd	2.303	0.027	2.424
fixDA	0.001	0.001	0.001
fixExpName	0.000	0.001	0.001
fixFM1	0.001	0.001	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0.000	0.000	0.001
fixFM4	0.001	0.000	0.001
fixFM5	0.000	0.000	0.001
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.000	0.001
fixMSD	0.000	0.001	0.001
fixPER1	0.001	0.001	0.001
fixPER2	0.000	0.001	0.001
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	2.876	0.021	3.049
getCellImages	0.839	2.597	3.605
getCellMigSlot	0.833	1.636	2.565
getCellTrackMeta	0.020	0.009	0.031
getCellTrackStats	0.027	0.010	0.038
getCellTracks	0.020	0.011	0.031
getCellsMeta	0.019	0.007	0.030
getCellsStats	0.025	0.008	0.047
getDACtable	6.027	0.035	6.324
getDiRatio	0.039	0.007	0.054
getFMItable	1.418	0.013	1.468
getForMigtable	1.752	0.016	1.780
getImageCentroids	0.032	0.010	0.044
getImageStacks	0.087	0.017	0.103
getMSDtable	10.622	0.071	11.018
getOptimizedParameters	0.018	0.007	0.025
getOptimizedParams	0.023	0.009	0.031
getPerAndSpeed	0.622	0.044	0.697
getPopulationStats	0.021	0.007	0.029
getProcessedImages	0.851	3.854	4.969
getProcessingStatus	0.018	0.006	0.025
getResults	1.878	0.029	2.057
getTracks	0.022	0.007	0.041
getVACtable	3.244	0.029	3.523
initializeTrackParams	0.001	0.001	0.002
innerBondRaster	0.002	0.000	0.004
internalPermutation	0.002	0.001	0.003
matfix	0.002	0.001	0.003
nontrivialBondTracking	0.002	0.001	0.002
pkfnd	2.252	0.027	2.346
plot3DAllTracks	0.001	0.001	0.001
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.032	0.008	0.045
plotSampleTracks	0.023	0.008	0.033
preProcCellMig	0.008	0.006	0.015
rmPreProcessing	0.224	0.007	0.241
runTrackingPermutation	0.003	0.001	0.005
setAnalyticParams	0.019	0.007	0.034
setCellMigSlot	0.032	0.006	0.043
setCellTracks	0.019	0.006	0.027
setCellsMeta	0.019	0.007	0.029
setExpName	0.033	0.006	0.043
setOptimizedParams	0.019	0.006	0.026
setProcessedImages	0.019	0.007	0.026
setProcessingStatus	0.036	0.007	0.044
setTrackedCellsMeta	0.020	0.006	0.027
setTrackedCentroids	0.019	0.006	0.034
setTrackedPositions	0.019	0.006	0.033
setTrackingStats	0.020	0.007	0.047
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.000	0.002
track	0.019	0.002	0.026
trackHypercubeBuild	0.001	0.000	0.002
trackSlideProcessing	0.001	0.000	0.002
trackSlideWrapUp	0.001	0.000	0.002
trivialBondRaster	0.003	0.000	0.003
trivialBondTracking	0.001	0.001	0.002
visualizeCellTracks	0.095	0.017	0.142
visualizeTrcks	0.043	0.003	0.057
warnMessage	0.001	0.001	0.001
wsaPreProcessing	0.145	0.007	0.183