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) (2024-10-21 r87258) -- "Unsuffered Consequences"	4756
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4475
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4435
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4390
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4383
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: 2025-01-03 19:28:38 -0500 (Fri, 03 Jan 2025)

EndedAt: 2025-01-03 19:31:00 -0500 (Fri, 03 Jan 2025)

EllapsedTime: 141.6 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) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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’ ...
** 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) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 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 Jan  3 19:30:48 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 
  3.145   0.344   3.495

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.003
CellMig-class	0.032	0.004	0.035
CellMigPCA	1.659	0.034	1.706
CellMigPCAclust	0.006	0.002	0.008
CellMigPCAclustALL	0.924	0.040	0.978
CellTracker	0.016	0.003	0.019
CellTrackerMainLoop	0.005	0.007	0.029
CentroidArray	0.015	0.002	0.016
CentroidValidation	0.492	0.020	0.514
ComputeTracksStats	0.028	0.003	0.032
DetectRadii	0.002	0.000	0.002
DiAutoCor	1.495	0.021	1.526
DiRatio	0.015	0.001	0.016
DiRatioPlot	0.036	0.014	0.053
EstimateDiameterRange	0.017	0.002	0.019
FMI	0.498	0.006	0.508
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.003	0.000	0.004
FinRes	0.714	0.014	0.735
ForwardMigration	1.051	0.009	1.065
GenAllCombos	0.002	0.001	0.002
LinearConv2	0.020	0.001	0.022
LoadTiff	0.001	0.000	0.002
MSD	1.784	0.028	1.826
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.001	0.001	0.001
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.002
NonParallelTrackLoop	0.001	0.000	0.000
OptimizeParams	0.016	0.002	0.018
OptimizeParamsMainLoop	0.004	0.007	0.022
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.345	0.033	0.392
PlotTracksSeparately	0.010	0.002	0.012
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.119	0.007	0.129
ThreeConditions	0.012	0.003	0.016
TrackCellsDataset	0.015	0.003	0.017
TrajectoryDataset	0.023	0.002	0.025
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.201	0.016	1.224
VisualizeCntr	0.001	0.001	0.003
VisualizeImg	0.004	0.001	0.005
VisualizeStackCentroids	0.052	0.007	0.061
WSADataset	0.008	0.001	0.009
aggregateFR	0.730	0.006	0.738
aggregateTrackedCells	0.019	0.003	0.022
bpass	0.062	0.003	0.065
circshift	0.000	0.001	0.001
cntrd	0.709	0.012	0.722
fixDA	0.000	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.000	0.000	0.001
fixFM5	0.001	0.000	0.000
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.001	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	1.030	0.010	1.045
getCellImages	0.266	0.770	1.050
getCellMigSlot	0.350	0.509	0.866
getCellTrackMeta	0.014	0.001	0.016
getCellTrackStats	0.017	0.002	0.019
getCellTracks	0.017	0.004	0.021
getCellsMeta	0.016	0.002	0.018
getCellsStats	0.016	0.003	0.019
getDACtable	2.234	0.020	2.263
getDiRatio	0.020	0.002	0.022
getFMItable	0.557	0.005	0.566
getForMigtable	0.901	0.008	0.914
getImageCentroids	0.021	0.003	0.024
getImageStacks	0.058	0.007	0.066
getMSDtable	3.703	0.037	3.762
getOptimizedParameters	0.012	0.001	0.014
getOptimizedParams	0.016	0.002	0.017
getPerAndSpeed	0.286	0.025	0.320
getPopulationStats	0.014	0.001	0.016
getProcessedImages	0.237	0.764	1.009
getProcessingStatus	0.012	0.001	0.013
getResults	0.692	0.015	0.714
getTracks	0.017	0.002	0.019
getVACtable	1.152	0.010	1.169
initializeTrackParams	0	0	0
innerBondRaster	0.001	0.000	0.001
internalPermutation	0.002	0.001	0.002
matfix	0.002	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.002
pkfnd	0.770	0.012	0.785
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.018	0.002	0.022
plotSampleTracks	0.017	0.003	0.020
preProcCellMig	0.007	0.002	0.009
rmPreProcessing	0.094	0.002	0.097
runTrackingPermutation	0.001	0.000	0.002
setAnalyticParams	0.014	0.001	0.016
setCellMigSlot	0.025	0.001	0.027
setCellTracks	0.013	0.001	0.015
setCellsMeta	0.013	0.002	0.015
setExpName	0.025	0.002	0.027
setOptimizedParams	0.014	0.002	0.015
setProcessedImages	0.015	0.002	0.017
setProcessingStatus	0.014	0.002	0.017
setTrackedCellsMeta	0.013	0.002	0.015
setTrackedCentroids	0.014	0.002	0.015
setTrackedPositions	0.015	0.001	0.017
setTrackingStats	0.041	0.006	0.047
sinkAway	0.001	0.000	0.001
subNetworkTracking	0.002	0.000	0.001
track	0.012	0.000	0.013
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.052	0.007	0.059
visualizeTrcks	0.027	0.002	0.029
warnMessage	0.000	0.001	0.000
wsaPreProcessing	0.051	0.001	0.052