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 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 merida1

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: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2024-12-20 00:52:55 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 00:57:42 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 286.9 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.14.0’
* 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 11.236  0.058  11.327
getDACtable  6.395  0.038   6.478
MSD          5.083  0.141   5.366
* 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

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-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

cellmigRation.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 Dec 20 00:57:22 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 
  6.052   0.536   6.600

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.004
CellMig-class	0.047	0.006	0.053
CellMigPCA	3.553	0.054	3.636
CellMigPCAclust	0.012	0.003	0.015
CellMigPCAclustALL	2.155	0.020	2.258
CellTracker	0.028	0.006	0.034
CellTrackerMainLoop	0.007	0.010	0.021
CentroidArray	0.029	0.006	0.035
CentroidValidation	1.582	0.029	1.640
ComputeTracksStats	0.048	0.005	0.054
DetectRadii	0.006	0.001	0.006
DiAutoCor	4.560	0.032	4.637
DiRatio	0.038	0.002	0.040
DiRatioPlot	0.061	0.021	0.085
EstimateDiameterRange	0.032	0.003	0.035
FMI	1.585	0.011	1.618
FianlizeOptiParams	0.000	0.000	0.001
FilterTrackedCells	0.006	0.002	0.007
FinRes	2.157	0.028	2.204
ForwardMigration	3.180	0.020	3.217
GenAllCombos	0.006	0.001	0.007
LinearConv2	0.052	0.002	0.054
LoadTiff	0.001	0.001	0.002
MSD	5.083	0.141	5.366
MakeHypercube	0.003	0.003	0.006
MigrationStats	0.002	0.002	0.004
NextOdd	0.001	0.001	0.001
NonParallel4OptimizeParams	0.002	0.000	0.003
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.023	0.003	0.026
OptimizeParamsMainLoop	0.007	0.010	0.019
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.001	0.001
PerAndSpeed	0.691	0.040	0.780
PlotTracksSeparately	0.015	0.003	0.019
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.230	0.009	0.240
ThreeConditions	0.019	0.004	0.023
TrackCellsDataset	0.023	0.005	0.028
TrajectoryDataset	0.036	0.004	0.040
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	3.539	0.036	3.622
VisualizeCntr	0.004	0.002	0.005
VisualizeImg	0.009	0.002	0.012
VisualizeStackCentroids	0.091	0.014	0.107
WSADataset	0.010	0.003	0.013
aggregateFR	2.070	0.016	2.103
aggregateTrackedCells	0.035	0.011	0.046
bpass	0.155	0.005	0.160
circshift	0.001	0.000	0.001
cntrd	2.445	0.033	2.513
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.001	0.001
fixFM1	0.001	0.000	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0.001	0.000	0.001
fixFM4	0.000	0.000	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.000	0.001	0.001
fixID1	0.001	0.001	0.002
fixMSD	0.001	0.000	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0.000	0.000	0.001
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	3.028	0.022	3.085
getCellImages	0.886	2.603	3.583
getCellMigSlot	0.853	1.606	2.476
getCellTrackMeta	0.023	0.005	0.028
getCellTrackStats	0.029	0.006	0.036
getCellTracks	0.024	0.006	0.034
getCellsMeta	0.024	0.006	0.030
getCellsStats	0.029	0.005	0.034
getDACtable	6.395	0.038	6.478
getDiRatio	0.043	0.004	0.047
getFMItable	1.536	0.011	1.564
getForMigtable	1.841	0.011	1.873
getImageCentroids	0.037	0.006	0.044
getImageStacks	0.083	0.015	0.099
getMSDtable	11.236	0.058	11.327
getOptimizedParameters	0.020	0.004	0.025
getOptimizedParams	0.027	0.006	0.033
getPerAndSpeed	0.667	0.044	0.714
getPopulationStats	0.024	0.005	0.029
getProcessedImages	0.863	3.356	4.234
getProcessingStatus	0.022	0.004	0.025
getResults	2.044	0.023	2.079
getTracks	0.025	0.004	0.029
getVACtable	3.453	0.016	3.489
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.003	0.000	0.003
internalPermutation	0.002	0.001	0.002
matfix	0.002	0.001	0.003
nontrivialBondTracking	0.002	0.000	0.003
pkfnd	2.399	0.033	2.436
plot3DAllTracks	0.001	0.001	0.001
plot3DTracks	0.000	0.001	0.001
plotAllTracks	0.034	0.005	0.039
plotSampleTracks	0.026	0.006	0.031
preProcCellMig	0.011	0.003	0.015
rmPreProcessing	0.242	0.004	0.247
runTrackingPermutation	0.003	0.001	0.004
setAnalyticParams	0.022	0.003	0.025
setCellMigSlot	0.037	0.003	0.039
setCellTracks	0.021	0.003	0.024
setCellsMeta	0.023	0.003	0.026
setExpName	0.029	0.002	0.031
setOptimizedParams	0.022	0.004	0.027
setProcessedImages	0.022	0.003	0.025
setProcessingStatus	0.023	0.003	0.025
setTrackedCellsMeta	0.023	0.005	0.028
setTrackedCentroids	0.024	0.003	0.027
setTrackedPositions	0.023	0.003	0.026
setTrackingStats	0.023	0.005	0.028
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.001	0.003
track	0.037	0.003	0.041
trackHypercubeBuild	0.002	0.000	0.002
trackSlideProcessing	0.001	0.000	0.002
trackSlideWrapUp	0.001	0.001	0.001
trivialBondRaster	0.004	0.001	0.004
trivialBondTracking	0.001	0.000	0.002
visualizeCellTracks	0.096	0.015	0.114
visualizeTrcks	0.046	0.003	0.050
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.154	0.004	0.159