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"	4769
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4504
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4527
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4480
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4416
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: 2025-03-04 00:42:08 -0500 (Tue, 04 Mar 2025)

EndedAt: 2025-03-04 00:47:01 -0500 (Tue, 04 Mar 2025)

EllapsedTime: 293.5 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_1.14.0.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 11.331  0.065  11.570
getDACtable  6.432  0.037   6.541
MSD          5.150  0.132   5.334
* 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 -- Tue Mar  4 00:46:41 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 
  6.032   0.533   6.580

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.005
CellMig-class	0.048	0.006	0.053
CellMigPCA	3.591	0.058	3.697
CellMigPCAclust	0.012	0.003	0.015
CellMigPCAclustALL	2.148	0.019	2.183
CellTracker	0.028	0.006	0.034
CellTrackerMainLoop	0.008	0.011	0.021
CentroidArray	0.029	0.005	0.034
CentroidValidation	1.571	0.026	1.616
ComputeTracksStats	0.049	0.006	0.055
DetectRadii	0.006	0.000	0.007
DiAutoCor	4.579	0.030	4.670
DiRatio	0.038	0.003	0.043
DiRatioPlot	0.064	0.024	0.133
EstimateDiameterRange	0.032	0.003	0.035
FMI	1.592	0.012	1.619
FianlizeOptiParams	0.000	0.001	0.001
FilterTrackedCells	0.007	0.002	0.009
FinRes	2.211	0.030	2.263
ForwardMigration	3.262	0.017	3.348
GenAllCombos	0.007	0.001	0.008
LinearConv2	0.055	0.002	0.058
LoadTiff	0.001	0.001	0.003
MSD	5.150	0.132	5.334
MakeHypercube	0.003	0.002	0.006
MigrationStats	0.002	0.002	0.004
NextOdd	0.001	0.001	0.000
NonParallel4OptimizeParams	0.001	0.000	0.003
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.023	0.004	0.028
OptimizeParamsMainLoop	0.005	0.009	0.017
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.002
PerAndSpeed	0.692	0.044	0.746
PlotTracksSeparately	0.016	0.003	0.018
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.237	0.008	0.246
ThreeConditions	0.018	0.005	0.023
TrackCellsDataset	0.023	0.004	0.028
TrajectoryDataset	0.035	0.003	0.038
ValidateTrackingArgs	0.001	0.001	0.002
VeAutoCor	3.569	0.036	3.638
VisualizeCntr	0.004	0.002	0.006
VisualizeImg	0.010	0.002	0.012
VisualizeStackCentroids	0.092	0.015	0.109
WSADataset	0.011	0.003	0.013
aggregateFR	2.106	0.020	2.149
aggregateTrackedCells	0.035	0.011	0.047
bpass	0.158	0.006	0.166
circshift	0.001	0.000	0.001
cntrd	2.456	0.049	2.587
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0.000	0.000	0.001
fixFM2	0.001	0.000	0.001
fixFM3	0.000	0.001	0.001
fixFM4	0.001	0.000	0.001
fixFM5	0.000	0.000	0.001
fixFM6	0.001	0.000	0.000
fixID1	0.001	0.001	0.002
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.001	0.001
fixPER2	0.000	0.001	0.001
fixPER3	0.001	0.000	0.002
getAvailableAggrMetrics	3.116	0.022	3.173
getCellImages	0.877	2.565	3.510
getCellMigSlot	0.854	1.628	2.505
getCellTrackMeta	0.022	0.003	0.025
getCellTrackStats	0.030	0.005	0.035
getCellTracks	0.023	0.006	0.031
getCellsMeta	0.023	0.003	0.026
getCellsStats	0.027	0.005	0.033
getDACtable	6.432	0.037	6.541
getDiRatio	0.044	0.004	0.049
getFMItable	1.538	0.013	1.577
getForMigtable	1.883	0.011	1.919
getImageCentroids	0.039	0.007	0.049
getImageStacks	0.090	0.015	0.107
getMSDtable	11.331	0.065	11.570
getOptimizedParameters	0.033	0.004	0.038
getOptimizedParams	0.025	0.006	0.030
getPerAndSpeed	0.671	0.041	0.716
getPopulationStats	0.025	0.005	0.030
getProcessedImages	0.809	2.649	3.471
getProcessingStatus	0.021	0.003	0.024
getResults	2.072	0.024	2.130
getTracks	0.026	0.003	0.032
getVACtable	3.470	0.016	3.493
initializeTrackParams	0.000	0.001	0.001
innerBondRaster	0.002	0.001	0.004
internalPermutation	0.003	0.000	0.003
matfix	0.002	0.001	0.004
nontrivialBondTracking	0.003	0.000	0.003
pkfnd	2.398	0.027	2.433
plot3DAllTracks	0.000	0.001	0.001
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.035	0.005	0.041
plotSampleTracks	0.026	0.005	0.031
preProcCellMig	0.011	0.002	0.013
rmPreProcessing	0.234	0.008	0.243
runTrackingPermutation	0.003	0.001	0.004
setAnalyticParams	0.022	0.003	0.025
setCellMigSlot	0.036	0.004	0.041
setCellTracks	0.023	0.003	0.026
setCellsMeta	0.023	0.004	0.028
setExpName	0.036	0.004	0.040
setOptimizedParams	0.023	0.003	0.026
setProcessedImages	0.021	0.003	0.025
setProcessingStatus	0.023	0.004	0.027
setTrackedCellsMeta	0.024	0.004	0.028
setTrackedCentroids	0.024	0.004	0.029
setTrackedPositions	0.024	0.004	0.027
setTrackingStats	0.040	0.007	0.049
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.000	0.003
track	0.021	0.001	0.022
trackHypercubeBuild	0.001	0.001	0.002
trackSlideProcessing	0.001	0.001	0.001
trackSlideWrapUp	0.001	0.001	0.001
trivialBondRaster	0.004	0.001	0.003
trivialBondTracking	0.002	0.001	0.002
visualizeCellTracks	0.096	0.013	0.110
visualizeTrcks	0.044	0.004	0.049
warnMessage	0.001	0.000	0.002
wsaPreProcessing	0.153	0.004	0.156