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"	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 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: 2024-12-31 13:41:22 -0500 (Tue, 31 Dec 2024)

EndedAt: 2024-12-31 13:43:39 -0500 (Tue, 31 Dec 2024)

EllapsedTime: 137.2 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 Dec 31 13:43:24 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 
  3.447   0.315   3.773

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.002	0.001	0.002
CellMig-class	0.039	0.003	0.042
CellMigPCA	1.478	0.032	1.523
CellMigPCAclust	0.009	0.002	0.012
CellMigPCAclustALL	0.709	0.006	0.718
CellTracker	0.027	0.003	0.030
CellTrackerMainLoop	0.006	0.010	0.020
CentroidArray	0.027	0.002	0.030
CentroidValidation	0.516	0.015	0.535
ComputeTracksStats	0.034	0.003	0.037
DetectRadii	0.002	0.000	0.003
DiAutoCor	1.482	0.017	1.505
DiRatio	0.021	0.002	0.023
DiRatioPlot	0.040	0.012	0.054
EstimateDiameterRange	0.017	0.002	0.021
FMI	0.516	0.005	0.523
FianlizeOptiParams	0.001	0.000	0.001
FilterTrackedCells	0.004	0.001	0.004
FinRes	0.734	0.016	0.754
ForwardMigration	1.076	0.007	1.086
GenAllCombos	0.003	0.000	0.003
LinearConv2	0.020	0.001	0.022
LoadTiff	0.001	0.000	0.001
MSD	1.873	0.047	1.929
MakeHypercube	0.001	0.001	0.001
MigrationStats	0.000	0.000	0.001
NextOdd	0	0	0
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.024	0.002	0.026
OptimizeParamsMainLoop	0.005	0.010	0.020
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.001	0.001	0.000
PerAndSpeed	0.309	0.033	0.349
PlotTracksSeparately	0.011	0.002	0.013
PostProcessTracking	0.000	0.000	0.001
Prep4OptimizeParams	0.101	0.004	0.105
ThreeConditions	0.020	0.003	0.024
TrackCellsDataset	0.025	0.002	0.027
TrajectoryDataset	0.031	0.002	0.034
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	1.099	0.019	1.121
VisualizeCntr	0.003	0.001	0.003
VisualizeImg	0.006	0.001	0.006
VisualizeStackCentroids	0.067	0.008	0.075
WSADataset	0.010	0.002	0.012
aggregateFR	0.667	0.008	0.679
aggregateTrackedCells	0.031	0.005	0.036
bpass	0.082	0.003	0.086
circshift	0	0	0
cntrd	0.731	0.018	0.752
fixDA	0.000	0.000	0.001
fixExpName	0	0	0
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.001	0.000	0.000
fixFM5	0	0	0
fixFM6	0.001	0.000	0.000
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0.001	0.000	0.000
fixPER2	0	0	0
fixPER3	0.001	0.001	0.000
getAvailableAggrMetrics	0.943	0.011	0.960
getCellImages	0.252	0.829	1.096
getCellMigSlot	0.407	0.503	0.924
getCellTrackMeta	0.024	0.003	0.027
getCellTrackStats	0.026	0.003	0.030
getCellTracks	0.025	0.003	0.029
getCellsMeta	0.024	0.003	0.026
getCellsStats	0.025	0.003	0.028
getDACtable	1.975	0.023	2.013
getDiRatio	0.023	0.002	0.026
getFMItable	0.504	0.007	0.515
getForMigtable	0.594	0.006	0.604
getImageCentroids	0.029	0.004	0.032
getImageStacks	0.067	0.008	0.078
getMSDtable	3.284	0.048	3.353
getOptimizedParameters	0.010	0.002	0.011
getOptimizedParams	0.011	0.002	0.013
getPerAndSpeed	0.226	0.028	0.260
getPopulationStats	0.010	0.001	0.012
getProcessedImages	0.188	0.674	0.883
getProcessingStatus	0.025	0.003	0.028
getResults	0.676	0.016	0.696
getTracks	0.025	0.003	0.028
getVACtable	1.099	0.012	1.117
initializeTrackParams	0.000	0.001	0.001
innerBondRaster	0.001	0.000	0.002
internalPermutation	0.001	0.000	0.001
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.001	0.001	0.002
pkfnd	0.776	0.021	0.800
plot3DAllTracks	0.000	0.000	0.001
plot3DTracks	0.001	0.000	0.000
plotAllTracks	0.021	0.005	0.026
plotSampleTracks	0.019	0.004	0.023
preProcCellMig	0.011	0.001	0.013
rmPreProcessing	0.097	0.004	0.101
runTrackingPermutation	0.002	0.001	0.003
setAnalyticParams	0.022	0.003	0.026
setCellMigSlot	0.032	0.003	0.035
setCellTracks	0.024	0.003	0.027
setCellsMeta	0.026	0.002	0.028
setExpName	0.031	0.002	0.034
setOptimizedParams	0.023	0.003	0.026
setProcessedImages	0.022	0.004	0.025
setProcessingStatus	0.024	0.003	0.027
setTrackedCellsMeta	0.024	0.003	0.027
setTrackedCentroids	0.025	0.003	0.028
setTrackedPositions	0.024	0.004	0.029
setTrackingStats	0.023	0.004	0.027
sinkAway	0.000	0.001	0.001
subNetworkTracking	0.001	0.000	0.001
track	0.024	0.003	0.027
trackHypercubeBuild	0.001	0.000	0.001
trackSlideProcessing	0	0	0
trackSlideWrapUp	0.000	0.001	0.001
trivialBondRaster	0.002	0.000	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.068	0.008	0.075
visualizeTrcks	0.046	0.003	0.049
warnMessage	0.000	0.000	0.001
wsaPreProcessing	0.057	0.002	0.059