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	4.4.3 (2025-02-28) -- "Trophy Case"	4670
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4355
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4446
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4439
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4306
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: 2025-03-07 01:05:56 -0500 (Fri, 07 Mar 2025)

EndedAt: 2025-03-07 01:10:41 -0500 (Fri, 07 Mar 2025)

EllapsedTime: 284.4 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 11.407  0.088  11.764
getDACtable  6.331  0.047   6.471
MSD          4.917  0.132   5.070
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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 Mar  7 01:10:19 2025 
*********************************************** 
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 
  6.019   0.574   6.679

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.001	0.004
CellMig-class	0.041	0.010	0.050
CellMigPCA	3.454	0.062	3.593
CellMigPCAclust	0.011	0.010	0.021
CellMigPCAclustALL	2.112	0.023	2.165
CellTracker	0.023	0.013	0.036
CellTrackerMainLoop	0.007	0.010	0.020
CentroidArray	0.025	0.010	0.034
CentroidValidation	1.528	0.035	1.575
ComputeTracksStats	0.047	0.013	0.061
DetectRadii	0.006	0.001	0.007
DiAutoCor	4.432	0.033	4.485
DiRatio	0.035	0.010	0.045
DiRatioPlot	0.060	0.030	0.091
EstimateDiameterRange	0.033	0.003	0.036
FMI	1.553	0.016	1.575
FianlizeOptiParams	0.000	0.000	0.001
FilterTrackedCells	0.006	0.001	0.006
FinRes	2.063	0.030	2.102
ForwardMigration	3.129	0.021	3.163
GenAllCombos	0.006	0.001	0.007
LinearConv2	0.067	0.003	0.070
LoadTiff	0.001	0.000	0.002
MSD	4.917	0.132	5.070
MakeHypercube	0.003	0.002	0.005
MigrationStats	0.002	0.002	0.003
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.002	0.001	0.002
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.020	0.011	0.030
OptimizeParamsMainLoop	0.006	0.010	0.018
Parallel4OptimizeParams	0.001	0.001	0.002
ParallelTrackLoop	0.001	0.001	0.001
PerAndSpeed	0.687	0.047	0.768
PlotTracksSeparately	0.013	0.009	0.021
PostProcessTracking	0.000	0.001	0.001
Prep4OptimizeParams	0.221	0.011	0.233
ThreeConditions	0.018	0.011	0.030
TrackCellsDataset	0.018	0.010	0.029
TrajectoryDataset	0.029	0.009	0.040
ValidateTrackingArgs	0.000	0.001	0.001
VeAutoCor	3.434	0.038	3.491
VisualizeCntr	0.003	0.001	0.005
VisualizeImg	0.010	0.002	0.011
VisualizeStackCentroids	0.084	0.019	0.103
WSADataset	0.009	0.009	0.018
aggregateFR	2.069	0.025	2.122
aggregateTrackedCells	0.033	0.020	0.053
bpass	0.159	0.004	0.171
circshift	0.001	0.001	0.001
cntrd	2.444	0.038	2.562
fixDA	0.000	0.000	0.002
fixExpName	0.001	0.000	0.001
fixFM1	0.001	0.001	0.001
fixFM2	0.000	0.001	0.001
fixFM3	0.001	0.000	0.002
fixFM4	0.000	0.000	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.001	0.000	0.001
fixID1	0.001	0.001	0.002
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.000	0.001
fixPER2	0.000	0.000	0.001
fixPER3	0.001	0.001	0.001
getAvailableAggrMetrics	3.070	0.038	3.252
getCellImages	0.871	2.574	3.501
getCellMigSlot	0.843	1.639	2.520
getCellTrackMeta	0.019	0.012	0.031
getCellTrackStats	0.027	0.013	0.041
getCellTracks	0.021	0.014	0.036
getCellsMeta	0.019	0.011	0.030
getCellsStats	0.024	0.013	0.037
getDACtable	6.331	0.047	6.471
getDiRatio	0.040	0.012	0.052
getFMItable	1.492	0.017	1.526
getForMigtable	1.877	0.019	1.925
getImageCentroids	0.034	0.014	0.049
getImageStacks	0.086	0.020	0.106
getMSDtable	11.407	0.088	11.764
getOptimizedParameters	0.019	0.010	0.029
getOptimizedParams	0.022	0.011	0.034
getPerAndSpeed	0.675	0.048	0.776
getPopulationStats	0.021	0.011	0.035
getProcessedImages	0.900	3.546	4.574
getProcessingStatus	0.020	0.009	0.029
getResults	2.035	0.032	2.106
getTracks	0.022	0.010	0.055
getVACtable	3.454	0.030	3.651
initializeTrackParams	0.001	0.001	0.002
innerBondRaster	0.002	0.000	0.003
internalPermutation	0.002	0.000	0.003
matfix	0.002	0.001	0.002
nontrivialBondTracking	0.002	0.000	0.002
pkfnd	2.429	0.039	2.492
plot3DAllTracks	0.001	0.000	0.001
plot3DTracks	0.000	0.001	0.001
plotAllTracks	0.033	0.012	0.049
plotSampleTracks	0.024	0.011	0.036
preProcCellMig	0.008	0.009	0.017
rmPreProcessing	0.241	0.024	0.270
runTrackingPermutation	0.003	0.001	0.004
setAnalyticParams	0.019	0.010	0.031
setCellMigSlot	0.032	0.011	0.043
setCellTracks	0.019	0.009	0.028
setCellsMeta	0.019	0.010	0.030
setExpName	0.033	0.010	0.043
setOptimizedParams	0.020	0.010	0.031
setProcessedImages	0.019	0.011	0.030
setProcessingStatus	0.020	0.009	0.030
setTrackedCellsMeta	0.018	0.010	0.028
setTrackedCentroids	0.020	0.011	0.031
setTrackedPositions	0.041	0.013	0.055
setTrackingStats	0.019	0.010	0.030
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.000	0.002
track	0.021	0.002	0.024
trackHypercubeBuild	0.002	0.001	0.002
trackSlideProcessing	0.001	0.000	0.002
trackSlideWrapUp	0.002	0.000	0.002
trivialBondRaster	0.003	0.001	0.005
trivialBondTracking	0.001	0.001	0.002
visualizeCellTracks	0.091	0.021	0.117
visualizeTrcks	0.045	0.003	0.051
warnMessage	0.001	0.000	0.002
wsaPreProcessing	0.150	0.010	0.164