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	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4518
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: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2025-03-27 20:09:00 -0400 (Thu, 27 Mar 2025)

EndedAt: 2025-03-27 20:11:22 -0400 (Thu, 27 Mar 2025)

EllapsedTime: 142.1 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* 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 ‘1.15.0’
* 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 ‘1.15.0’
** 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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
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 -- Thu Mar 27 20:11:10 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 
  3.208   0.360   3.584

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.002
CellMig-class	0.024	0.003	0.028
CellMigPCA	1.516	0.034	1.561
CellMigPCAclust	0.007	0.001	0.008
CellMigPCAclustALL	0.921	0.047	0.971
CellTracker	0.015	0.004	0.018
CellTrackerMainLoop	0.006	0.013	0.039
CentroidArray	0.015	0.002	0.017
CentroidValidation	0.488	0.018	0.508
ComputeTracksStats	0.022	0.003	0.025
DetectRadii	0.003	0.001	0.002
DiAutoCor	1.426	0.018	1.451
DiRatio	0.016	0.001	0.018
DiRatioPlot	0.035	0.015	0.054
EstimateDiameterRange	0.017	0.001	0.019
FMI	0.489	0.006	0.496
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.002	0.000	0.002
FinRes	0.718	0.018	0.749
ForwardMigration	1.056	0.010	1.072
GenAllCombos	0.003	0.000	0.004
LinearConv2	0.021	0.001	0.023
LoadTiff	0.001	0.000	0.003
MSD	1.607	0.020	1.638
MakeHypercube	0.002	0.001	0.002
MigrationStats	0.001	0.001	0.001
NextOdd	0.000	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.001	0.000
OptimizeParams	0.010	0.003	0.014
OptimizeParamsMainLoop	0.004	0.008	0.027
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.001	0.001
PerAndSpeed	0.314	0.028	0.352
PlotTracksSeparately	0.008	0.001	0.009
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.142	0.011	0.157
ThreeConditions	0.010	0.004	0.014
TrackCellsDataset	0.011	0.002	0.012
TrajectoryDataset	0.015	0.002	0.016
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	1.226	0.022	1.255
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.005	0.001	0.007
VisualizeStackCentroids	0.049	0.008	0.059
WSADataset	0.005	0.001	0.006
aggregateFR	0.743	0.007	0.751
aggregateTrackedCells	0.017	0.005	0.021
bpass	0.067	0.003	0.070
circshift	0	0	0
cntrd	0.787	0.018	0.807
fixDA	0.000	0.000	0.001
fixExpName	0	0	0
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0.000	0.000	0.001
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	1.103	0.008	1.117
getCellImages	0.281	0.882	1.170
getCellMigSlot	0.377	0.536	0.919
getCellTrackMeta	0.009	0.002	0.012
getCellTrackStats	0.015	0.003	0.018
getCellTracks	0.009	0.003	0.011
getCellsMeta	0.009	0.002	0.012
getCellsStats	0.012	0.002	0.014
getDACtable	2.286	0.024	2.321
getDiRatio	0.021	0.002	0.023
getFMItable	0.607	0.007	0.619
getForMigtable	0.933	0.010	0.948
getImageCentroids	0.018	0.003	0.021
getImageStacks	0.044	0.007	0.052
getMSDtable	3.837	0.038	3.895
getOptimizedParameters	0.013	0.002	0.016
getOptimizedParams	0.012	0.002	0.014
getPerAndSpeed	0.305	0.027	0.341
getPopulationStats	0.010	0.002	0.012
getProcessedImages	0.271	0.914	1.196
getProcessingStatus	0.010	0.003	0.012
getResults	0.670	0.016	0.694
getTracks	0.010	0.002	0.013
getVACtable	1.113	0.008	1.124
initializeTrackParams	0.000	0.001	0.001
innerBondRaster	0.002	0.001	0.002
internalPermutation	0.002	0.000	0.001
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.000	0.000	0.001
pkfnd	0.684	0.012	0.697
plot3DAllTracks	0.001	0.000	0.001
plot3DTracks	0	0	0
plotAllTracks	0.015	0.004	0.019
plotSampleTracks	0.012	0.003	0.017
preProcCellMig	0.006	0.001	0.007
rmPreProcessing	0.079	0.002	0.080
runTrackingPermutation	0.002	0.001	0.002
setAnalyticParams	0.012	0.002	0.014
setCellMigSlot	0.018	0.002	0.020
setCellTracks	0.011	0.002	0.013
setCellsMeta	0.010	0.003	0.013
setExpName	0.021	0.002	0.023
setOptimizedParams	0.009	0.002	0.012
setProcessedImages	0.009	0.002	0.012
setProcessingStatus	0.010	0.003	0.013
setTrackedCellsMeta	0.009	0.002	0.012
setTrackedCentroids	0.009	0.003	0.012
setTrackedPositions	0.009	0.002	0.011
setTrackingStats	0.021	0.006	0.028
sinkAway	0.000	0.001	0.001
subNetworkTracking	0.001	0.001	0.001
track	0.008	0.001	0.009
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.001	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.001	0.000	0.002
trivialBondTracking	0	0	0
visualizeCellTracks	0.052	0.008	0.060
visualizeTrcks	0.026	0.002	0.029
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.049	0.001	0.051