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

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"	4720
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4482
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4493
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4446
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 lconway

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.15.0.tar.gz

StartedAt: 2025-02-14 19:19:34 -0500 (Fri, 14 Feb 2025)

EndedAt: 2025-02-14 19:21:55 -0500 (Fri, 14 Feb 2025)

EllapsedTime: 140.9 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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) (2025-01-22 r87618) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 -- Fri Feb 14 19:21:43 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 
  3.069   0.336   3.418

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.002
CellMig-class	0.022	0.002	0.025
CellMigPCA	1.522	0.032	1.565
CellMigPCAclust	0.007	0.002	0.009
CellMigPCAclustALL	0.957	0.045	1.007
CellTracker	0.015	0.004	0.019
CellTrackerMainLoop	0.005	0.008	0.023
CentroidArray	0.013	0.003	0.015
CentroidValidation	0.485	0.022	0.521
ComputeTracksStats	0.020	0.003	0.022
DetectRadii	0.004	0.001	0.004
DiAutoCor	1.377	0.016	1.397
DiRatio	0.017	0.001	0.020
DiRatioPlot	0.032	0.013	0.049
EstimateDiameterRange	0.014	0.002	0.017
FMI	0.504	0.005	0.509
FianlizeOptiParams	0.000	0.000	0.001
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.702	0.013	0.719
ForwardMigration	1.048	0.009	1.060
GenAllCombos	0.002	0.000	0.003
LinearConv2	0.016	0.001	0.018
LoadTiff	0.001	0.001	0.001
MSD	1.543	0.018	1.569
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.001	0.001	0.001
NextOdd	0.001	0.001	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.001	0.000	0.000
OptimizeParams	0.015	0.003	0.017
OptimizeParamsMainLoop	0.005	0.011	0.028
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.302	0.027	0.339
PlotTracksSeparately	0.007	0.001	0.008
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.133	0.007	0.140
ThreeConditions	0.009	0.003	0.011
TrackCellsDataset	0.009	0.002	0.010
TrajectoryDataset	0.019	0.001	0.020
ValidateTrackingArgs	0.001	0.000	0.000
VeAutoCor	1.161	0.021	1.186
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.005	0.001	0.007
VisualizeStackCentroids	0.046	0.007	0.054
WSADataset	0.005	0.002	0.007
aggregateFR	0.726	0.007	0.738
aggregateTrackedCells	0.018	0.004	0.023
bpass	0.066	0.003	0.069
circshift	0.001	0.000	0.000
cntrd	0.799	0.015	0.819
fixDA	0.001	0.000	0.000
fixExpName	0.001	0.000	0.001
fixFM1	0	0	0
fixFM2	0.000	0.001	0.000
fixFM3	0	0	0
fixFM4	0.001	0.000	0.000
fixFM5	0.000	0.000	0.001
fixFM6	0	0	0
fixID1	0.000	0.001	0.001
fixMSD	0.001	0.000	0.000
fixPER1	0.001	0.000	0.001
fixPER2	0	0	0
fixPER3	0.000	0.000	0.001
getAvailableAggrMetrics	1.122	0.009	1.137
getCellImages	0.282	0.813	1.102
getCellMigSlot	0.346	0.533	0.883
getCellTrackMeta	0.009	0.002	0.011
getCellTrackStats	0.014	0.003	0.017
getCellTracks	0.010	0.003	0.013
getCellsMeta	0.008	0.002	0.010
getCellsStats	0.012	0.003	0.014
getDACtable	2.120	0.021	2.149
getDiRatio	0.019	0.002	0.021
getFMItable	0.520	0.005	0.527
getForMigtable	0.844	0.007	0.854
getImageCentroids	0.015	0.003	0.018
getImageStacks	0.042	0.006	0.048
getMSDtable	3.668	0.035	3.722
getOptimizedParameters	0.011	0.002	0.012
getOptimizedParams	0.012	0.002	0.014
getPerAndSpeed	0.305	0.026	0.341
getPopulationStats	0.010	0.001	0.011
getProcessedImages	0.276	0.930	1.215
getProcessingStatus	0.010	0.002	0.012
getResults	0.627	0.013	0.646
getTracks	0.009	0.001	0.011
getVACtable	1.092	0.008	1.105
initializeTrackParams	0.001	0.000	0.000
innerBondRaster	0.001	0.000	0.001
internalPermutation	0.001	0.000	0.002
matfix	0.002	0.001	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.682	0.012	0.699
plot3DAllTracks	0	0	0
plot3DTracks	0.001	0.000	0.000
plotAllTracks	0.017	0.004	0.021
plotSampleTracks	0.013	0.003	0.016
preProcCellMig	0.005	0.002	0.006
rmPreProcessing	0.092	0.002	0.094
runTrackingPermutation	0.002	0.000	0.001
setAnalyticParams	0.010	0.001	0.011
setCellMigSlot	0.019	0.002	0.020
setCellTracks	0.010	0.002	0.011
setCellsMeta	0.011	0.002	0.014
setExpName	0.020	0.002	0.022
setOptimizedParams	0.010	0.002	0.011
setProcessedImages	0.009	0.002	0.011
setProcessingStatus	0.011	0.002	0.012
setTrackedCellsMeta	0.010	0.001	0.012
setTrackedCentroids	0.010	0.002	0.013
setTrackedPositions	0.020	0.005	0.025
setTrackingStats	0.011	0.003	0.014
sinkAway	0.001	0.000	0.001
subNetworkTracking	0.001	0.000	0.001
track	0.007	0.001	0.008
trackHypercubeBuild	0.001	0.001	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.001	0.001
visualizeCellTracks	0.048	0.008	0.057
visualizeTrcks	0.029	0.002	0.031
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.052	0.001	0.054