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 (2025-06-13) -- "Great Square Root"	4821
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4610
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4553
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4539
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: 2025-08-25 19:38:23 -0400 (Mon, 25 Aug 2025)

EndedAt: 2025-08-25 19:40:47 -0400 (Mon, 25 Aug 2025)

EllapsedTime: 144.3 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 (2025-06-13)
* 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 (2025-06-13) -- "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 -- Mon Aug 25 19:40:34 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 
  3.322   0.339   3.664

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.002
CellMig-class	0.023	0.002	0.025
CellMigPCA	1.721	0.030	1.761
CellMigPCAclust	0.006	0.001	0.007
CellMigPCAclustALL	0.718	0.042	0.764
CellTracker	0.012	0.002	0.014
CellTrackerMainLoop	0.005	0.008	0.023
CentroidArray	0.013	0.002	0.015
CentroidValidation	0.492	0.018	0.514
ComputeTracksStats	0.020	0.003	0.022
DetectRadii	0.002	0.001	0.002
DiAutoCor	1.376	0.017	1.401
DiRatio	0.016	0.002	0.018
DiRatioPlot	0.035	0.015	0.054
EstimateDiameterRange	0.012	0.002	0.015
FMI	0.485	0.007	0.493
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.002	0.000	0.004
FinRes	0.677	0.015	0.697
ForwardMigration	1.093	0.010	1.107
GenAllCombos	0.002	0.001	0.003
LinearConv2	0.019	0.002	0.020
LoadTiff	0.000	0.001	0.002
MSD	1.671	0.021	1.704
MakeHypercube	0.002	0.001	0.002
MigrationStats	0.001	0.001	0.002
NextOdd	0.000	0.001	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.013	0.003	0.014
OptimizeParamsMainLoop	0.005	0.008	0.022
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.000	0.000	0.001
PerAndSpeed	0.303	0.027	0.341
PlotTracksSeparately	0.008	0.002	0.009
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.129	0.012	0.142
ThreeConditions	0.009	0.004	0.013
TrackCellsDataset	0.011	0.002	0.013
TrajectoryDataset	0.020	0.002	0.023
ValidateTrackingArgs	0	0	0
VeAutoCor	1.166	0.022	1.193
VisualizeCntr	0.001	0.001	0.002
VisualizeImg	0.005	0.001	0.006
VisualizeStackCentroids	0.044	0.007	0.051
WSADataset	0.006	0.001	0.007
aggregateFR	0.719	0.009	0.734
aggregateTrackedCells	0.018	0.005	0.022
bpass	0.065	0.003	0.068
circshift	0.000	0.000	0.001
cntrd	0.801	0.014	0.820
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0.000	0.001	0.000
fixFM4	0	0	0
fixFM5	0.000	0.000	0.001
fixFM6	0.000	0.000	0.001
fixID1	0.000	0.000	0.001
fixMSD	0	0	0
fixPER1	0.001	0.001	0.000
fixPER2	0.000	0.000	0.001
fixPER3	0.000	0.001	0.001
getAvailableAggrMetrics	1.024	0.007	1.035
getCellImages	0.255	0.791	1.052
getCellMigSlot	0.372	0.527	0.905
getCellTrackMeta	0.011	0.002	0.013
getCellTrackStats	0.014	0.002	0.016
getCellTracks	0.009	0.002	0.011
getCellsMeta	0.009	0.002	0.011
getCellsStats	0.012	0.002	0.014
getDACtable	2.046	0.015	2.067
getDiRatio	0.015	0.001	0.016
getFMItable	0.480	0.005	0.486
getForMigtable	0.625	0.005	0.633
getImageCentroids	0.018	0.003	0.021
getImageStacks	0.048	0.007	0.056
getMSDtable	4.142	0.042	4.207
getOptimizedParameters	0.010	0.003	0.013
getOptimizedParams	0.012	0.002	0.014
getPerAndSpeed	0.309	0.027	0.345
getPopulationStats	0.012	0.002	0.013
getProcessedImages	0.252	0.832	1.090
getProcessingStatus	0.011	0.002	0.012
getResults	0.708	0.014	0.729
getTracks	0.013	0.002	0.015
getVACtable	1.132	0.010	1.147
initializeTrackParams	0	0	0
innerBondRaster	0.001	0.000	0.001
internalPermutation	0.001	0.001	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.702	0.010	0.714
plot3DAllTracks	0.001	0.000	0.001
plot3DTracks	0.001	0.000	0.000
plotAllTracks	0.018	0.003	0.022
plotSampleTracks	0.012	0.004	0.016
preProcCellMig	0.005	0.001	0.007
rmPreProcessing	0.102	0.004	0.106
runTrackingPermutation	0.001	0.000	0.002
setAnalyticParams	0.010	0.002	0.012
setCellMigSlot	0.018	0.002	0.020
setCellTracks	0.011	0.003	0.015
setCellsMeta	0.013	0.002	0.014
setExpName	0.021	0.001	0.022
setOptimizedParams	0.013	0.002	0.015
setProcessedImages	0.009	0.001	0.012
setProcessingStatus	0.009	0.001	0.010
setTrackedCellsMeta	0.012	0.001	0.014
setTrackedCentroids	0.012	0.002	0.013
setTrackedPositions	0.013	0.002	0.014
setTrackingStats	0.012	0.003	0.014
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.001	0.000	0.001
track	0.012	0.001	0.013
trackHypercubeBuild	0.001	0.000	0.002
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.002	0.001	0.002
trivialBondTracking	0.000	0.001	0.001
visualizeCellTracks	0.058	0.010	0.092
visualizeTrcks	0.029	0.002	0.031
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.059	0.001	0.061