Multiple platform build/check report for BioC 3.17 - CHECK results for cellmigRation on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)	x86_64	R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"	4536
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"	4298
merida1	macOS 10.14.6 Mojave	x86_64	R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"	4290
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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.7.0’
* 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 R 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 ... OK
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMSDtable 9.937  0.039  14.520
getDACtable 5.638  0.016   8.113
MSD         4.149  0.023   5.945
DiAutoCor   3.950  0.021   5.699
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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/4.3/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 -- Thu Mar 23 00:06:34 2023 
*********************************************** 
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 
  6.139   0.398   9.208

Example timings

name	user	system	elapsed
AddDimension	0.004	0.000	0.005
CellMig-class	0.051	0.004	0.084
CellMigPCA	3.266	0.033	4.702
CellMigPCAclust	0.014	0.002	0.023
CellMigPCAclustALL	2.113	0.091	3.126
CellTracker	0.037	0.004	0.054
CellTrackerMainLoop	0.006	0.005	0.024
CentroidArray	0.039	0.003	0.055
CentroidValidation	1.382	0.022	2.032
ComputeTracksStats	0.056	0.003	0.082
DetectRadii	0.005	0.000	0.005
DiAutoCor	3.950	0.021	5.699
DiRatio	0.035	0.002	0.055
DiRatioPlot	0.058	0.011	0.097
EstimateDiameterRange	0.029	0.001	0.040
FMI	1.340	0.009	1.852
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.005	0.000	0.009
FinRes	1.816	0.014	2.543
ForwardMigration	2.705	0.009	3.883
GenAllCombos	0.006	0.000	0.009
LinearConv2	0.047	0.001	0.068
LoadTiff	0.002	0.001	0.002
MSD	4.149	0.023	5.945
MakeHypercube	0.003	0.001	0.007
MigrationStats	0.002	0.001	0.002
NextOdd	0	0	0
NonParallel4OptimizeParams	0.002	0.000	0.007
NonParallelTrackLoop	0	0	0
OptimizeParams	0.071	0.004	0.099
OptimizeParamsMainLoop	0.005	0.005	0.020
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.001	0.001
PerAndSpeed	0.618	0.024	0.898
PlotTracksSeparately	0.014	0.003	0.026
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.216	0.004	0.302
ThreeConditions	0.033	0.003	0.057
TrackCellsDataset	0.032	0.003	0.049
TrajectoryDataset	0.038	0.002	0.059
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	3.145	0.028	4.618
VisualizeCntr	0.003	0.001	0.008
VisualizeImg	0.009	0.001	0.014
VisualizeStackCentroids	0.101	0.008	0.172
WSADataset	0.011	0.001	0.021
aggregateFR	1.836	0.007	2.640
aggregateTrackedCells	0.043	0.004	0.063
bpass	0.138	0.002	0.196
circshift	0.001	0.000	0.008
cntrd	2.174	0.013	3.134
fixDA	0.000	0.000	0.001
fixExpName	0.001	0.001	0.005
fixFM1	0	0	0
fixFM2	0.001	0.000	0.001
fixFM3	0.001	0.000	0.001
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0.001	0.001	0.001
fixID1	0.001	0.000	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0.001	0.000	0.001
fixPER3	0.001	0.000	0.004
getAvailableAggrMetrics	2.686	0.012	3.823
getCellImages	0.577	0.765	1.903
getCellMigSlot	0.654	0.496	1.616
getCellTrackMeta	0.032	0.004	0.047
getCellTrackStats	0.040	0.004	0.056
getCellTracks	0.032	0.003	0.055
getCellsMeta	0.033	0.003	0.047
getCellsStats	0.037	0.003	0.060
getDACtable	5.638	0.016	8.113
getDiRatio	0.040	0.002	0.057
getFMItable	1.354	0.005	1.981
getForMigtable	1.975	0.007	2.879
getImageCentroids	0.046	0.003	0.075
getImageStacks	0.102	0.007	0.156
getMSDtable	9.937	0.039	14.520
getOptimizedParameters	0.032	0.002	0.048
getOptimizedParams	0.035	0.002	0.054
getPerAndSpeed	0.614	0.021	1.026
getPopulationStats	0.035	0.002	0.060
getProcessedImages	0.538	0.769	2.109
getProcessingStatus	0.032	0.002	0.051
getResults	1.779	0.013	2.774
getTracks	0.035	0.002	0.058
getVACtable	3.058	0.014	4.866
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.003	0.000	0.003
internalPermutation	0.002	0.001	0.002
matfix	0.002	0.000	0.003
nontrivialBondTracking	0.002	0.000	0.009
pkfnd	2.117	0.009	3.188
plot3DAllTracks	0	0	0
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.033	0.003	0.056
plotSampleTracks	0.025	0.003	0.043
preProcCellMig	0.011	0.002	0.019
rmPreProcessing	0.225	0.003	0.329
runTrackingPermutation	0.003	0.000	0.003
setAnalyticParams	0.032	0.002	0.045
setCellMigSlot	0.041	0.002	0.061
setCellTracks	0.032	0.002	0.046
setCellsMeta	0.033	0.002	0.047
setExpName	0.040	0.002	0.063
setOptimizedParams	0.033	0.003	0.047
setProcessedImages	0.032	0.002	0.049
setProcessingStatus	0.033	0.003	0.049
setTrackedCellsMeta	0.051	0.003	0.073
setTrackedCentroids	0.031	0.002	0.044
setTrackedPositions	0.033	0.002	0.062
setTrackingStats	0.032	0.002	0.049
sinkAway	0.001	0.000	0.002
subNetworkTracking	0.002	0.000	0.002
track	0.020	0.001	0.029
trackHypercubeBuild	0.001	0.000	0.006
trackSlideProcessing	0.002	0.000	0.005
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.003	0.000	0.008
trivialBondTracking	0.001	0.000	0.002
visualizeCellTracks	0.103	0.007	0.161
visualizeTrcks	0.038	0.002	0.060
warnMessage	0.001	0.001	0.001
wsaPreProcessing	0.143	0.002	0.213

CHECK results for cellmigRation on merida1

Summary

Command output

Installation output

Tests output

Example timings