Multiple platform build/check report for BioC 3.19 - CHECK results for cellmigRation on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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*

CHECK results for cellmigRation on kjohnson3

To the developers/maintainers of the cellmigRation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellmigRation.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: cellmigRation

Version: 1.12.0

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_1.12.0.tar.gz

StartedAt: 2024-06-10 09:58:59 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 10:02:09 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 190.5 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMSDtable 3.959  0.069   5.458
* 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

cellmigRation.Rcheck/00install.out

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

cellmigRation.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24) -- "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 -- Mon Jun 10 10:01:50 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 
  3.276   0.381   4.787

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.004
CellMig-class	0.026	0.004	0.037
CellMigPCA	1.581	0.052	2.187
CellMigPCAclust	0.007	0.002	0.012
CellMigPCAclustALL	0.793	0.011	1.049
CellTracker	0.016	0.003	0.023
CellTrackerMainLoop	0.005	0.012	0.039
CentroidArray	0.016	0.002	0.028
CentroidValidation	0.560	0.018	0.757
ComputeTracksStats	0.046	0.004	0.068
DetectRadii	0.003	0.000	0.004
DiAutoCor	1.628	0.020	2.123
DiRatio	0.017	0.002	0.028
DiRatioPlot	0.035	0.018	0.070
EstimateDiameterRange	0.015	0.003	0.022
FMI	0.615	0.008	0.817
FianlizeOptiParams	0.001	0.000	0.000
FilterTrackedCells	0.004	0.000	0.004
FinRes	0.826	0.023	1.150
ForwardMigration	1.224	0.011	1.608
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.021	0.002	0.032
LoadTiff	0.001	0.001	0.001
MSD	2.135	0.077	2.940
MakeHypercube	0.002	0.001	0.001
MigrationStats	0.001	0.001	0.005
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.001	0.003
NonParallelTrackLoop	0.001	0.000	0.000
OptimizeParams	0.014	0.003	0.029
OptimizeParamsMainLoop	0.006	0.013	0.043
Parallel4OptimizeParams	0.001	0.001	0.000
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.298	0.045	0.477
PlotTracksSeparately	0.008	0.001	0.011
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.086	0.005	0.109
ThreeConditions	0.011	0.003	0.019
TrackCellsDataset	0.013	0.002	0.023
TrajectoryDataset	0.020	0.003	0.033
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	1.152	0.020	1.576
VisualizeCntr	0.003	0.002	0.005
VisualizeImg	0.005	0.002	0.008
VisualizeStackCentroids	0.048	0.007	0.079
WSADataset	0.006	0.002	0.008
aggregateFR	0.664	0.010	0.857
aggregateTrackedCells	0.020	0.004	0.030
bpass	0.060	0.004	0.075
circshift	0.000	0.000	0.001
cntrd	0.745	0.017	1.020
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0.001	0.000	0.000
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.000	0.000	0.001
fixFM5	0	0	0
fixFM6	0.001	0.000	0.000
fixID1	0.000	0.000	0.001
fixMSD	0.000	0.001	0.004
fixPER1	0.000	0.000	0.001
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.973	0.013	1.327
getCellImages	0.180	0.572	0.974
getCellMigSlot	0.284	0.378	0.887
getCellTrackMeta	0.013	0.002	0.024
getCellTrackStats	0.017	0.003	0.028
getCellTracks	0.014	0.003	0.019
getCellsMeta	0.013	0.002	0.021
getCellsStats	0.016	0.004	0.032
getDACtable	2.053	0.031	2.765
getDiRatio	0.019	0.003	0.033
getFMItable	0.504	0.007	0.696
getForMigtable	0.621	0.009	0.858
getImageCentroids	0.020	0.003	0.031
getImageStacks	0.047	0.009	0.075
getMSDtable	3.959	0.069	5.458
getOptimizedParameters	0.014	0.003	0.023
getOptimizedParams	0.014	0.003	0.021
getPerAndSpeed	0.301	0.046	0.497
getPopulationStats	0.015	0.003	0.024
getProcessedImages	0.180	0.813	1.338
getProcessingStatus	0.014	0.002	0.024
getResults	0.692	0.023	0.966
getTracks	0.015	0.003	0.021
getVACtable	1.163	0.016	1.523
initializeTrackParams	0.000	0.001	0.001
innerBondRaster	0.001	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.803	0.023	1.056
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.017	0.005	0.028
plotSampleTracks	0.015	0.005	0.027
preProcCellMig	0.006	0.002	0.010
rmPreProcessing	0.095	0.009	0.141
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.014	0.002	0.021
setCellMigSlot	0.020	0.002	0.029
setCellTracks	0.013	0.002	0.020
setCellsMeta	0.014	0.003	0.017
setExpName	0.020	0.003	0.031
setOptimizedParams	0.013	0.003	0.016
setProcessedImages	0.013	0.003	0.024
setProcessingStatus	0.014	0.003	0.023
setTrackedCellsMeta	0.013	0.002	0.016
setTrackedCentroids	0.013	0.002	0.016
setTrackedPositions	0.044	0.005	0.060
setTrackingStats	0.014	0.003	0.019
sinkAway	0.000	0.001	0.001
subNetworkTracking	0.002	0.000	0.003
track	0.012	0.000	0.021
trackHypercubeBuild	0.001	0.000	0.002
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.003
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.049	0.009	0.071
visualizeTrcks	0.027	0.002	0.035
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.055	0.002	0.078