Multiple platform build/check report for BioC 3.20 - CHECK results for cellmigRation on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2025-04-01 00:28:50 -0400 (Tue, 01 Apr 2025)

EndedAt: 2025-04-01 00:33:37 -0400 (Tue, 01 Apr 2025)

EllapsedTime: 287.0 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.14.0’
* 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 11.529  0.087  11.698
getDACtable  6.405  0.047   6.509
MSD          5.062  0.146   5.453
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘cellmigRation’ ...
** 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 4.4.3 (2025-02-28) -- "Trophy Case"
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 Apr  1 00:33:16 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 
  6.039   0.574   6.632

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.002	0.004
CellMig-class	0.044	0.008	0.052
CellMigPCA	3.583	0.060	3.671
CellMigPCAclust	0.011	0.007	0.018
CellMigPCAclustALL	2.179	0.019	2.218
CellTracker	0.024	0.010	0.034
CellTrackerMainLoop	0.007	0.009	0.018
CentroidArray	0.027	0.008	0.034
CentroidValidation	1.630	0.044	1.722
ComputeTracksStats	0.045	0.009	0.056
DetectRadii	0.006	0.000	0.006
DiAutoCor	4.587	0.035	4.666
DiRatio	0.033	0.007	0.039
DiRatioPlot	0.071	0.026	0.098
EstimateDiameterRange	0.033	0.003	0.042
FMI	1.583	0.015	1.607
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.006	0.001	0.008
FinRes	2.204	0.031	2.260
ForwardMigration	3.248	0.021	3.294
GenAllCombos	0.006	0.001	0.007
LinearConv2	0.054	0.002	0.058
LoadTiff	0.001	0.001	0.002
MSD	5.062	0.146	5.453
MakeHypercube	0.003	0.002	0.006
MigrationStats	0.002	0.001	0.004
NextOdd	0.000	0.001	0.001
NonParallel4OptimizeParams	0.002	0.001	0.002
NonParallelTrackLoop	0.001	0.000	0.001
OptimizeParams	0.020	0.008	0.029
OptimizeParamsMainLoop	0.006	0.009	0.017
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.001	0.001
PerAndSpeed	0.695	0.046	0.749
PlotTracksSeparately	0.012	0.006	0.018
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.247	0.014	0.268
ThreeConditions	0.018	0.009	0.034
TrackCellsDataset	0.021	0.009	0.030
TrajectoryDataset	0.031	0.007	0.038
ValidateTrackingArgs	0.000	0.001	0.001
VeAutoCor	3.537	0.033	3.610
VisualizeCntr	0.004	0.002	0.007
VisualizeImg	0.009	0.001	0.012
VisualizeStackCentroids	0.09	0.02	0.11
WSADataset	0.009	0.006	0.016
aggregateFR	2.072	0.019	2.103
aggregateTrackedCells	0.031	0.014	0.045
bpass	0.159	0.004	0.165
circshift	0.001	0.001	0.002
cntrd	2.474	0.038	2.533
fixDA	0.000	0.000	0.001
fixExpName	0.000	0.001	0.001
fixFM1	0.001	0.001	0.001
fixFM2	0.000	0.001	0.001
fixFM3	0.001	0.001	0.001
fixFM4	0.000	0.000	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.000	0.001	0.001
fixID1	0.001	0.001	0.002
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0	0	0
fixPER3	0.001	0.001	0.002
getAvailableAggrMetrics	3.083	0.026	3.125
getCellImages	0.836	2.524	3.392
getCellMigSlot	0.830	1.618	2.461
getCellTrackMeta	0.019	0.008	0.027
getCellTrackStats	0.028	0.012	0.040
getCellTracks	0.020	0.012	0.032
getCellsMeta	0.020	0.008	0.029
getCellsStats	0.024	0.010	0.035
getDACtable	6.405	0.047	6.509
getDiRatio	0.041	0.009	0.049
getFMItable	1.537	0.017	1.568
getForMigtable	1.882	0.019	1.930
getImageCentroids	0.036	0.015	0.052
getImageStacks	0.088	0.020	0.108
getMSDtable	11.529	0.087	11.698
getOptimizedParameters	0.019	0.008	0.028
getOptimizedParams	0.021	0.012	0.033
getPerAndSpeed	0.680	0.048	0.732
getPopulationStats	0.022	0.010	0.031
getProcessedImages	0.860	3.436	4.343
getProcessingStatus	0.019	0.008	0.029
getResults	2.046	0.032	2.090
getTracks	0.022	0.008	0.030
getVACtable	3.538	0.025	3.586
initializeTrackParams	0.001	0.001	0.002
innerBondRaster	0.002	0.001	0.004
internalPermutation	0.002	0.000	0.003
matfix	0.003	0.001	0.003
nontrivialBondTracking	0.002	0.000	0.002
pkfnd	2.514	0.037	2.565
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.033	0.011	0.088
plotSampleTracks	0.024	0.010	0.036
preProcCellMig	0.007	0.007	0.016
rmPreProcessing	0.249	0.022	0.272
runTrackingPermutation	0.003	0.000	0.003
setAnalyticParams	0.020	0.008	0.028
setCellMigSlot	0.032	0.008	0.041
setCellTracks	0.018	0.008	0.027
setCellsMeta	0.020	0.009	0.029
setExpName	0.032	0.008	0.039
setOptimizedParams	0.019	0.008	0.028
setProcessedImages	0.021	0.011	0.032
setProcessingStatus	0.019	0.009	0.028
setTrackedCellsMeta	0.019	0.009	0.030
setTrackedCentroids	0.041	0.012	0.052
setTrackedPositions	0.019	0.007	0.028
setTrackingStats	0.020	0.008	0.027
sinkAway	0.001	0.001	0.001
subNetworkTracking	0.002	0.001	0.003
track	0.021	0.001	0.022
trackHypercubeBuild	0.002	0.001	0.002
trackSlideProcessing	0.001	0.001	0.002
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.003	0.000	0.004
trivialBondTracking	0.001	0.001	0.002
visualizeCellTracks	0.093	0.020	0.113
visualizeTrcks	0.044	0.004	0.049
warnMessage	0.001	0.001	0.002
wsaPreProcessing	0.149	0.008	0.158