Multiple platform build/check report for BioC 3.21 - CHECK results for cellmigRation on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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: 1.16.0

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_1.16.0.tar.gz

StartedAt: 2025-04-21 19:38:01 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 19:40:20 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 138.7 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.16.0’
* 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-3.21-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 ‘1.16.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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 Apr 21 19:40:07 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 
  3.149   0.343   3.505

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.002
CellMig-class	0.024	0.002	0.027
CellMigPCA	1.443	0.029	1.482
CellMigPCAclust	0.005	0.001	0.007
CellMigPCAclustALL	0.895	0.038	0.935
CellTracker	0.013	0.003	0.016
CellTrackerMainLoop	0.004	0.007	0.023
CentroidArray	0.011	0.002	0.013
CentroidValidation	0.466	0.018	0.486
ComputeTracksStats	0.020	0.003	0.022
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.419	0.017	1.442
DiRatio	0.016	0.001	0.018
DiRatioPlot	0.034	0.014	0.052
EstimateDiameterRange	0.017	0.002	0.019
FMI	0.520	0.006	0.529
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.002	0.001	0.002
FinRes	0.686	0.015	0.708
ForwardMigration	1.049	0.009	1.064
GenAllCombos	0.003	0.001	0.003
LinearConv2	0.020	0.001	0.023
LoadTiff	0.001	0.000	0.001
MSD	1.566	0.020	1.593
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.001	0.001	0.001
NextOdd	0.001	0.001	0.000
NonParallel4OptimizeParams	0.001	0.000	0.002
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.013	0.003	0.016
OptimizeParamsMainLoop	0.005	0.007	0.021
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.313	0.027	0.351
PlotTracksSeparately	0.006	0.001	0.007
PostProcessTracking	0.000	0.001	0.000
Prep4OptimizeParams	0.131	0.010	0.142
ThreeConditions	0.009	0.002	0.011
TrackCellsDataset	0.012	0.002	0.014
TrajectoryDataset	0.020	0.002	0.021
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.242	0.023	1.273
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.004	0.001	0.006
VisualizeStackCentroids	0.043	0.007	0.050
WSADataset	0.007	0.001	0.008
aggregateFR	0.747	0.009	0.761
aggregateTrackedCells	0.015	0.004	0.019
bpass	0.063	0.003	0.066
circshift	0.000	0.001	0.001
cntrd	0.759	0.015	0.777
fixDA	0.001	0.001	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.001	0.000	0.001
fixFM5	0.001	0.000	0.000
fixFM6	0.000	0.001	0.000
fixID1	0.000	0.000	0.001
fixMSD	0.000	0.000	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0.001	0.000	0.001
fixPER3	0	0	0
getAvailableAggrMetrics	0.976	0.007	0.986
getCellImages	0.275	0.855	1.138
getCellMigSlot	0.371	0.551	0.929
getCellTrackMeta	0.011	0.002	0.013
getCellTrackStats	0.014	0.003	0.017
getCellTracks	0.011	0.002	0.013
getCellsMeta	0.012	0.002	0.013
getCellsStats	0.011	0.002	0.013
getDACtable	2.102	0.018	2.129
getDiRatio	0.019	0.002	0.020
getFMItable	0.511	0.006	0.517
getForMigtable	0.896	0.009	0.911
getImageCentroids	0.014	0.003	0.160
getImageStacks	0.050	0.008	0.058
getMSDtable	3.803	0.042	3.873
getOptimizedParameters	0.012	0.002	0.014
getOptimizedParams	0.012	0.003	0.014
getPerAndSpeed	0.269	0.026	0.304
getPopulationStats	0.010	0.002	0.012
getProcessedImages	0.272	1.323	1.606
getProcessingStatus	0.010	0.002	0.012
getResults	0.710	0.016	0.732
getTracks	0.012	0.002	0.013
getVACtable	1.061	0.009	1.076
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.001	0.001	0.001
internalPermutation	0.000	0.001	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.695	0.011	0.709
plot3DAllTracks	0	0	0
plot3DTracks	0.000	0.001	0.001
plotAllTracks	0.015	0.003	0.019
plotSampleTracks	0.013	0.003	0.017
preProcCellMig	0.004	0.001	0.006
rmPreProcessing	0.079	0.002	0.081
runTrackingPermutation	0.001	0.001	0.002
setAnalyticParams	0.009	0.001	0.011
setCellMigSlot	0.022	0.002	0.023
setCellTracks	0.009	0.002	0.010
setCellsMeta	0.009	0.002	0.010
setExpName	0.019	0.002	0.020
setOptimizedParams	0.010	0.001	0.012
setProcessedImages	0.011	0.002	0.014
setProcessingStatus	0.009	0.002	0.011
setTrackedCellsMeta	0.012	0.003	0.015
setTrackedCentroids	0.011	0.002	0.012
setTrackedPositions	0.010	0.001	0.011
setTrackingStats	0.020	0.004	0.024
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.002	0.001	0.001
track	0.011	0.001	0.011
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.000	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.001	0.000	0.002
trivialBondTracking	0.000	0.000	0.001
visualizeCellTracks	0.047	0.007	0.057
visualizeTrcks	0.026	0.002	0.027
warnMessage	0	0	0
wsaPreProcessing	0.053	0.001	0.054