Mac ARM64 build report for BioC 3.20 - CHECK results for cellmigRation on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4381
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*

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### Running command:
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###   /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_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/cellmigRation.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.13.0’
* 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-mac-arm64/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

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


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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 -- Sun May 19 07:52:39 2024 
*********************************************** 
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 
  3.440   0.319   3.771

Example timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.002
CellMig-class	0.038	0.003	0.040
CellMigPCA	1.460	0.031	1.502
CellMigPCAclust	0.011	0.002	0.013
CellMigPCAclustALL	0.711	0.008	0.721
CellTracker	0.029	0.004	0.032
CellTrackerMainLoop	0.007	0.012	0.024
CentroidArray	0.028	0.003	0.031
CentroidValidation	0.523	0.016	0.540
ComputeTracksStats	0.031	0.003	0.035
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.527	0.017	1.554
DiRatio	0.020	0.002	0.022
DiRatioPlot	0.046	0.013	0.060
EstimateDiameterRange	0.016	0.002	0.019
FMI	0.519	0.005	0.525
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.736	0.015	0.752
ForwardMigration	1.033	0.007	1.041
GenAllCombos	0.003	0.001	0.003
LinearConv2	0.020	0.002	0.021
LoadTiff	0.001	0.000	0.001
MSD	1.835	0.071	1.952
MakeHypercube	0.000	0.000	0.001
MigrationStats	0.000	0.001	0.000
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.002
OptimizeParams	0.009	0.003	0.021
OptimizeParamsMainLoop	0.002	0.005	0.010
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.210	0.027	0.245
PlotTracksSeparately	0.005	0.001	0.006
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.049	0.003	0.054
ThreeConditions	0.007	0.002	0.009
TrackCellsDataset	0.010	0.001	0.011
TrajectoryDataset	0.012	0.001	0.014
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	0.836	0.012	0.884
VisualizeCntr	0.002	0.001	0.004
VisualizeImg	0.006	0.001	0.006
VisualizeStackCentroids	0.069	0.007	0.078
WSADataset	0.009	0.002	0.011
aggregateFR	0.661	0.008	0.704
aggregateTrackedCells	0.030	0.004	0.035
bpass	0.085	0.003	0.109
circshift	0	0	0
cntrd	0.744	0.016	0.774
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.001	0.000
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.000	0.000	0.001
fixFM5	0.000	0.000	0.001
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0.001	0.001	0.000
getAvailableAggrMetrics	0.974	0.011	1.018
getCellImages	0.250	0.782	1.088
getCellMigSlot	0.407	0.504	0.963
getCellTrackMeta	0.024	0.003	0.027
getCellTrackStats	0.026	0.003	0.029
getCellTracks	0.023	0.003	0.026
getCellsMeta	0.023	0.003	0.027
getCellsStats	0.027	0.003	0.030
getDACtable	2.009	0.021	2.038
getDiRatio	0.023	0.003	0.025
getFMItable	0.502	0.007	0.511
getForMigtable	0.595	0.005	0.603
getImageCentroids	0.029	0.003	0.033
getImageStacks	0.066	0.007	0.075
getMSDtable	3.632	0.047	3.694
getOptimizedParameters	0.024	0.002	0.027
getOptimizedParams	0.027	0.003	0.029
getPerAndSpeed	0.311	0.031	0.347
getPopulationStats	0.026	0.002	0.029
getProcessedImages	0.241	0.808	1.069
getProcessingStatus	0.024	0.003	0.026
getResults	0.655	0.017	0.675
getTracks	0.026	0.004	0.030
getVACtable	1.122	0.012	1.136
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.002	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.770	0.033	0.808
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0	0	0
plotAllTracks	0.024	0.004	0.028
plotSampleTracks	0.021	0.004	0.024
preProcCellMig	0.011	0.002	0.014
rmPreProcessing	0.102	0.008	0.111
runTrackingPermutation	0.002	0.001	0.002
setAnalyticParams	0.026	0.002	0.028
setCellMigSlot	0.033	0.002	0.037
setCellTracks	0.025	0.002	0.027
setCellsMeta	0.026	0.002	0.028
setExpName	0.032	0.002	0.034
setOptimizedParams	0.024	0.002	0.027
setProcessedImages	0.025	0.002	0.028
setProcessingStatus	0.043	0.004	0.049
setTrackedCellsMeta	0.023	0.002	0.027
setTrackedCentroids	0.023	0.002	0.026
setTrackedPositions	0.023	0.002	0.026
setTrackingStats	0.026	0.002	0.028
sinkAway	0.001	0.000	0.002
subNetworkTracking	0.002	0.001	0.003
track	0.010	0.001	0.010
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0	0	0
trackSlideWrapUp	0	0	0
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.000
visualizeCellTracks	0.068	0.007	0.075
visualizeTrcks	0.047	0.003	0.049
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.055	0.003	0.058

CHECK results for cellmigRation on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings