Multiple platform build/check report for BioC 3.20 - CHECK results for cellmigRation on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4753
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4501
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4524
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4476
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4407
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 kjohnson1

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: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2025-02-04 14:13:04 -0500 (Tue, 04 Feb 2025)

EndedAt: 2025-02-04 14:15:23 -0500 (Tue, 04 Feb 2025)

EllapsedTime: 139.2 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.14.0’
* 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-3.20-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/4.4-arm64/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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 -- Tue Feb  4 14:15:08 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 
  3.453   0.308   3.790

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.002
CellMig-class	0.041	0.003	0.045
CellMigPCA	1.454	0.031	1.510
CellMigPCAclust	0.010	0.003	0.011
CellMigPCAclustALL	0.702	0.007	0.714
CellTracker	0.026	0.004	0.029
CellTrackerMainLoop	0.007	0.011	0.022
CentroidArray	0.025	0.002	0.028
CentroidValidation	0.512	0.013	0.533
ComputeTracksStats	0.033	0.002	0.036
DetectRadii	0.002	0.000	0.002
DiAutoCor	1.512	0.015	1.533
DiRatio	0.019	0.002	0.020
DiRatioPlot	0.040	0.012	0.053
EstimateDiameterRange	0.017	0.003	0.019
FMI	0.519	0.004	0.527
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.003	0.001	0.004
FinRes	0.744	0.016	0.765
ForwardMigration	1.072	0.006	1.085
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.022	0.002	0.023
LoadTiff	0.001	0.001	0.001
MSD	1.838	0.060	1.912
MakeHypercube	0.002	0.001	0.001
MigrationStats	0.001	0.001	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.026	0.002	0.028
OptimizeParamsMainLoop	0.006	0.010	0.022
Parallel4OptimizeParams	0.001	0.001	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.316	0.031	0.349
PlotTracksSeparately	0.009	0.001	0.010
PostProcessTracking	0.001	0.000	0.000
Prep4OptimizeParams	0.046	0.002	0.050
ThreeConditions	0.007	0.002	0.009
TrackCellsDataset	0.011	0.001	0.013
TrajectoryDataset	0.013	0.001	0.014
ValidateTrackingArgs	0	0	0
VeAutoCor	0.647	0.015	0.683
VisualizeCntr	0.001	0.001	0.002
VisualizeImg	0.003	0.001	0.003
VisualizeStackCentroids	0.043	0.005	0.051
WSADataset	0.004	0.001	0.006
aggregateFR	0.568	0.006	0.582
aggregateTrackedCells	0.031	0.004	0.036
bpass	0.083	0.004	0.087
circshift	0.001	0.000	0.001
cntrd	0.746	0.015	0.781
fixDA	0.000	0.000	0.001
fixExpName	0.000	0.001	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0.000	0.001	0.000
fixID1	0	0	0
fixMSD	0.000	0.000	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0.000	0.000	0.001
fixPER3	0.001	0.001	0.001
getAvailableAggrMetrics	0.963	0.010	0.979
getCellImages	0.252	0.787	1.063
getCellMigSlot	0.397	0.492	0.904
getCellTrackMeta	0.023	0.003	0.026
getCellTrackStats	0.026	0.003	0.030
getCellTracks	0.026	0.003	0.028
getCellsMeta	0.025	0.002	0.028
getCellsStats	0.027	0.003	0.030
getDACtable	1.981	0.022	2.021
getDiRatio	0.023	0.002	0.025
getFMItable	0.499	0.008	0.510
getForMigtable	0.601	0.006	0.609
getImageCentroids	0.032	0.004	0.035
getImageStacks	0.070	0.008	0.078
getMSDtable	3.601	0.050	3.681
getOptimizedParameters	0.025	0.002	0.027
getOptimizedParams	0.027	0.003	0.030
getPerAndSpeed	0.316	0.033	0.352
getPopulationStats	0.027	0.003	0.030
getProcessedImages	0.242	0.800	1.073
getProcessingStatus	0.024	0.003	0.028
getResults	0.671	0.018	0.695
getTracks	0.025	0.003	0.028
getVACtable	1.101	0.012	1.125
initializeTrackParams	0.001	0.001	0.000
innerBondRaster	0.002	0.000	0.003
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.001	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.737	0.027	0.768
plot3DAllTracks	0.001	0.000	0.000
plot3DTracks	0.001	0.000	0.000
plotAllTracks	0.023	0.004	0.026
plotSampleTracks	0.019	0.004	0.024
preProcCellMig	0.011	0.002	0.012
rmPreProcessing	0.101	0.003	0.105
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.026	0.003	0.028
setCellMigSlot	0.034	0.002	0.036
setCellTracks	0.026	0.003	0.028
setCellsMeta	0.025	0.002	0.028
setExpName	0.032	0.002	0.034
setOptimizedParams	0.024	0.003	0.027
setProcessedImages	0.025	0.002	0.029
setProcessingStatus	0.023	0.003	0.026
setTrackedCellsMeta	0.024	0.003	0.027
setTrackedCentroids	0.025	0.003	0.028
setTrackedPositions	0.025	0.002	0.028
setTrackingStats	0.026	0.003	0.029
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.002	0.000	0.004
track	0.022	0.005	0.027
trackHypercubeBuild	0.000	0.000	0.001
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	0.070	0.008	0.079
visualizeTrcks	0.047	0.003	0.050
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.056	0.002	0.058