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"	4882
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: 2025-12-12 01:58:51 -0500 (Fri, 12 Dec 2025)

EndedAt: 2025-12-12 02:03:54 -0500 (Fri, 12 Dec 2025)

EllapsedTime: 302.9 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 10.738  0.076  11.175
getDACtable  5.925  0.033   6.097
* 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 12 02:03:34 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 
  6.731   0.581   7.694

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.004
CellMig-class	0.042	0.008	0.049
CellMigPCA	4.364	0.183	4.897
CellMigPCAclust	0.011	0.006	0.018
CellMigPCAclustALL	1.973	0.042	2.139
CellTracker	0.024	0.010	0.034
CellTrackerMainLoop	0.007	0.009	0.019
CentroidArray	0.025	0.007	0.033
CentroidValidation	1.487	0.048	1.605
ComputeTracksStats	0.044	0.007	0.053
DetectRadii	0.005	0.000	0.007
DiAutoCor	4.093	0.040	4.286
DiRatio	0.034	0.005	0.040
DiRatioPlot	0.056	0.024	0.083
EstimateDiameterRange	0.029	0.003	0.033
FMI	1.418	0.014	1.487
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.006	0.001	0.007
FinRes	1.910	0.026	2.038
ForwardMigration	2.878	0.018	3.026
GenAllCombos	0.006	0.001	0.008
LinearConv2	0.051	0.002	0.054
LoadTiff	0.001	0.001	0.003
MSD	4.435	0.078	4.764
MakeHypercube	0.003	0.002	0.005
MigrationStats	0.002	0.001	0.004
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.003
NonParallelTrackLoop	0.001	0.001	0.001
OptimizeParams	0.019	0.006	0.027
OptimizeParamsMainLoop	0.006	0.009	0.021
Parallel4OptimizeParams	0.001	0.001	0.002
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.659	0.042	0.730
PlotTracksSeparately	0.013	0.005	0.017
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.222	0.007	0.240
ThreeConditions	0.017	0.007	0.025
TrackCellsDataset	0.019	0.006	0.024
TrajectoryDataset	0.030	0.006	0.036
ValidateTrackingArgs	0.001	0.001	0.002
VeAutoCor	3.318	0.026	3.500
VisualizeCntr	0.004	0.001	0.007
VisualizeImg	0.009	0.002	0.011
VisualizeStackCentroids	0.084	0.017	0.109
WSADataset	0.010	0.006	0.015
aggregateFR	1.960	0.015	2.063
aggregateTrackedCells	0.032	0.014	0.057
bpass	0.157	0.005	0.169
circshift	0.000	0.001	0.002
cntrd	2.331	0.027	2.467
fixDA	0.001	0.001	0.001
fixExpName	0.000	0.000	0.002
fixFM1	0.001	0.001	0.001
fixFM2	0.000	0.001	0.001
fixFM3	0.000	0.000	0.001
fixFM4	0.001	0.001	0.002
fixFM5	0.001	0.000	0.001
fixFM6	0.000	0.000	0.001
fixID1	0.001	0.000	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.001	0.001
fixPER2	0.000	0.001	0.001
fixPER3	0.001	0.001	0.002
getAvailableAggrMetrics	2.879	0.020	3.035
getCellImages	0.824	2.530	3.509
getCellMigSlot	0.803	1.574	2.408
getCellTrackMeta	0.018	0.007	0.025
getCellTrackStats	0.027	0.010	0.038
getCellTracks	0.020	0.011	0.032
getCellsMeta	0.019	0.008	0.027
getCellsStats	0.023	0.008	0.032
getDACtable	5.925	0.033	6.097
getDiRatio	0.038	0.008	0.046
getFMItable	1.430	0.012	1.519
getForMigtable	1.751	0.018	1.824
getImageCentroids	0.035	0.010	0.046
getImageStacks	0.085	0.019	0.106
getMSDtable	10.738	0.076	11.175
getOptimizedParameters	0.019	0.006	0.028
getOptimizedParams	0.022	0.008	0.032
getPerAndSpeed	0.624	0.042	0.699
getPopulationStats	0.022	0.008	0.032
getProcessedImages	0.854	3.495	4.542
getProcessingStatus	0.019	0.006	0.027
getResults	1.879	0.029	2.026
getTracks	0.021	0.007	0.031
getVACtable	3.224	0.026	3.380
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.002	0.001	0.003
internalPermutation	0.002	0.001	0.003
matfix	0.003	0.000	0.003
nontrivialBondTracking	0.001	0.000	0.002
pkfnd	2.279	0.029	2.542
plot3DAllTracks	0.001	0.001	0.001
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.029	0.007	0.036
plotSampleTracks	0.023	0.008	0.031
preProcCellMig	0.008	0.006	0.015
rmPreProcessing	0.228	0.007	0.239
runTrackingPermutation	0.002	0.000	0.003
setAnalyticParams	0.019	0.005	0.025
setCellMigSlot	0.033	0.006	0.038
setCellTracks	0.019	0.006	0.028
setCellsMeta	0.019	0.007	0.027
setExpName	0.033	0.006	0.043
setOptimizedParams	0.020	0.007	0.030
setProcessedImages	0.020	0.008	0.030
setProcessingStatus	0.037	0.009	0.051
setTrackedCellsMeta	0.020	0.006	0.027
setTrackedCentroids	0.019	0.006	0.043
setTrackedPositions	0.020	0.006	0.028
setTrackingStats	0.019	0.006	0.026
sinkAway	0.001	0.001	0.001
subNetworkTracking	0.002	0.000	0.003
track	0.019	0.001	0.025
trackHypercubeBuild	0.001	0.001	0.002
trackSlideProcessing	0.001	0.001	0.001
trackSlideWrapUp	0.001	0.000	0.002
trivialBondRaster	0.003	0.000	0.006
trivialBondTracking	0.001	0.001	0.002
visualizeCellTracks	0.091	0.017	0.116
visualizeTrcks	0.044	0.004	0.056
warnMessage	0.001	0.000	0.002
wsaPreProcessing	0.142	0.007	0.168