Multiple platform build/check report for BioC 3.22 - CHECK results for cellmigRation on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4810
palomino8	Windows Server 2022 Datacenter	x64	4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six"	4548
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"	4528
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4493
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: 1.17.0

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_1.17.0.tar.gz

StartedAt: 2025-06-18 21:33:45 -0400 (Wed, 18 Jun 2025)

EndedAt: 2025-06-18 21:37:34 -0400 (Wed, 18 Jun 2025)

EllapsedTime: 229.2 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 24.04.2 LTS
* using session charset: UTF-8
* 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 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 ‘1.17.0’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 -- Wed Jun 18 21:35:29 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 
  2.758   0.204   2.949

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.000	0.000	0.001
CellMig-class	0.027	0.002	0.028
CellMigPCA	1.150	0.067	1.219
CellMigPCAclust	0.007	0.001	0.008
CellMigPCAclustALL	0.603	0.001	0.604
CellTracker	0.015	0.005	0.020
CellTrackerMainLoop	0.001	0.006	0.007
CentroidArray	0.017	0.003	0.020
CentroidValidation	0.443	0.006	0.449
ComputeTracksStats	0.022	0.005	0.027
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.276	0.044	1.321
DiRatio	0.017	0.000	0.017
DiRatioPlot	0.039	0.001	0.040
EstimateDiameterRange	0.021	0.000	0.021
FMI	0.520	0.002	0.522
FianlizeOptiParams	0.001	0.000	0.000
FilterTrackedCells	0.003	0.000	0.002
FinRes	0.682	0.003	0.685
ForwardMigration	0.911	0.009	0.920
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.017	0.002	0.019
LoadTiff	0.000	0.001	0.000
MSD	1.671	0.087	1.759
MakeHypercube	0.001	0.000	0.001
MigrationStats	0.001	0.000	0.000
NextOdd	0	0	0
NonParallel4OptimizeParams	0.000	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.017	0.001	0.017
OptimizeParamsMainLoop	0.001	0.008	0.007
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.270	0.006	0.277
PlotTracksSeparately	0.009	0.000	0.009
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.080	0.004	0.084
ThreeConditions	0.010	0.005	0.015
TrackCellsDataset	0.013	0.004	0.017
TrajectoryDataset	0.022	0.000	0.021
ValidateTrackingArgs	0	0	0
VeAutoCor	0.974	0.039	1.013
VisualizeCntr	0.001	0.001	0.002
VisualizeImg	0.005	0.000	0.005
VisualizeStackCentroids	0.055	0.002	0.057
WSADataset	0.006	0.001	0.007
aggregateFR	0.577	0.020	0.597
aggregateTrackedCells	0.018	0.004	0.022
bpass	0.055	0.002	0.057
circshift	0.001	0.000	0.000
cntrd	0.655	0.004	0.659
fixDA	0.001	0.000	0.000
fixExpName	0.000	0.001	0.000
fixFM1	0.000	0.000	0.001
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	0	0
getAvailableAggrMetrics	0.854	0.029	0.883
getCellImages	0.139	0.118	0.258
getCellMigSlot	0.217	0.069	0.286
getCellTrackMeta	0.014	0.004	0.017
getCellTrackStats	0.019	0.002	0.021
getCellTracks	0.016	0.003	0.019
getCellsMeta	0.016	0.002	0.018
getCellsStats	0.016	0.004	0.020
getDACtable	1.775	0.025	1.801
getDiRatio	0.018	0.000	0.018
getFMItable	0.429	0.000	0.429
getForMigtable	0.528	0.028	0.557
getImageCentroids	0.021	0.002	0.023
getImageStacks	0.055	0.003	0.058
getMSDtable	3.389	0.028	3.419
getOptimizedParameters	0.016	0.000	0.016
getOptimizedParams	0.016	0.002	0.018
getPerAndSpeed	0.257	0.011	0.267
getPopulationStats	0.014	0.004	0.017
getProcessedImages	0.137	0.102	0.239
getProcessingStatus	0.013	0.003	0.017
getResults	0.607	0.038	0.646
getTracks	0.016	0.002	0.018
getVACtable	0.992	0.005	0.997
initializeTrackParams	0	0	0
innerBondRaster	0.001	0.001	0.001
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.000
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.656	0.015	0.671
plot3DAllTracks	0.104	0.027	0.131
plot3DTracks	0.007	0.001	0.008
plotAllTracks	0.017	0.001	0.018
plotSampleTracks	0.014	0.001	0.014
preProcCellMig	0.007	0.001	0.007
rmPreProcessing	0.077	0.004	0.080
runTrackingPermutation	0.000	0.001	0.001
setAnalyticParams	0.015	0.002	0.016
setCellMigSlot	0.022	0.000	0.022
setCellTracks	0.013	0.003	0.017
setCellsMeta	0.014	0.003	0.017
setExpName	0.022	0.000	0.023
setOptimizedParams	0.014	0.003	0.017
setProcessedImages	0.013	0.003	0.017
setProcessingStatus	0.015	0.002	0.017
setTrackedCellsMeta	0.016	0.001	0.017
setTrackedCentroids	0.017	0.000	0.017
setTrackedPositions	0.015	0.002	0.018
setTrackingStats	0.016	0.002	0.018
sinkAway	0.008	0.002	0.010
subNetworkTracking	0.001	0.000	0.001
track	0.008	0.001	0.008
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.000
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0	0	0
visualizeCellTracks	0.056	0.002	0.058
visualizeTrcks	0.023	0.001	0.024
warnMessage	0	0	0
wsaPreProcessing	0.047	0.001	0.047