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"	4756
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4514
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4441
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4406
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: 2025-03-18 01:24:09 -0400 (Tue, 18 Mar 2025)

EndedAt: 2025-03-18 01:28:55 -0400 (Tue, 18 Mar 2025)

EllapsedTime: 286.6 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 11.320  0.079  11.498
getDACtable  6.263  0.037   6.378
MSD          4.946  0.149   5.327
* 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 Mar 18 01:28:34 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 
  5.949   0.556   6.511

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.004
CellMig-class	0.041	0.008	0.049
CellMigPCA	3.469	0.060	3.546
CellMigPCAclust	0.011	0.005	0.017
CellMigPCAclustALL	2.195	0.023	2.243
CellTracker	0.024	0.009	0.033
CellTrackerMainLoop	0.007	0.010	0.018
CentroidArray	0.024	0.008	0.032
CentroidValidation	1.602	0.034	1.659
ComputeTracksStats	0.045	0.009	0.055
DetectRadii	0.006	0.001	0.007
DiAutoCor	4.483	0.031	4.567
DiRatio	0.034	0.006	0.041
DiRatioPlot	0.073	0.026	0.099
EstimateDiameterRange	0.030	0.003	0.034
FMI	1.553	0.012	1.581
FianlizeOptiParams	0.001	0.001	0.001
FilterTrackedCells	0.006	0.002	0.009
FinRes	2.110	0.031	2.212
ForwardMigration	3.179	0.020	3.241
GenAllCombos	0.006	0.001	0.007
LinearConv2	0.054	0.002	0.088
LoadTiff	0.001	0.001	0.002
MSD	4.946	0.149	5.327
MakeHypercube	0.003	0.002	0.005
MigrationStats	0.002	0.001	0.004
NextOdd	0.001	0.001	0.001
NonParallel4OptimizeParams	0.001	0.001	0.002
NonParallelTrackLoop	0.001	0.000	0.001
OptimizeParams	0.020	0.006	0.027
OptimizeParamsMainLoop	0.006	0.011	0.019
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.683	0.042	0.777
PlotTracksSeparately	0.013	0.005	0.019
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.239	0.014	0.256
ThreeConditions	0.018	0.007	0.025
TrackCellsDataset	0.019	0.006	0.025
TrajectoryDataset	0.031	0.007	0.038
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	3.441	0.026	3.488
VisualizeCntr	0.004	0.002	0.005
VisualizeImg	0.010	0.002	0.012
VisualizeStackCentroids	0.086	0.018	0.105
WSADataset	0.009	0.006	0.015
aggregateFR	2.028	0.018	2.065
aggregateTrackedCells	0.032	0.015	0.050
bpass	0.160	0.005	0.180
circshift	0.001	0.000	0.002
cntrd	2.423	0.037	2.531
fixDA	0.001	0.001	0.001
fixExpName	0.001	0.001	0.001
fixFM1	0.000	0.000	0.001
fixFM2	0.001	0.000	0.000
fixFM3	0.000	0.001	0.001
fixFM4	0.001	0.000	0.001
fixFM5	0.000	0.000	0.001
fixFM6	0.000	0.000	0.001
fixID1	0.001	0.001	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0.000	0.000	0.002
fixPER3	0.001	0.001	0.002
getAvailableAggrMetrics	3.075	0.029	3.145
getCellImages	0.855	2.512	3.458
getCellMigSlot	0.851	1.624	2.498
getCellTrackMeta	0.019	0.008	0.027
getCellTrackStats	0.027	0.010	0.037
getCellTracks	0.02	0.01	0.03
getCellsMeta	0.018	0.007	0.026
getCellsStats	0.026	0.009	0.035
getDACtable	6.263	0.037	6.378
getDiRatio	0.041	0.009	0.051
getFMItable	1.506	0.016	1.545
getForMigtable	1.818	0.017	1.841
getImageCentroids	0.035	0.013	0.048
getImageStacks	0.086	0.017	0.104
getMSDtable	11.320	0.079	11.498
getOptimizedParameters	0.019	0.007	0.026
getOptimizedParams	0.022	0.010	0.032
getPerAndSpeed	0.685	0.047	0.738
getPopulationStats	0.022	0.009	0.032
getProcessedImages	0.884	3.463	4.377
getProcessingStatus	0.019	0.009	0.027
getResults	2.009	0.030	2.050
getTracks	0.021	0.006	0.027
getVACtable	3.455	0.020	3.500
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.002	0.001	0.003
internalPermutation	0.002	0.001	0.002
matfix	0.003	0.001	0.003
nontrivialBondTracking	0.002	0.001	0.002
pkfnd	2.375	0.040	2.425
plot3DAllTracks	0.000	0.001	0.001
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.032	0.008	0.041
plotSampleTracks	0.023	0.008	0.032
preProcCellMig	0.009	0.006	0.015
rmPreProcessing	0.242	0.022	0.268
runTrackingPermutation	0.003	0.001	0.003
setAnalyticParams	0.019	0.007	0.027
setCellMigSlot	0.032	0.007	0.040
setCellTracks	0.020	0.007	0.027
setCellsMeta	0.019	0.008	0.027
setExpName	0.034	0.007	0.041
setOptimizedParams	0.020	0.007	0.027
setProcessedImages	0.019	0.007	0.026
setProcessingStatus	0.018	0.006	0.025
setTrackedCellsMeta	0.020	0.007	0.027
setTrackedCentroids	0.042	0.012	0.055
setTrackedPositions	0.020	0.005	0.027
setTrackingStats	0.020	0.008	0.028
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.000	0.003
track	0.020	0.002	0.023
trackHypercubeBuild	0.002	0.001	0.002
trackSlideProcessing	0.001	0.000	0.002
trackSlideWrapUp	0.002	0.000	0.002
trivialBondRaster	0.003	0.001	0.004
trivialBondTracking	0.001	0.001	0.001
visualizeCellTracks	0.091	0.016	0.112
visualizeTrcks	0.045	0.003	0.049
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.152	0.007	0.160