Multiple platform build/check report for BioC 3.19 - CHECK results for cellmigRation on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.12.0’
* 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-3.19-bioc/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-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 (2024-04-24) -- "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 -- Wed May 29 19:40:20 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 
  3.435   0.374   3.820

Example timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.002
CellMig-class	0.023	0.002	0.026
CellMigPCA	1.542	0.040	1.597
CellMigPCAclust	0.007	0.002	0.009
CellMigPCAclustALL	0.788	0.011	0.805
CellTracker	0.016	0.003	0.018
CellTrackerMainLoop	0.006	0.007	0.025
CentroidArray	0.019	0.003	0.022
CentroidValidation	0.510	0.015	0.529
ComputeTracksStats	0.035	0.003	0.040
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.665	0.024	1.702
DiRatio	0.021	0.002	0.022
DiRatioPlot	0.042	0.015	0.062
EstimateDiameterRange	0.020	0.002	0.024
FMI	0.576	0.007	0.586
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.002	0.000	0.003
FinRes	0.802	0.017	0.828
ForwardMigration	1.186	0.014	1.209
GenAllCombos	0.004	0.000	0.005
LinearConv2	0.023	0.001	0.025
LoadTiff	0.000	0.000	0.001
MSD	2.022	0.066	2.107
MakeHypercube	0.001	0.000	0.002
MigrationStats	0.001	0.000	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.001	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.014	0.002	0.016
OptimizeParamsMainLoop	0.005	0.010	0.024
Parallel4OptimizeParams	0.001	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.331	0.032	0.376
PlotTracksSeparately	0.009	0.002	0.012
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.108	0.005	0.114
ThreeConditions	0.012	0.003	0.015
TrackCellsDataset	0.015	0.002	0.018
TrajectoryDataset	0.020	0.002	0.022
ValidateTrackingArgs	0.001	0.001	0.001
VeAutoCor	1.377	0.032	1.429
VisualizeCntr	0.003	0.002	0.004
VisualizeImg	0.005	0.002	0.007
VisualizeStackCentroids	0.052	0.010	0.063
WSADataset	0.006	0.001	0.008
aggregateFR	0.692	0.011	0.708
aggregateTrackedCells	0.020	0.004	0.023
bpass	0.068	0.003	0.072
circshift	0.001	0.000	0.000
cntrd	0.764	0.018	0.789
fixDA	0	0	0
fixExpName	0.000	0.000	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.001	0.001	0.001
fixFM5	0.001	0.000	0.000
fixFM6	0.001	0.000	0.001
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0.001	0.000	0.000
fixPER2	0.000	0.001	0.000
fixPER3	0.000	0.000	0.001
getAvailableAggrMetrics	1.085	0.015	1.110
getCellImages	0.269	0.848	1.133
getCellMigSlot	0.381	0.577	0.969
getCellTrackMeta	0.013	0.001	0.015
getCellTrackStats	0.018	0.002	0.021
getCellTracks	0.015	0.003	0.017
getCellsMeta	0.015	0.003	0.017
getCellsStats	0.017	0.003	0.020
getDACtable	2.182	0.032	2.232
getDiRatio	0.023	0.004	0.028
getFMItable	0.557	0.012	0.575
getForMigtable	0.714	0.014	0.737
getImageCentroids	0.023	0.005	0.029
getImageStacks	0.060	0.009	0.071
getMSDtable	4.347	0.072	4.465
getOptimizedParameters	0.014	0.002	0.017
getOptimizedParams	0.015	0.002	0.018
getPerAndSpeed	0.310	0.033	0.354
getPopulationStats	0.017	0.004	0.020
getProcessedImages	0.306	1.937	2.290
getProcessingStatus	0.016	0.002	0.019
getResults	0.804	0.018	0.832
getTracks	0.016	0.002	0.018
getVACtable	1.328	0.021	1.363
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.001	0.001	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.002	0.000	0.001
pkfnd	0.886	0.023	0.918
plot3DAllTracks	0.000	0.001	0.000
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.019	0.003	0.023
plotSampleTracks	0.016	0.003	0.020
preProcCellMig	0.007	0.001	0.009
rmPreProcessing	0.110	0.006	0.118
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.016	0.002	0.017
setCellMigSlot	0.021	0.001	0.023
setCellTracks	0.014	0.002	0.017
setCellsMeta	0.016	0.002	0.018
setExpName	0.020	0.001	0.022
setOptimizedParams	0.015	0.001	0.018
setProcessedImages	0.015	0.002	0.018
setProcessingStatus	0.015	0.003	0.018
setTrackedCellsMeta	0.016	0.003	0.019
setTrackedCentroids	0.028	0.004	0.032
setTrackedPositions	0.015	0.002	0.017
setTrackingStats	0.014	0.003	0.016
sinkAway	0.001	0.000	0.001
subNetworkTracking	0.002	0.001	0.001
track	0.009	0.000	0.009
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.000	0.001	0.001
trackSlideWrapUp	0	0	0
trivialBondRaster	0.001	0.000	0.002
trivialBondTracking	0.000	0.000	0.001
visualizeCellTracks	0.060	0.008	0.069
visualizeTrcks	0.025	0.003	0.028
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.062	0.003	0.067

CHECK results for cellmigRation on lconway

Summary

Command output

Installation output

Tests output

Example timings