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"	4378
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*

##############################################################################
##############################################################################
###
### 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* 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

##############################################################################
##############################################################################
###
### 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


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 12 08:02:51 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 
  3.379   0.277   3.658

Example timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.003
CellMig-class	0.035	0.003	0.039
CellMigPCA	1.467	0.032	1.509
CellMigPCAclust	0.011	0.003	0.015
CellMigPCAclustALL	0.717	0.007	0.747
CellTracker	0.027	0.003	0.030
CellTrackerMainLoop	0.007	0.013	0.027
CentroidArray	0.029	0.003	0.031
CentroidValidation	0.537	0.015	0.558
ComputeTracksStats	0.036	0.003	0.039
DetectRadii	0.003	0.000	0.002
DiAutoCor	1.457	0.020	1.482
DiRatio	0.022	0.003	0.025
DiRatioPlot	0.055	0.014	0.073
EstimateDiameterRange	0.019	0.002	0.021
FMI	0.528	0.006	0.558
FianlizeOptiParams	0.000	0.001	0.001
FilterTrackedCells	0.002	0.000	0.003
FinRes	0.560	0.015	0.591
ForwardMigration	0.888	0.007	0.923
GenAllCombos	0.002	0.000	0.003
LinearConv2	0.020	0.001	0.021
LoadTiff	0.001	0.001	0.002
MSD	1.888	0.063	2.022
MakeHypercube	0.002	0.000	0.002
MigrationStats	0.001	0.000	0.001
NextOdd	0.000	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.025	0.003	0.030
OptimizeParamsMainLoop	0.005	0.012	0.025
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.311	0.032	0.349
PlotTracksSeparately	0.013	0.001	0.014
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.115	0.005	0.126
ThreeConditions	0.020	0.003	0.024
TrackCellsDataset	0.025	0.002	0.028
TrajectoryDataset	0.033	0.002	0.038
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.109	0.015	1.144
VisualizeCntr	0.002	0.001	0.004
VisualizeImg	0.006	0.002	0.010
VisualizeStackCentroids	0.070	0.008	0.080
WSADataset	0.010	0.001	0.012
aggregateFR	0.662	0.007	0.678
aggregateTrackedCells	0.030	0.005	0.035
bpass	0.082	0.003	0.084
circshift	0.001	0.001	0.000
cntrd	0.744	0.019	0.767
fixDA	0.000	0.000	0.001
fixExpName	0.000	0.000	0.001
fixFM1	0	0	0
fixFM2	0.001	0.000	0.001
fixFM3	0.000	0.000	0.001
fixFM4	0.000	0.000	0.001
fixFM5	0.001	0.000	0.000
fixFM6	0	0	0
fixID1	0.000	0.000	0.001
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0.001	0.000	0.000
fixPER3	0	0	0
getAvailableAggrMetrics	0.962	0.009	0.973
getCellImages	0.254	0.796	1.062
getCellMigSlot	0.404	0.496	0.909
getCellTrackMeta	0.026	0.002	0.027
getCellTrackStats	0.027	0.003	0.031
getCellTracks	0.023	0.004	0.027
getCellsMeta	0.025	0.003	0.028
getCellsStats	0.025	0.003	0.029
getDACtable	2.018	0.021	2.050
getDiRatio	0.023	0.003	0.026
getFMItable	0.500	0.007	0.507
getForMigtable	0.599	0.005	0.605
getImageCentroids	0.029	0.003	0.032
getImageStacks	0.069	0.007	0.076
getMSDtable	3.642	0.047	3.703
getOptimizedParameters	0.023	0.002	0.026
getOptimizedParams	0.026	0.004	0.031
getPerAndSpeed	0.308	0.033	0.342
getPopulationStats	0.025	0.004	0.030
getProcessedImages	0.246	1.151	1.426
getProcessingStatus	0.025	0.002	0.028
getResults	0.675	0.017	0.693
getTracks	0.025	0.004	0.028
getVACtable	1.124	0.013	1.140
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.001	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.755	0.030	0.787
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.022	0.004	0.025
plotSampleTracks	0.019	0.004	0.024
preProcCellMig	0.011	0.003	0.014
rmPreProcessing	0.100	0.009	0.110
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.023	0.002	0.028
setCellMigSlot	0.033	0.003	0.042
setCellTracks	0.026	0.004	0.046
setCellsMeta	0.026	0.006	0.049
setExpName	0.034	0.004	0.064
setOptimizedParams	0.024	0.003	0.027
setProcessedImages	0.024	0.002	0.027
setProcessingStatus	0.041	0.004	0.046
setTrackedCellsMeta	0.024	0.002	0.026
setTrackedCentroids	0.024	0.003	0.027
setTrackedPositions	0.025	0.002	0.027
setTrackingStats	0.026	0.002	0.028
sinkAway	0.001	0.001	0.001
subNetworkTracking	0.001	0.000	0.002
track	0.011	0.000	0.012
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.000	0.001
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.002	0.000	0.003
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.071	0.007	0.078
visualizeTrcks	0.049	0.002	0.052
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.057	0.002	0.059

CHECK results for cellmigRation on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings