Multiple platform build/check report for BioC 3.22 - CHECK results for cellmigRation on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4826
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4616
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4563
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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: 1.17.0

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_1.17.0.tar.gz

StartedAt: 2025-09-02 19:41:50 -0400 (Tue, 02 Sep 2025)

EndedAt: 2025-09-02 19:44:15 -0400 (Tue, 02 Sep 2025)

EllapsedTime: 145.3 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.17.0’
* 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-3.22-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 ‘1.17.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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 Sep  2 19:44:02 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 
  3.439   0.362   3.825

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.002
CellMig-class	0.025	0.002	0.028
CellMigPCA	1.826	0.033	1.873
CellMigPCAclust	0.007	0.001	0.008
CellMigPCAclustALL	0.732	0.045	0.783
CellTracker	0.014	0.003	0.017
CellTrackerMainLoop	0.006	0.007	0.024
CentroidArray	0.012	0.002	0.014
CentroidValidation	0.502	0.018	0.523
ComputeTracksStats	0.023	0.003	0.026
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.488	0.019	1.514
DiRatio	0.016	0.002	0.018
DiRatioPlot	0.033	0.015	0.051
EstimateDiameterRange	0.013	0.002	0.015
FMI	0.531	0.007	0.540
FianlizeOptiParams	0.000	0.001	0.001
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.711	0.016	0.733
ForwardMigration	1.107	0.008	1.120
GenAllCombos	0.003	0.001	0.004
LinearConv2	0.024	0.002	0.026
LoadTiff	0.001	0.001	0.001
MSD	1.719	0.021	1.750
MakeHypercube	0.001	0.000	0.002
MigrationStats	0.001	0.000	0.001
NextOdd	0.001	0.000	0.000
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.001	0.000
OptimizeParams	0.013	0.003	0.016
OptimizeParamsMainLoop	0.004	0.009	0.022
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.311	0.025	0.347
PlotTracksSeparately	0.007	0.001	0.008
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.135	0.006	0.141
ThreeConditions	0.009	0.003	0.012
TrackCellsDataset	0.011	0.001	0.012
TrajectoryDataset	0.020	0.002	0.022
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	1.275	0.027	1.309
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.005	0.001	0.007
VisualizeStackCentroids	0.051	0.009	0.062
WSADataset	0.004	0.002	0.006
aggregateFR	0.792	0.007	0.803
aggregateTrackedCells	0.016	0.004	0.021
bpass	0.065	0.001	0.068
circshift	0	0	0
cntrd	0.809	0.014	0.826
fixDA	0.000	0.000	0.001
fixExpName	0	0	0
fixFM1	0.000	0.001	0.000
fixFM2	0.001	0.000	0.001
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.000	0.000	0.001
fixFM6	0.001	0.001	0.000
fixID1	0.001	0.000	0.001
fixMSD	0.001	0.000	0.001
fixPER1	0.000	0.001	0.000
fixPER2	0	0	0
fixPER3	0.000	0.001	0.001
getAvailableAggrMetrics	1.052	0.008	1.063
getCellImages	0.261	0.830	1.097
getCellMigSlot	0.363	0.518	0.887
getCellTrackMeta	0.010	0.002	0.012
getCellTrackStats	0.014	0.003	0.018
getCellTracks	0.010	0.003	0.013
getCellsMeta	0.012	0.003	0.014
getCellsStats	0.013	0.003	0.015
getDACtable	2.115	0.016	2.135
getDiRatio	0.020	0.002	0.021
getFMItable	0.477	0.004	0.482
getForMigtable	0.608	0.004	0.615
getImageCentroids	0.016	0.003	0.019
getImageStacks	0.046	0.007	0.053
getMSDtable	3.995	0.038	4.051
getOptimizedParameters	0.010	0.002	0.012
getOptimizedParams	0.013	0.003	0.016
getPerAndSpeed	0.308	0.029	0.348
getPopulationStats	0.011	0.002	0.014
getProcessedImages	0.249	0.844	1.098
getProcessingStatus	0.011	0.001	0.012
getResults	0.648	0.014	0.666
getTracks	0.013	0.003	0.016
getVACtable	1.148	0.011	1.164
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.001	0.002
matfix	0.002	0.001	0.001
nontrivialBondTracking	0.001	0.000	0.002
pkfnd	0.733	0.011	0.747
plot3DAllTracks	0.001	0.000	0.001
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.019	0.004	0.023
plotSampleTracks	0.012	0.003	0.016
preProcCellMig	0.004	0.001	0.006
rmPreProcessing	0.107	0.004	0.111
runTrackingPermutation	0.001	0.000	0.001
setAnalyticParams	0.010	0.002	0.012
setCellMigSlot	0.021	0.002	0.023
setCellTracks	0.009	0.002	0.011
setCellsMeta	0.010	0.001	0.012
setExpName	0.017	0.002	0.020
setOptimizedParams	0.010	0.002	0.011
setProcessedImages	0.011	0.002	0.013
setProcessingStatus	0.011	0.003	0.015
setTrackedCellsMeta	0.012	0.003	0.019
setTrackedCentroids	0.011	0.002	0.015
setTrackedPositions	0.010	0.002	0.013
setTrackingStats	0.012	0.003	0.015
sinkAway	0.001	0.000	0.002
subNetworkTracking	0.002	0.000	0.002
track	0.009	0.001	0.010
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.003	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.062	0.010	0.074
visualizeTrcks	0.029	0.002	0.032
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.055	0.003	0.061