Multiple platform build/check report for BioC 3.20 - CHECK results for cellmigRation on kjohnson1

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 kjohnson1

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 13:49:33 -0500 (Tue, 04 Mar 2025)

EndedAt: 2025-03-04 13:51:48 -0500 (Tue, 04 Mar 2025)

EllapsedTime: 134.4 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 4.4.2 (2024-10-31)
* 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 13.7.1
* 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
* 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-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 -- Tue Mar  4 13:51:33 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 
  3.396   0.324   3.753

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.000	0.002
CellMig-class	0.040	0.003	0.043
CellMigPCA	1.445	0.033	1.515
CellMigPCAclust	0.009	0.002	0.011
CellMigPCAclustALL	0.691	0.007	0.702
CellTracker	0.027	0.003	0.031
CellTrackerMainLoop	0.008	0.010	0.019
CentroidArray	0.029	0.002	0.032
CentroidValidation	0.526	0.013	0.542
ComputeTracksStats	0.033	0.003	0.036
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.536	0.017	1.563
DiRatio	0.021	0.002	0.022
DiRatioPlot	0.039	0.013	0.053
EstimateDiameterRange	0.017	0.002	0.020
FMI	0.523	0.005	0.529
FianlizeOptiParams	0	0	0
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.736	0.015	0.764
ForwardMigration	1.046	0.007	1.060
GenAllCombos	0.003	0.001	0.003
LinearConv2	0.022	0.002	0.024
LoadTiff	0.000	0.000	0.001
MSD	1.889	0.055	1.958
MakeHypercube	0.001	0.001	0.002
MigrationStats	0.001	0.001	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.026	0.002	0.028
OptimizeParamsMainLoop	0.006	0.010	0.019
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.311	0.033	0.349
PlotTracksSeparately	0.014	0.002	0.015
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.100	0.003	0.105
ThreeConditions	0.021	0.004	0.024
TrackCellsDataset	0.023	0.003	0.027
TrajectoryDataset	0.032	0.003	0.035
ValidateTrackingArgs	0.000	0.001	0.001
VeAutoCor	1.128	0.017	1.154
VisualizeCntr	0.002	0.000	0.003
VisualizeImg	0.005	0.001	0.006
VisualizeStackCentroids	0.069	0.007	0.076
WSADataset	0.010	0.002	0.011
aggregateFR	0.659	0.007	0.672
aggregateTrackedCells	0.031	0.005	0.035
bpass	0.083	0.003	0.085
circshift	0.001	0.001	0.001
cntrd	0.749	0.015	0.766
fixDA	0.001	0.000	0.001
fixExpName	0.000	0.000	0.001
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0.001	0.000	0.001
fixFM4	0.000	0.000	0.001
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0.001	0.000	0.001
fixMSD	0.000	0.000	0.001
fixPER1	0.000	0.000	0.001
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.941	0.011	0.959
getCellImages	0.250	0.775	1.043
getCellMigSlot	0.400	0.489	0.896
getCellTrackMeta	0.025	0.003	0.028
getCellTrackStats	0.026	0.003	0.029
getCellTracks	0.024	0.004	0.027
getCellsMeta	0.026	0.003	0.029
getCellsStats	0.028	0.004	0.032
getDACtable	1.992	0.019	2.020
getDiRatio	0.023	0.002	0.025
getFMItable	0.494	0.009	0.507
getForMigtable	0.600	0.006	0.610
getImageCentroids	0.030	0.005	0.037
getImageStacks	0.068	0.008	0.076
getMSDtable	3.650	0.049	3.718
getOptimizedParameters	0.025	0.002	0.027
getOptimizedParams	0.025	0.004	0.028
getPerAndSpeed	0.305	0.031	0.342
getPopulationStats	0.025	0.003	0.028
getProcessedImages	0.241	1.168	1.437
getProcessingStatus	0.024	0.003	0.026
getResults	0.688	0.018	0.720
getTracks	0.027	0.002	0.030
getVACtable	1.154	0.014	1.192
initializeTrackParams	0.001	0.001	0.001
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.001	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.001	0.001
pkfnd	0.763	0.022	0.796
plot3DAllTracks	0	0	0
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.023	0.004	0.027
plotSampleTracks	0.020	0.003	0.025
preProcCellMig	0.009	0.001	0.011
rmPreProcessing	0.103	0.007	0.112
runTrackingPermutation	0.002	0.000	0.002
setAnalyticParams	0.024	0.003	0.025
setCellMigSlot	0.032	0.002	0.034
setCellTracks	0.023	0.003	0.026
setCellsMeta	0.025	0.003	0.028
setExpName	0.031	0.003	0.035
setOptimizedParams	0.024	0.003	0.026
setProcessedImages	0.026	0.003	0.029
setProcessingStatus	0.026	0.003	0.029
setTrackedCellsMeta	0.024	0.002	0.028
setTrackedCentroids	0.025	0.002	0.027
setTrackedPositions	0.041	0.004	0.046
setTrackingStats	0.023	0.002	0.028
sinkAway	0.001	0.001	0.001
subNetworkTracking	0.001	0.000	0.002
track	0.013	0.000	0.013
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.071	0.008	0.081
visualizeTrcks	0.047	0.002	0.049
warnMessage	0.001	0.001	0.000
wsaPreProcessing	0.055	0.002	0.057