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 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4833
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4621
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4566
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4563
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: 2025-09-28 22:11:39 -0400 (Sun, 28 Sep 2025)

EndedAt: 2025-09-28 22:17:26 -0400 (Sun, 28 Sep 2025)

EllapsedTime: 347.4 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 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.17.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMSDtable 5.184  0.157   5.681
* 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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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 -- Sun Sep 28 22:14:26 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 
  4.204   0.297   4.733

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.002
CellMig-class	0.034	0.001	0.045
CellMigPCA	2.368	0.061	2.667
CellMigPCAclust	0.007	0.002	0.013
CellMigPCAclustALL	0.766	0.057	0.949
CellTracker	0.017	0.005	0.022
CellTrackerMainLoop	0.004	0.005	0.015
CentroidArray	0.021	0.003	0.050
CentroidValidation	0.544	0.018	0.707
ComputeTracksStats	0.029	0.003	0.041
DetectRadii	0.003	0.000	0.007
DiAutoCor	1.637	0.050	1.884
DiRatio	0.023	0.002	0.024
DiRatioPlot	0.042	0.003	0.045
EstimateDiameterRange	0.020	0.001	0.021
FMI	0.818	0.054	0.877
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.004	0.000	0.004
FinRes	1.091	0.064	1.156
ForwardMigration	1.641	0.079	1.737
GenAllCombos	0.005	0.000	0.005
LinearConv2	0.033	0.000	0.033
LoadTiff	0.001	0.000	0.001
MSD	2.400	0.090	2.603
MakeHypercube	0.001	0.000	0.001
MigrationStats	0.001	0.000	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.017	0.003	0.020
OptimizeParamsMainLoop	0.001	0.008	0.015
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0	0	0
PerAndSpeed	0.326	0.007	0.352
PlotTracksSeparately	0.008	0.002	0.010
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.104	0.004	0.116
ThreeConditions	0.014	0.004	0.029
TrackCellsDataset	0.017	0.002	0.020
TrajectoryDataset	0.027	0.000	0.043
ValidateTrackingArgs	0	0	0
VeAutoCor	1.452	0.046	1.810
VisualizeCntr	0.003	0.000	0.003
VisualizeImg	0.006	0.001	0.007
VisualizeStackCentroids	0.084	0.003	0.088
WSADataset	0.009	0.002	0.010
aggregateFR	1.096	0.041	1.197
aggregateTrackedCells	0.021	0.002	0.022
bpass	0.070	0.001	0.070
circshift	0.001	0.000	0.000
cntrd	1.021	0.013	1.207
fixDA	0	0	0
fixExpName	0.001	0.000	0.001
fixFM1	0.001	0.000	0.001
fixFM2	0	0	0
fixFM3	0.000	0.000	0.001
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.000	0.000
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0.000	0.000	0.001
getAvailableAggrMetrics	1.417	0.071	1.546
getCellImages	0.176	0.133	0.309
getCellMigSlot	0.269	0.074	0.355
getCellTrackMeta	0.018	0.002	0.020
getCellTrackStats	0.021	0.002	0.023
getCellTracks	0.018	0.002	0.020
getCellsMeta	0.015	0.011	0.026
getCellsStats	0.017	0.006	0.023
getDACtable	2.287	0.061	2.713
getDiRatio	0.018	0.002	0.021
getFMItable	0.555	0.002	0.577
getForMigtable	0.668	0.001	0.670
getImageCentroids	0.022	0.004	0.026
getImageStacks	0.067	0.001	0.069
getMSDtable	5.184	0.157	5.681
getOptimizedParameters	0.018	0.006	0.024
getOptimizedParams	0.020	0.006	0.026
getPerAndSpeed	0.438	0.008	0.447
getPopulationStats	0.022	0.003	0.025
getProcessedImages	0.224	0.163	0.387
getProcessingStatus	0.021	0.003	0.024
getResults	0.952	0.001	1.028
getTracks	0.020	0.006	0.026
getVACtable	1.356	0.033	1.474
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.001	0.001	0.003
internalPermutation	0.001	0.000	0.002
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.001	0.000	0.002
pkfnd	1.278	0.053	1.331
plot3DAllTracks	0.109	0.032	0.153
plot3DTracks	0.010	0.001	0.011
plotAllTracks	0.023	0.000	0.024
plotSampleTracks	0.020	0.001	0.021
preProcCellMig	0.008	0.001	0.009
rmPreProcessing	0.110	0.004	0.114
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.019	0.000	0.019
setCellMigSlot	0.025	0.002	0.027
setCellTracks	0.016	0.003	0.019
setCellsMeta	0.016	0.004	0.020
setExpName	0.024	0.002	0.027
setOptimizedParams	0.049	0.006	0.083
setProcessedImages	0.016	0.003	0.019
setProcessingStatus	0.016	0.003	0.019
setTrackedCellsMeta	0.017	0.002	0.019
setTrackedCentroids	0.017	0.002	0.019
setTrackedPositions	0.017	0.002	0.019
setTrackingStats	0.017	0.002	0.019
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.002	0.000	0.002
track	0.011	0.001	0.012
trackHypercubeBuild	0.001	0.000	0.000
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	0.083	0.004	0.087
visualizeTrcks	0.034	0.000	0.034
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.093	0.001	0.093