Multiple platform build/check report for BioC 3.20 - CHECK results for cellmigRation on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4669
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4404
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4431
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4384
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/meat/cellmigRation.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-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 Monterey 12.7.4
* 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getMSDtable 11.697  0.082  12.938
getDACtable  6.465  0.046   7.430
MSD          5.162  0.144   5.930
DiAutoCor    4.594  0.032   5.157
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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: x86_64-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 May 31 06:04:01 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 
  6.164   0.544   7.451

Example timings

name	user	system	elapsed
AddDimension	0.003	0.001	0.004
CellMig-class	0.048	0.006	0.063
CellMigPCA	3.660	0.062	4.323
CellMigPCAclust	0.012	0.003	0.017
CellMigPCAclustALL	2.200	0.018	2.450
CellTracker	0.028	0.005	0.037
CellTrackerMainLoop	0.007	0.010	0.023
CentroidArray	0.030	0.004	0.034
CentroidValidation	1.618	0.026	1.808
ComputeTracksStats	0.063	0.006	0.075
DetectRadii	0.006	0.000	0.009
DiAutoCor	4.594	0.032	5.157
DiRatio	0.039	0.003	0.045
DiRatioPlot	0.063	0.021	0.095
EstimateDiameterRange	0.032	0.003	0.040
FMI	1.628	0.012	1.843
FianlizeOptiParams	0.001	0.001	0.001
FilterTrackedCells	0.006	0.001	0.008
FinRes	2.193	0.027	2.470
ForwardMigration	3.270	0.021	3.702
GenAllCombos	0.007	0.001	0.008
LinearConv2	0.053	0.002	0.062
LoadTiff	0.002	0.001	0.002
MSD	5.162	0.144	5.930
MakeHypercube	0.003	0.003	0.005
MigrationStats	0.002	0.002	0.004
NextOdd	0.000	0.000	0.001
NonParallel4OptimizeParams	0.001	0.001	0.003
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.022	0.003	0.027
OptimizeParamsMainLoop	0.007	0.010	0.020
Parallel4OptimizeParams	0.001	0.001	0.001
ParallelTrackLoop	0.001	0.001	0.002
PerAndSpeed	0.708	0.041	0.820
PlotTracksSeparately	0.016	0.003	0.021
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.235	0.007	0.271
ThreeConditions	0.019	0.004	0.026
TrackCellsDataset	0.022	0.005	0.033
TrajectoryDataset	0.034	0.003	0.044
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	3.568	0.037	4.193
VisualizeCntr	0.004	0.002	0.007
VisualizeImg	0.009	0.001	0.012
VisualizeStackCentroids	0.093	0.015	0.130
WSADataset	0.010	0.002	0.013
aggregateFR	2.097	0.018	2.429
aggregateTrackedCells	0.035	0.010	0.049
bpass	0.162	0.005	0.185
circshift	0.001	0.001	0.002
cntrd	2.511	0.038	3.074
fixDA	0.000	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0.001	0.001	0.001
fixFM2	0.000	0.001	0.001
fixFM3	0.001	0.001	0.000
fixFM4	0.000	0.001	0.001
fixFM5	0.001	0.001	0.001
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.000	0.002
fixMSD	0.001	0.001	0.001
fixPER1	0.000	0.001	0.001
fixPER2	0.001	0.001	0.000
fixPER3	0.001	0.001	0.001
getAvailableAggrMetrics	3.108	0.027	3.806
getCellImages	0.889	2.599	4.138
getCellMigSlot	0.888	1.630	2.963
getCellTrackMeta	0.023	0.004	0.030
getCellTrackStats	0.031	0.006	0.045
getCellTracks	0.024	0.006	0.035
getCellsMeta	0.023	0.005	0.032
getCellsStats	0.029	0.006	0.038
getDACtable	6.465	0.046	7.430
getDiRatio	0.042	0.004	0.052
getFMItable	1.529	0.012	1.708
getForMigtable	1.910	0.013	2.139
getImageCentroids	0.037	0.006	0.047
getImageStacks	0.092	0.014	0.116
getMSDtable	11.697	0.082	12.938
getOptimizedParameters	0.023	0.003	0.026
getOptimizedParams	0.026	0.005	0.032
getPerAndSpeed	0.692	0.043	0.770
getPopulationStats	0.024	0.005	0.032
getProcessedImages	0.911	3.486	4.911
getProcessingStatus	0.023	0.003	0.026
getResults	2.082	0.027	2.363
getTracks	0.026	0.004	0.030
getVACtable	3.570	0.028	3.994
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.003	0.000	0.003
internalPermutation	0.002	0.001	0.003
matfix	0.003	0.001	0.004
nontrivialBondTracking	0.002	0.000	0.002
pkfnd	2.521	0.032	2.820
plot3DAllTracks	0.001	0.001	0.001
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.035	0.005	0.041
plotSampleTracks	0.025	0.005	0.034
preProcCellMig	0.011	0.003	0.014
rmPreProcessing	0.250	0.010	0.291
runTrackingPermutation	0.003	0.001	0.003
setAnalyticParams	0.022	0.004	0.031
setCellMigSlot	0.036	0.003	0.041
setCellTracks	0.022	0.003	0.030
setCellsMeta	0.022	0.002	0.026
setExpName	0.035	0.003	0.043
setOptimizedParams	0.023	0.004	0.030
setProcessedImages	0.024	0.005	0.031
setProcessingStatus	0.023	0.004	0.028
setTrackedCellsMeta	0.023	0.004	0.028
setTrackedCentroids	0.023	0.005	0.029
setTrackedPositions	0.042	0.006	0.048
setTrackingStats	0.023	0.003	0.027
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.000	0.004
track	0.021	0.001	0.023
trackHypercubeBuild	0.002	0.000	0.002
trackSlideProcessing	0.001	0.001	0.002
trackSlideWrapUp	0.001	0.001	0.001
trivialBondRaster	0.004	0.001	0.004
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.098	0.013	0.120
visualizeTrcks	0.043	0.003	0.051
warnMessage	0.001	0.001	0.002
wsaPreProcessing	0.156	0.004	0.175

CHECK results for cellmigRation on merida1

Summary

Command output

Installation output

Tests output

Example timings