Multiple platform build/check report for BioC 3.21 - CHECK results for cellmigRation on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
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: 1.15.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cellmigRation_1.15.0.tar.gz

StartedAt: 2025-02-05 20:46:47 -0500 (Wed, 05 Feb 2025)

EndedAt: 2025-02-05 20:50:39 -0500 (Wed, 05 Feb 2025)

EllapsedTime: 232.2 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cellmigRation_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.15.0’
* 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-3.21-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.15.0’
** 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) (2025-01-20 r87609) -- "Unsuffered Consequences"
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 Feb  5 20:48:32 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 
  2.800   0.206   2.996

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.002
CellMig-class	0.025	0.002	0.027
CellMigPCA	1.184	0.066	1.251
CellMigPCAclust	0.007	0.001	0.008
CellMigPCAclustALL	0.658	0.003	0.661
CellTracker	0.016	0.003	0.019
CellTrackerMainLoop	0.003	0.005	0.006
CentroidArray	0.012	0.008	0.020
CentroidValidation	0.451	0.004	0.456
ComputeTracksStats	0.025	0.001	0.026
DetectRadii	0.002	0.000	0.002
DiAutoCor	1.324	0.044	1.369
DiRatio	0.017	0.001	0.018
DiRatioPlot	0.035	0.002	0.037
EstimateDiameterRange	0.016	0.000	0.016
FMI	0.488	0.001	0.490
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.616	0.000	0.616
ForwardMigration	0.901	0.013	0.915
GenAllCombos	0.002	0.001	0.003
LinearConv2	0.017	0.001	0.019
LoadTiff	0.001	0.000	0.001
MSD	1.639	0.029	1.668
MakeHypercube	0.001	0.000	0.001
MigrationStats	0.000	0.001	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.000
NonParallelTrackLoop	0	0	0
OptimizeParams	0.015	0.002	0.018
OptimizeParamsMainLoop	0.004	0.004	0.006
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.268	0.011	0.279
PlotTracksSeparately	0.008	0.001	0.010
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.082	0.006	0.089
ThreeConditions	0.012	0.003	0.016
TrackCellsDataset	0.015	0.003	0.017
TrajectoryDataset	0.021	0.000	0.022
ValidateTrackingArgs	0	0	0
VeAutoCor	1.041	0.045	1.088
VisualizeCntr	0.002	0.001	0.002
VisualizeImg	0.005	0.001	0.005
VisualizeStackCentroids	0.056	0.003	0.059
WSADataset	0.006	0.001	0.007
aggregateFR	0.571	0.004	0.575
aggregateTrackedCells	0.023	0.002	0.024
bpass	0.058	0.000	0.058
circshift	0.001	0.000	0.000
cntrd	0.651	0.006	0.658
fixDA	0.000	0.000	0.001
fixExpName	0.000	0.000	0.001
fixFM1	0.000	0.001	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0	0	0
fixFM4	0.001	0.000	0.000
fixFM5	0.001	0.000	0.000
fixFM6	0	0	0
fixID1	0.000	0.001	0.001
fixMSD	0.000	0.001	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0	0	0
fixPER3	0.000	0.000	0.001
getAvailableAggrMetrics	0.862	0.006	0.869
getCellImages	0.218	1.006	1.224
getCellMigSlot	0.271	0.643	0.915
getCellTrackMeta	0.016	0.002	0.017
getCellTrackStats	0.015	0.007	0.022
getCellTracks	0.015	0.005	0.019
getCellsMeta	0.016	0.003	0.018
getCellsStats	0.016	0.004	0.020
getDACtable	1.756	0.038	1.795
getDiRatio	0.018	0.002	0.020
getFMItable	0.423	0.013	0.437
getForMigtable	0.531	0.002	0.533
getImageCentroids	0.019	0.006	0.025
getImageStacks	0.051	0.007	0.058
getMSDtable	3.419	0.102	3.522
getOptimizedParameters	0.013	0.004	0.018
getOptimizedParams	0.016	0.003	0.019
getPerAndSpeed	0.262	0.007	0.269
getPopulationStats	0.014	0.005	0.019
getProcessedImages	0.190	1.044	1.234
getProcessingStatus	0.015	0.002	0.018
getResults	0.618	0.015	0.633
getTracks	0.017	0.002	0.019
getVACtable	1.043	0.043	1.085
initializeTrackParams	0.001	0.000	0.001
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.000	0.001	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.706	0.006	0.715
plot3DAllTracks	0.092	0.038	0.131
plot3DTracks	0.008	0.000	0.009
plotAllTracks	0.017	0.002	0.019
plotSampleTracks	0.014	0.002	0.015
preProcCellMig	0.008	0.000	0.007
rmPreProcessing	0.104	0.001	0.104
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.016	0.001	0.017
setCellMigSlot	0.022	0.001	0.023
setCellTracks	0.015	0.002	0.018
setCellsMeta	0.016	0.002	0.017
setExpName	0.020	0.003	0.023
setOptimizedParams	0.015	0.002	0.018
setProcessedImages	0.012	0.005	0.018
setProcessingStatus	0.016	0.001	0.017
setTrackedCellsMeta	0.015	0.002	0.017
setTrackedCentroids	0.013	0.004	0.017
setTrackedPositions	0.015	0.003	0.018
setTrackingStats	0.015	0.003	0.019
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.000	0.001	0.001
track	0.008	0.001	0.009
trackHypercubeBuild	0.001	0.000	0.000
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.002	0.000	0.001
trivialBondTracking	0.000	0.001	0.000
visualizeCellTracks	0.071	0.009	0.080
visualizeTrcks	0.025	0.002	0.027
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.054	0.003	0.057