Build/check report for BioC 3.23 - CHECK results for cellmigRation on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4877
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 nebbiolo1

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: 1.19.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings cellmigRation_1.19.0.tar.gz

StartedAt: 2026-02-26 22:04:53 -0500 (Thu, 26 Feb 2026)

EndedAt: 2026-02-26 22:08:53 -0500 (Thu, 26 Feb 2026)

EllapsedTime: 240.4 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings cellmigRation_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘1.19.0’
* 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-3.23-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.19.0’
** 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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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 22:06:49 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 
  3.019   0.250   3.258

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.002
CellMig-class	0.026	0.002	0.028
CellMigPCA	1.447	0.013	1.461
CellMigPCAclust	0.008	0.000	0.008
CellMigPCAclustALL	0.621	0.002	0.623
CellTracker	0.016	0.004	0.020
CellTrackerMainLoop	0.001	0.007	0.007
CentroidArray	0.017	0.003	0.021
CentroidValidation	0.455	0.009	0.464
ComputeTracksStats	0.023	0.003	0.026
DetectRadii	0.003	0.000	0.002
DiAutoCor	1.289	0.035	1.325
DiRatio	0.016	0.000	0.017
DiRatioPlot	0.027	0.005	0.033
EstimateDiameterRange	0.012	0.001	0.014
FMI	0.498	0.007	0.506
FianlizeOptiParams	0.000	0.000	0.001
FilterTrackedCells	0.000	0.002	0.003
FinRes	0.625	0.004	0.628
ForwardMigration	0.901	0.015	0.916
GenAllCombos	0.002	0.001	0.003
LinearConv2	0.018	0.001	0.019
LoadTiff	0.001	0.000	0.001
MSD	1.426	0.006	1.433
MakeHypercube	0.000	0.001	0.002
MigrationStats	0.001	0.000	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.012	0.005	0.018
OptimizeParamsMainLoop	0.001	0.018	0.018
Parallel4OptimizeParams	0.002	0.000	0.002
ParallelTrackLoop	0.000	0.001	0.001
PerAndSpeed	0.297	0.122	0.420
PlotTracksSeparately	0.009	0.001	0.010
PostProcessTracking	0.000	0.001	0.001
Prep4OptimizeParams	0.098	0.005	0.103
ThreeConditions	0.010	0.004	0.014
TrackCellsDataset	0.015	0.002	0.017
TrajectoryDataset	0.020	0.002	0.022
ValidateTrackingArgs	0.000	0.001	0.000
VeAutoCor	1.348	0.039	1.387
VisualizeCntr	0.002	0.000	0.002
VisualizeImg	0.005	0.000	0.005
VisualizeStackCentroids	0.058	0.014	0.071
WSADataset	0.009	0.000	0.009
aggregateFR	0.588	0.102	0.689
aggregateTrackedCells	0.018	0.006	0.024
bpass	0.056	0.002	0.058
circshift	0	0	0
cntrd	0.655	0.026	0.681
fixDA	0.000	0.001	0.000
fixExpName	0.000	0.001	0.000
fixFM1	0.001	0.000	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.000	0.001	0.001
fixFM6	0.000	0.001	0.001
fixID1	0.000	0.000	0.001
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0.000	0.001	0.000
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	0.862	0.024	0.886
getCellImages	0.193	0.984	1.176
getCellMigSlot	0.248	0.636	0.884
getCellTrackMeta	0.013	0.004	0.018
getCellTrackStats	0.017	0.005	0.022
getCellTracks	0.013	0.007	0.019
getCellsMeta	0.015	0.003	0.018
getCellsStats	0.017	0.003	0.020
getDACtable	1.776	0.056	1.832
getDiRatio	0.018	0.001	0.019
getFMItable	0.424	0.004	0.429
getForMigtable	0.526	0.001	0.527
getImageCentroids	0.019	0.005	0.025
getImageStacks	0.054	0.006	0.060
getMSDtable	3.446	0.042	3.496
getOptimizedParameters	0.015	0.002	0.018
getOptimizedParams	0.016	0.003	0.019
getPerAndSpeed	0.255	0.009	0.265
getPopulationStats	0.015	0.003	0.019
getProcessedImages	0.184	0.997	1.182
getProcessingStatus	0.014	0.003	0.018
getResults	0.599	0.024	0.623
getTracks	0.016	0.003	0.018
getVACtable	0.998	0.005	1.003
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.000	0.001	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.000	0.001	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.668	0.002	0.670
plot3DAllTracks	0.073	0.031	0.103
plot3DTracks	0.009	0.000	0.009
plotAllTracks	0.019	0.000	0.019
plotSampleTracks	0.014	0.002	0.016
preProcCellMig	0.006	0.002	0.007
rmPreProcessing	0.096	0.016	0.112
runTrackingPermutation	0.001	0.001	0.001
setAnalyticParams	0.015	0.003	0.018
setCellMigSlot	0.022	0.002	0.023
setCellTracks	0.015	0.004	0.019
setCellsMeta	0.015	0.003	0.018
setExpName	0.020	0.003	0.023
setOptimizedParams	0.017	0.001	0.018
setProcessedImages	0.017	0.001	0.018
setProcessingStatus	0.014	0.004	0.018
setTrackedCellsMeta	0.015	0.003	0.018
setTrackedCentroids	0.016	0.002	0.018
setTrackedPositions	0.013	0.006	0.019
setTrackingStats	0.023	0.001	0.024
sinkAway	0.000	0.001	0.000
subNetworkTracking	0.001	0.001	0.002
track	0.008	0.001	0.009
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0	0	0
visualizeCellTracks	0.058	0.003	0.061
visualizeTrcks	0.025	0.000	0.025
warnMessage	0.000	0.001	0.001
wsaPreProcessing	0.048	0.001	0.049