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"	4832
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4620
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4565
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4563
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: 2025-09-26 20:02:06 -0400 (Fri, 26 Sep 2025)

EndedAt: 2025-09-26 20:04:42 -0400 (Fri, 26 Sep 2025)

EllapsedTime: 156.1 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_1.17.0.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 -- Fri Sep 26 20:04:29 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 
  3.731   0.364   4.118

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.003
CellMig-class	0.028	0.003	0.032
CellMigPCA	2.035	0.079	2.123
CellMigPCAclust	0.006	0.002	0.008
CellMigPCAclustALL	0.727	0.009	0.739
CellTracker	0.014	0.003	0.017
CellTrackerMainLoop	0.005	0.007	0.023
CentroidArray	0.013	0.003	0.016
CentroidValidation	0.492	0.018	0.513
ComputeTracksStats	0.022	0.003	0.025
DetectRadii	0.003	0.000	0.004
DiAutoCor	1.539	0.018	1.564
DiRatio	0.019	0.001	0.020
DiRatioPlot	0.036	0.015	0.055
EstimateDiameterRange	0.015	0.002	0.017
FMI	0.561	0.007	0.572
FianlizeOptiParams	0.001	0.001	0.001
FilterTrackedCells	0.003	0.001	0.004
FinRes	0.784	0.017	0.809
ForwardMigration	1.107	0.009	1.122
GenAllCombos	0.003	0.001	0.003
LinearConv2	0.022	0.002	0.024
LoadTiff	0.001	0.001	0.001
MSD	1.755	0.020	1.786
MakeHypercube	0.001	0.001	0.003
MigrationStats	0.001	0.001	0.002
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.011	0.002	0.013
OptimizeParamsMainLoop	0.004	0.007	0.024
Parallel4OptimizeParams	0.001	0.001	0.001
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.313	0.029	0.353
PlotTracksSeparately	0.007	0.001	0.007
PostProcessTracking	0.000	0.001	0.000
Prep4OptimizeParams	0.095	0.004	0.100
ThreeConditions	0.010	0.003	0.013
TrackCellsDataset	0.011	0.001	0.013
TrajectoryDataset	0.031	0.003	0.034
ValidateTrackingArgs	0	0	0
VeAutoCor	1.266	0.019	1.292
VisualizeCntr	0.003	0.001	0.003
VisualizeImg	0.004	0.001	0.005
VisualizeStackCentroids	0.049	0.008	0.058
WSADataset	0.005	0.001	0.006
aggregateFR	0.743	0.007	0.752
aggregateTrackedCells	0.017	0.004	0.021
bpass	0.079	0.003	0.082
circshift	0.000	0.000	0.001
cntrd	0.819	0.013	0.838
fixDA	0.001	0.000	0.001
fixExpName	0.000	0.001	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0.001	0.001	0.001
fixFM4	0.001	0.000	0.000
fixFM5	0.001	0.000	0.001
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.001	0.001
fixMSD	0.001	0.000	0.001
fixPER1	0.001	0.000	0.000
fixPER2	0.001	0.001	0.000
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	1.102	0.011	1.119
getCellImages	0.274	0.983	1.268
getCellMigSlot	0.354	0.674	1.036
getCellTrackMeta	0.010	0.002	0.012
getCellTrackStats	0.012	0.003	0.016
getCellTracks	0.009	0.003	0.012
getCellsMeta	0.009	0.002	0.011
getCellsStats	0.013	0.003	0.016
getDACtable	2.260	0.022	2.290
getDiRatio	0.020	0.002	0.023
getFMItable	0.522	0.005	0.527
getForMigtable	0.629	0.006	0.636
getImageCentroids	0.019	0.004	0.023
getImageStacks	0.045	0.008	0.054
getMSDtable	4.125	0.035	4.178
getOptimizedParameters	0.012	0.002	0.014
getOptimizedParams	0.014	0.003	0.017
getPerAndSpeed	0.313	0.031	0.358
getPopulationStats	0.009	0.002	0.011
getProcessedImages	0.265	1.281	1.558
getProcessingStatus	0.011	0.002	0.013
getResults	0.698	0.014	0.718
getTracks	0.012	0.002	0.014
getVACtable	1.154	0.013	1.175
initializeTrackParams	0	0	0
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.765	0.010	0.779
plot3DAllTracks	0.000	0.001	0.000
plot3DTracks	0	0	0
plotAllTracks	0.018	0.004	0.022
plotSampleTracks	0.013	0.004	0.017
preProcCellMig	0.006	0.002	0.007
rmPreProcessing	0.113	0.003	0.116
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.011	0.002	0.012
setCellMigSlot	0.020	0.002	0.022
setCellTracks	0.011	0.002	0.012
setCellsMeta	0.010	0.002	0.012
setExpName	0.018	0.002	0.019
setOptimizedParams	0.012	0.002	0.014
setProcessedImages	0.009	0.001	0.012
setProcessingStatus	0.009	0.002	0.010
setTrackedCellsMeta	0.011	0.002	0.015
setTrackedCentroids	0.012	0.002	0.014
setTrackedPositions	0.009	0.002	0.011
setTrackingStats	0.009	0.001	0.011
sinkAway	0.001	0.000	0.001
subNetworkTracking	0.024	0.006	0.029
track	0.011	0.001	0.012
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.001	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.000
visualizeCellTracks	0.048	0.007	0.055
visualizeTrcks	0.026	0.002	0.029
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.058	0.002	0.060