Build/check report for BioC 3.22 - CHECK results for cellmigRation on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4891
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 nebbiolo2

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: 1.18.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cellmigRation_1.18.0.tar.gz

StartedAt: 2026-02-26 21:52:43 -0500 (Thu, 26 Feb 2026)

EndedAt: 2026-02-26 21:56:43 -0500 (Thu, 26 Feb 2026)

EllapsedTime: 240.2 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cellmigRation_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.18.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.18.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 Feb 26 21:54:36 2026 
*********************************************** 
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 
  3.160   0.242   3.390

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.001
CellMig-class	0.026	0.002	0.028
CellMigPCA	1.507	0.006	1.513
CellMigPCAclust	0.007	0.001	0.008
CellMigPCAclustALL	0.634	0.000	0.633
CellTracker	0.016	0.005	0.020
CellTrackerMainLoop	0.002	0.006	0.006
CentroidArray	0.017	0.003	0.020
CentroidValidation	0.460	0.007	0.467
ComputeTracksStats	0.027	0.000	0.027
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.306	0.040	1.346
DiRatio	0.016	0.001	0.016
DiRatioPlot	0.031	0.001	0.033
EstimateDiameterRange	0.013	0.000	0.013
FMI	0.516	0.006	0.522
FianlizeOptiParams	0.001	0.000	0.000
FilterTrackedCells	0.002	0.000	0.003
FinRes	0.623	0.005	0.629
ForwardMigration	0.919	0.005	0.924
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.019	0.001	0.019
LoadTiff	0.001	0.000	0.001
MSD	1.426	0.003	1.430
MakeHypercube	0.001	0.000	0.001
MigrationStats	0.001	0.000	0.001
NextOdd	0.001	0.000	0.000
NonParallel4OptimizeParams	0.001	0.000	0.000
NonParallelTrackLoop	0	0	0
OptimizeParams	0.016	0.001	0.017
OptimizeParamsMainLoop	0.002	0.017	0.017
Parallel4OptimizeParams	0.002	0.001	0.002
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.306	0.098	0.450
PlotTracksSeparately	0.009	0.000	0.009
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.103	0.004	0.106
ThreeConditions	0.012	0.002	0.014
TrackCellsDataset	0.014	0.003	0.017
TrajectoryDataset	0.021	0.001	0.022
ValidateTrackingArgs	0	0	0
VeAutoCor	1.379	0.147	1.526
VisualizeCntr	0.002	0.001	0.004
VisualizeImg	0.005	0.002	0.007
VisualizeStackCentroids	0.052	0.008	0.059
WSADataset	0.007	0.000	0.007
aggregateFR	0.587	0.013	0.600
aggregateTrackedCells	0.020	0.002	0.022
bpass	0.059	0.004	0.063
circshift	0.001	0.000	0.001
cntrd	0.686	0.012	0.698
fixDA	0	0	0
fixExpName	0.000	0.000	0.001
fixFM1	0.000	0.001	0.000
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.000	0.000	0.001
fixFM6	0	0	0
fixID1	0.001	0.000	0.001
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.895	0.029	0.924
getCellImages	0.143	0.116	0.259
getCellMigSlot	0.208	0.077	0.285
getCellTrackMeta	0.012	0.005	0.017
getCellTrackStats	0.018	0.002	0.020
getCellTracks	0.016	0.002	0.018
getCellsMeta	0.015	0.003	0.019
getCellsStats	0.019	0.001	0.020
getDACtable	1.881	0.014	1.895
getDiRatio	0.018	0.000	0.019
getFMItable	0.438	0.001	0.439
getForMigtable	0.536	0.002	0.538
getImageCentroids	0.022	0.000	0.022
getImageStacks	0.054	0.004	0.057
getMSDtable	3.424	0.045	3.470
getOptimizedParameters	0.013	0.003	0.018
getOptimizedParams	0.017	0.002	0.018
getPerAndSpeed	0.259	0.009	0.268
getPopulationStats	0.015	0.003	0.017
getProcessedImages	0.122	0.117	0.239
getProcessingStatus	0.013	0.004	0.017
getResults	0.612	0.002	0.614
getTracks	0.016	0.002	0.017
getVACtable	1.015	0.002	1.017
initializeTrackParams	0.001	0.000	0.001
innerBondRaster	0.001	0.000	0.001
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.000	0.001	0.001
pkfnd	0.677	0.001	0.678
plot3DAllTracks	0.066	0.034	0.100
plot3DTracks	0.008	0.000	0.008
plotAllTracks	0.018	0.000	0.018
plotSampleTracks	0.015	0.000	0.015
preProcCellMig	0.008	0.000	0.008
rmPreProcessing	0.081	0.001	0.082
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.016	0.001	0.017
setCellMigSlot	0.023	0.000	0.023
setCellTracks	0.016	0.001	0.017
setCellsMeta	0.013	0.004	0.018
setExpName	0.022	0.001	0.023
setOptimizedParams	0.015	0.003	0.018
setProcessedImages	0.016	0.002	0.018
setProcessingStatus	0.015	0.002	0.017
setTrackedCellsMeta	0.028	0.004	0.032
setTrackedCentroids	0.015	0.002	0.017
setTrackedPositions	0.014	0.002	0.017
setTrackingStats	0.015	0.002	0.017
sinkAway	0.001	0.000	0.001
subNetworkTracking	0.001	0.000	0.001
track	0.008	0.000	0.008
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.058	0.001	0.059
visualizeTrcks	0.024	0.000	0.024
warnMessage	0	0	0
wsaPreProcessing	0.048	0.000	0.047