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"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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: 2025-03-20 19:50:59 -0400 (Thu, 20 Mar 2025)

EndedAt: 2025-03-20 19:53:26 -0400 (Thu, 20 Mar 2025)

EllapsedTime: 146.8 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 20 19:53:13 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 
  3.376   0.370   3.753

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.002
CellMig-class	0.027	0.003	0.030
CellMigPCA	1.634	0.033	1.675
CellMigPCAclust	0.006	0.002	0.008
CellMigPCAclustALL	0.971	0.045	1.021
CellTracker	0.016	0.003	0.020
CellTrackerMainLoop	0.005	0.007	0.024
CentroidArray	0.011	0.002	0.013
CentroidValidation	0.507	0.019	0.530
ComputeTracksStats	0.023	0.002	0.025
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.410	0.017	1.431
DiRatio	0.017	0.001	0.018
DiRatioPlot	0.034	0.014	0.051
EstimateDiameterRange	0.015	0.002	0.018
FMI	0.496	0.007	0.506
FianlizeOptiParams	0.001	0.000	0.000
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.737	0.016	0.758
ForwardMigration	1.037	0.008	1.049
GenAllCombos	0.002	0.000	0.002
LinearConv2	0.017	0.002	0.019
LoadTiff	0.001	0.001	0.001
MSD	1.684	0.024	1.729
MakeHypercube	0.002	0.000	0.002
MigrationStats	0.001	0.001	0.002
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.001	0.000	0.000
OptimizeParams	0.010	0.002	0.013
OptimizeParamsMainLoop	0.005	0.014	0.033
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.296	0.026	0.333
PlotTracksSeparately	0.007	0.001	0.008
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.128	0.006	0.134
ThreeConditions	0.010	0.002	0.011
TrackCellsDataset	0.011	0.002	0.013
TrajectoryDataset	0.017	0.002	0.020
ValidateTrackingArgs	0	0	0
VeAutoCor	1.166	0.025	1.196
VisualizeCntr	0.003	0.001	0.004
VisualizeImg	0.005	0.001	0.005
VisualizeStackCentroids	0.051	0.009	0.061
WSADataset	0.005	0.002	0.007
aggregateFR	0.732	0.008	0.746
aggregateTrackedCells	0.018	0.005	0.023
bpass	0.061	0.002	0.064
circshift	0	0	0
cntrd	0.796	0.017	0.816
fixDA	0	0	0
fixExpName	0.001	0.000	0.000
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	0.001	0.001	0.001
fixMSD	0.001	0.000	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0	0	0
fixPER3	0.001	0.000	0.000
getAvailableAggrMetrics	1.094	0.009	1.107
getCellImages	0.276	0.900	1.186
getCellMigSlot	0.372	0.541	0.918
getCellTrackMeta	0.009	0.002	0.011
getCellTrackStats	0.013	0.004	0.017
getCellTracks	0.012	0.004	0.016
getCellsMeta	0.012	0.003	0.015
getCellsStats	0.014	0.003	0.016
getDACtable	2.110	0.023	2.151
getDiRatio	0.016	0.002	0.018
getFMItable	0.510	0.005	0.517
getForMigtable	0.883	0.010	0.897
getImageCentroids	0.015	0.003	0.017
getImageStacks	0.045	0.007	0.051
getMSDtable	3.887	0.040	3.950
getOptimizedParameters	0.011	0.002	0.012
getOptimizedParams	0.013	0.002	0.015
getPerAndSpeed	0.300	0.028	0.338
getPopulationStats	0.011	0.002	0.013
getProcessedImages	0.267	0.910	1.185
getProcessingStatus	0.009	0.002	0.010
getResults	0.697	0.015	0.721
getTracks	0.011	0.002	0.013
getVACtable	1.180	0.011	1.197
initializeTrackParams	0.001	0.000	0.000
innerBondRaster	0.002	0.001	0.002
internalPermutation	0.001	0.000	0.002
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.751	0.012	0.768
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0	0	0
plotAllTracks	0.016	0.004	0.020
plotSampleTracks	0.014	0.003	0.018
preProcCellMig	0.006	0.001	0.007
rmPreProcessing	0.084	0.002	0.087
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.010	0.002	0.012
setCellMigSlot	0.021	0.002	0.024
setCellTracks	0.011	0.002	0.014
setCellsMeta	0.011	0.002	0.013
setExpName	0.020	0.002	0.023
setOptimizedParams	0.011	0.002	0.013
setProcessedImages	0.010	0.002	0.013
setProcessingStatus	0.011	0.002	0.014
setTrackedCellsMeta	0.011	0.003	0.013
setTrackedCentroids	0.012	0.003	0.015
setTrackedPositions	0.013	0.003	0.017
setTrackingStats	0.022	0.005	0.027
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.001	0.000	0.002
track	0.009	0.000	0.009
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.001	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.001	0.000	0.002
trivialBondTracking	0.000	0.001	0.000
visualizeCellTracks	0.051	0.010	0.063
visualizeTrcks	0.027	0.002	0.029
warnMessage	0.001	0.001	0.000
wsaPreProcessing	0.060	0.002	0.062