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"	4822
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4617
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4564
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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: 2025-09-03 19:42:17 -0400 (Wed, 03 Sep 2025)

EndedAt: 2025-09-03 19:44:38 -0400 (Wed, 03 Sep 2025)

EllapsedTime: 141.9 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 -- Wed Sep  3 19:44:26 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 
  3.375   0.343   3.723

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.003
CellMig-class	0.020	0.002	0.022
CellMigPCA	1.695	0.027	1.731
CellMigPCAclust	0.005	0.001	0.006
CellMigPCAclustALL	0.683	0.041	0.727
CellTracker	0.015	0.003	0.018
CellTrackerMainLoop	0.007	0.009	0.026
CentroidArray	0.014	0.002	0.017
CentroidValidation	0.436	0.014	0.452
ComputeTracksStats	0.018	0.002	0.021
DetectRadii	0.003	0.001	0.004
DiAutoCor	1.451	0.021	1.478
DiRatio	0.015	0.002	0.017
DiRatioPlot	0.033	0.015	0.054
EstimateDiameterRange	0.014	0.001	0.015
FMI	0.516	0.006	0.525
FianlizeOptiParams	0.000	0.001	0.000
FilterTrackedCells	0.002	0.001	0.003
FinRes	0.705	0.017	0.731
ForwardMigration	0.986	0.008	0.999
GenAllCombos	0.002	0.000	0.003
LinearConv2	0.017	0.001	0.018
LoadTiff	0.000	0.001	0.001
MSD	1.643	0.020	1.673
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.001	0.001	0.001
NextOdd	0.001	0.000	0.000
NonParallel4OptimizeParams	0.001	0.001	0.001
NonParallelTrackLoop	0.001	0.000	0.000
OptimizeParams	0.011	0.002	0.013
OptimizeParamsMainLoop	0.004	0.007	0.022
Parallel4OptimizeParams	0.001	0.001	0.001
ParallelTrackLoop	0.000	0.000	0.001
PerAndSpeed	0.308	0.026	0.345
PlotTracksSeparately	0.008	0.002	0.009
PostProcessTracking	0.001	0.000	0.000
Prep4OptimizeParams	0.139	0.016	0.160
ThreeConditions	0.008	0.003	0.011
TrackCellsDataset	0.012	0.002	0.013
TrajectoryDataset	0.017	0.001	0.018
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.111	0.021	1.136
VisualizeCntr	0.001	0.000	0.003
VisualizeImg	0.004	0.001	0.006
VisualizeStackCentroids	0.049	0.007	0.057
WSADataset	0.004	0.001	0.005
aggregateFR	0.690	0.006	0.698
aggregateTrackedCells	0.017	0.004	0.022
bpass	0.062	0.002	0.065
circshift	0.000	0.001	0.000
cntrd	0.744	0.017	0.764
fixDA	0.001	0.000	0.001
fixExpName	0	0	0
fixFM1	0.000	0.001	0.001
fixFM2	0	0	0
fixFM3	0.001	0.000	0.001
fixFM4	0	0	0
fixFM5	0.000	0.000	0.001
fixFM6	0.000	0.001	0.000
fixID1	0.001	0.000	0.001
fixMSD	0.001	0.000	0.000
fixPER1	0.000	0.001	0.001
fixPER2	0	0	0
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	0.985	0.008	0.997
getCellImages	0.264	1.077	1.351
getCellMigSlot	0.360	0.571	0.936
getCellTrackMeta	0.009	0.002	0.010
getCellTrackStats	0.014	0.003	0.017
getCellTracks	0.010	0.003	0.012
getCellsMeta	0.012	0.002	0.014
getCellsStats	0.012	0.003	0.014
getDACtable	1.992	0.018	2.018
getDiRatio	0.021	0.002	0.023
getFMItable	0.425	0.005	0.431
getForMigtable	0.607	0.006	0.617
getImageCentroids	0.018	0.003	0.021
getImageStacks	0.046	0.008	0.054
getMSDtable	4.168	0.043	4.233
getOptimizedParameters	0.009	0.001	0.011
getOptimizedParams	0.011	0.002	0.013
getPerAndSpeed	0.304	0.028	0.341
getPopulationStats	0.011	0.002	0.012
getProcessedImages	0.270	0.895	1.176
getProcessingStatus	0.009	0.001	0.010
getResults	0.649	0.012	0.666
getTracks	0.013	0.002	0.015
getVACtable	1.104	0.009	1.115
initializeTrackParams	0.001	0.000	0.000
innerBondRaster	0.002	0.000	0.001
internalPermutation	0.000	0.000	0.001
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.002	0.000	0.001
pkfnd	0.650	0.011	0.662
plot3DAllTracks	0.001	0.000	0.000
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.016	0.004	0.019
plotSampleTracks	0.014	0.004	0.020
preProcCellMig	0.005	0.001	0.007
rmPreProcessing	0.102	0.003	0.105
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.009	0.001	0.010
setCellMigSlot	0.020	0.001	0.021
setCellTracks	0.010	0.002	0.012
setCellsMeta	0.012	0.002	0.014
setExpName	0.018	0.001	0.019
setOptimizedParams	0.010	0.002	0.012
setProcessedImages	0.009	0.001	0.011
setProcessingStatus	0.009	0.002	0.011
setTrackedCellsMeta	0.010	0.001	0.012
setTrackedCentroids	0.012	0.003	0.015
setTrackedPositions	0.011	0.002	0.014
setTrackingStats	0.012	0.003	0.015
sinkAway	0.000	0.001	0.000
subNetworkTracking	0.001	0.000	0.001
track	0.008	0.001	0.008
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.001	0.002
trivialBondTracking	0.001	0.001	0.001
visualizeCellTracks	0.060	0.013	0.073
visualizeTrcks	0.027	0.002	0.029
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.056	0.002	0.058