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"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4494
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4400
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: 2025-01-31 13:47:25 -0500 (Fri, 31 Jan 2025)

EndedAt: 2025-01-31 13:49:42 -0500 (Fri, 31 Jan 2025)

EllapsedTime: 137.7 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 -- Fri Jan 31 13:49:27 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 
  3.438   0.309   3.756

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.003
CellMig-class	0.037	0.003	0.040
CellMigPCA	1.459	0.033	1.500
CellMigPCAclust	0.011	0.002	0.013
CellMigPCAclustALL	0.710	0.008	0.721
CellTracker	0.028	0.003	0.031
CellTrackerMainLoop	0.005	0.012	0.020
CentroidArray	0.026	0.003	0.029
CentroidValidation	0.529	0.015	0.547
ComputeTracksStats	0.035	0.003	0.038
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.493	0.017	1.519
DiRatio	0.021	0.002	0.023
DiRatioPlot	0.043	0.014	0.057
EstimateDiameterRange	0.016	0.002	0.019
FMI	0.519	0.005	0.531
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.742	0.015	0.761
ForwardMigration	1.050	0.006	1.065
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.022	0.002	0.023
LoadTiff	0.001	0.000	0.001
MSD	1.878	0.052	1.945
MakeHypercube	0.001	0.000	0.002
MigrationStats	0.000	0.001	0.002
NextOdd	0.000	0.001	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.024	0.003	0.028
OptimizeParamsMainLoop	0.006	0.012	0.023
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.311	0.031	0.347
PlotTracksSeparately	0.013	0.001	0.015
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.100	0.004	0.104
ThreeConditions	0.018	0.003	0.024
TrackCellsDataset	0.025	0.003	0.027
TrajectoryDataset	0.031	0.002	0.033
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.106	0.018	1.125
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.005	0.001	0.006
VisualizeStackCentroids	0.066	0.008	0.076
WSADataset	0.010	0.002	0.012
aggregateFR	0.667	0.008	0.679
aggregateTrackedCells	0.032	0.005	0.037
bpass	0.083	0.003	0.086
circshift	0.001	0.001	0.001
cntrd	0.741	0.015	0.758
fixDA	0.000	0.000	0.001
fixExpName	0.000	0.000	0.001
fixFM1	0.001	0.000	0.000
fixFM2	0.000	0.000	0.001
fixFM3	0.001	0.001	0.001
fixFM4	0	0	0
fixFM5	0.001	0.000	0.000
fixFM6	0	0	0
fixID1	0.001	0.000	0.000
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.000	0.000
fixPER2	0.000	0.001	0.000
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	0.957	0.009	0.970
getCellImages	0.251	0.803	1.073
getCellMigSlot	0.402	0.504	0.911
getCellTrackMeta	0.024	0.003	0.027
getCellTrackStats	0.027	0.003	0.030
getCellTracks	0.023	0.002	0.026
getCellsMeta	0.024	0.002	0.027
getCellsStats	0.025	0.003	0.029
getDACtable	1.526	0.023	1.572
getDiRatio	0.009	0.001	0.010
getFMItable	0.402	0.007	0.418
getForMigtable	0.599	0.006	0.606
getImageCentroids	0.032	0.004	0.037
getImageStacks	0.068	0.008	0.075
getMSDtable	3.647	0.047	3.713
getOptimizedParameters	0.026	0.003	0.028
getOptimizedParams	0.025	0.002	0.027
getPerAndSpeed	0.318	0.032	0.352
getPopulationStats	0.025	0.003	0.027
getProcessedImages	0.242	1.005	1.286
getProcessingStatus	0.026	0.003	0.029
getResults	0.671	0.016	0.691
getTracks	0.027	0.003	0.030
getVACtable	1.106	0.013	1.125
initializeTrackParams	0	0	0
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.001	0.001
pkfnd	0.779	0.024	0.807
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.022	0.004	0.025
plotSampleTracks	0.019	0.003	0.024
preProcCellMig	0.011	0.002	0.013
rmPreProcessing	0.101	0.004	0.105
runTrackingPermutation	0.002	0.000	0.003
setAnalyticParams	0.023	0.002	0.025
setCellMigSlot	0.033	0.003	0.035
setCellTracks	0.024	0.002	0.026
setCellsMeta	0.023	0.003	0.027
setExpName	0.034	0.002	0.036
setOptimizedParams	0.025	0.002	0.028
setProcessedImages	0.025	0.003	0.028
setProcessingStatus	0.023	0.003	0.027
setTrackedCellsMeta	0.026	0.003	0.028
setTrackedCentroids	0.022	0.003	0.025
setTrackedPositions	0.025	0.003	0.029
setTrackingStats	0.023	0.002	0.026
sinkAway	0.000	0.000	0.001
subNetworkTracking	0.001	0.001	0.001
track	0.024	0.003	0.028
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.001	0.001
trivialBondRaster	0.002	0.000	0.003
trivialBondTracking	0.000	0.000	0.001
visualizeCellTracks	0.070	0.006	0.076
visualizeTrcks	0.047	0.002	0.049
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.057	0.002	0.059