Multiple platform build/check report for BioC 3.19 - CHECK results for cellmigRation on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4466
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: 1.12.0

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: 2024-06-24 01:40:50 -0400 (Mon, 24 Jun 2024)

EndedAt: 2024-06-24 01:46:02 -0400 (Mon, 24 Jun 2024)

EllapsedTime: 312.3 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: 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 ‘1.12.0’
* 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 11.831  0.144  12.990
getDACtable  6.509  0.045   6.931
MSD          5.142  0.143   5.829
DiAutoCor    4.696  0.040   5.043
* 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-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 4.4.0 (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 -- Mon Jun 24 01:45:39 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 
  6.248   0.583   7.425

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.005
CellMig-class	0.049	0.006	0.077
CellMigPCA	3.660	0.057	4.044
CellMigPCAclust	0.012	0.003	0.018
CellMigPCAclustALL	2.194	0.018	2.416
CellTracker	0.028	0.005	0.036
CellTrackerMainLoop	0.007	0.014	0.028
CentroidArray	0.029	0.005	0.036
CentroidValidation	1.626	0.033	1.809
ComputeTracksStats	0.051	0.005	0.058
DetectRadii	0.006	0.000	0.007
DiAutoCor	4.696	0.040	5.043
DiRatio	0.038	0.003	0.044
DiRatioPlot	0.065	0.023	0.094
EstimateDiameterRange	0.036	0.003	0.041
FMI	1.637	0.012	1.726
FianlizeOptiParams	0.001	0.000	0.002
FilterTrackedCells	0.006	0.002	0.008
FinRes	2.165	0.027	2.290
ForwardMigration	3.300	0.022	3.554
GenAllCombos	0.007	0.001	0.009
LinearConv2	0.056	0.003	0.067
LoadTiff	0.001	0.001	0.001
MSD	5.142	0.143	5.829
MakeHypercube	0.003	0.002	0.005
MigrationStats	0.002	0.002	0.004
NextOdd	0.000	0.001	0.001
NonParallel4OptimizeParams	0.002	0.001	0.002
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.023	0.004	0.029
OptimizeParamsMainLoop	0.006	0.009	0.021
Parallel4OptimizeParams	0.001	0.001	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.702	0.043	0.874
PlotTracksSeparately	0.016	0.003	0.020
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.238	0.006	0.266
ThreeConditions	0.018	0.005	0.027
TrackCellsDataset	0.023	0.003	0.027
TrajectoryDataset	0.034	0.003	0.041
ValidateTrackingArgs	0.001	0.001	0.002
VeAutoCor	3.601	0.039	3.964
VisualizeCntr	0.004	0.002	0.005
VisualizeImg	0.009	0.002	0.013
VisualizeStackCentroids	0.091	0.014	0.116
WSADataset	0.010	0.002	0.013
aggregateFR	2.140	0.018	2.351
aggregateTrackedCells	0.037	0.011	0.054
bpass	0.162	0.004	0.180
circshift	0.001	0.001	0.002
cntrd	2.515	0.038	2.810
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0.000	0.000	0.001
fixFM2	0.001	0.001	0.001
fixFM3	0.001	0.001	0.001
fixFM4	0.000	0.001	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.000	0.000	0.001
fixID1	0.001	0.001	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.000	0.001	0.001
fixPER2	0.001	0.001	0.001
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	3.114	0.024	3.402
getCellImages	0.901	2.544	3.691
getCellMigSlot	0.846	1.605	2.610
getCellTrackMeta	0.022	0.003	0.026
getCellTrackStats	0.030	0.007	0.039
getCellTracks	0.023	0.007	0.031
getCellsMeta	0.022	0.004	0.028
getCellsStats	0.028	0.006	0.035
getDACtable	6.509	0.045	6.931
getDiRatio	0.045	0.005	0.052
getFMItable	1.568	0.016	1.680
getForMigtable	1.900	0.015	2.022
getImageCentroids	0.039	0.009	0.054
getImageStacks	0.089	0.015	0.112
getMSDtable	11.831	0.144	12.990
getOptimizedParameters	0.022	0.003	0.031
getOptimizedParams	0.026	0.006	0.034
getPerAndSpeed	0.700	0.042	0.823
getPopulationStats	0.025	0.005	0.036
getProcessedImages	0.923	3.636	4.961
getProcessingStatus	0.022	0.003	0.027
getResults	2.130	0.036	2.403
getTracks	0.024	0.004	0.029
getVACtable	3.659	0.035	4.018
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.002	0.000	0.003
internalPermutation	0.002	0.001	0.003
matfix	0.003	0.000	0.004
nontrivialBondTracking	0.002	0.001	0.003
pkfnd	2.548	0.036	2.808
plot3DAllTracks	0.000	0.001	0.001
plot3DTracks	0.001	0.001	0.001
plotAllTracks	0.036	0.005	0.047
plotSampleTracks	0.027	0.005	0.034
preProcCellMig	0.011	0.002	0.014
rmPreProcessing	0.254	0.011	0.278
runTrackingPermutation	0.002	0.001	0.004
setAnalyticParams	0.023	0.004	0.026
setCellMigSlot	0.036	0.004	0.043
setCellTracks	0.022	0.004	0.029
setCellsMeta	0.023	0.003	0.028
setExpName	0.036	0.004	0.040
setOptimizedParams	0.023	0.004	0.028
setProcessedImages	0.023	0.003	0.027
setProcessingStatus	0.023	0.004	0.027
setTrackedCellsMeta	0.023	0.004	0.029
setTrackedCentroids	0.023	0.004	0.029
setTrackedPositions	0.041	0.006	0.047
setTrackingStats	0.023	0.004	0.031
sinkAway	0.002	0.001	0.002
subNetworkTracking	0.002	0.001	0.003
track	0.021	0.002	0.026
trackHypercubeBuild	0.002	0.000	0.003
trackSlideProcessing	0.001	0.001	0.003
trackSlideWrapUp	0.002	0.001	0.003
trivialBondRaster	0.003	0.000	0.004
trivialBondTracking	0.002	0.001	0.002
visualizeCellTracks	0.095	0.015	0.120
visualizeTrcks	0.045	0.002	0.048
warnMessage	0.000	0.001	0.002
wsaPreProcessing	0.164	0.006	0.178