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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4522
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4468
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 lconway

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: 2024-06-09 19:18:36 -0400 (Sun, 09 Jun 2024)

EndedAt: 2024-06-09 19:20:51 -0400 (Sun, 09 Jun 2024)

EllapsedTime: 135.0 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.12.0’
* 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
* 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 -- Sun Jun  9 19:20:39 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 
  3.135   0.343   3.475

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.001
CellMig-class	0.032	0.003	0.036
CellMigPCA	1.426	0.030	1.460
CellMigPCAclust	0.008	0.001	0.009
CellMigPCAclustALL	0.685	0.007	0.695
CellTracker	0.019	0.003	0.022
CellTrackerMainLoop	0.005	0.008	0.026
CentroidArray	0.019	0.002	0.022
CentroidValidation	0.568	0.014	0.584
ComputeTracksStats	0.037	0.003	0.039
DetectRadii	0.003	0.000	0.004
DiAutoCor	1.451	0.010	1.463
DiRatio	0.020	0.001	0.022
DiRatioPlot	0.036	0.013	0.053
EstimateDiameterRange	0.016	0.002	0.019
FMI	0.528	0.006	0.535
FianlizeOptiParams	0.000	0.000	0.001
FilterTrackedCells	0.004	0.000	0.004
FinRes	0.637	0.012	0.652
ForwardMigration	1.098	0.007	1.107
GenAllCombos	0.002	0.000	0.002
LinearConv2	0.021	0.001	0.022
LoadTiff	0.001	0.000	0.001
MSD	1.918	0.051	1.976
MakeHypercube	0.001	0.001	0.001
MigrationStats	0.001	0.001	0.002
NextOdd	0.000	0.001	0.001
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0.000	0.000	0.001
OptimizeParams	0.016	0.002	0.018
OptimizeParamsMainLoop	0.004	0.010	0.043
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.000	0.001	0.001
PerAndSpeed	0.326	0.027	0.365
PlotTracksSeparately	0.009	0.001	0.011
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.093	0.004	0.097
ThreeConditions	0.010	0.003	0.013
TrackCellsDataset	0.014	0.002	0.016
TrajectoryDataset	0.026	0.002	0.029
ValidateTrackingArgs	0.000	0.001	0.000
VeAutoCor	1.037	0.016	1.056
VisualizeCntr	0.002	0.001	0.003
VisualizeImg	0.006	0.001	0.007
VisualizeStackCentroids	0.053	0.010	0.066
WSADataset	0.008	0.001	0.009
aggregateFR	0.591	0.006	0.598
aggregateTrackedCells	0.016	0.003	0.019
bpass	0.054	0.001	0.056
circshift	0.001	0.000	0.001
cntrd	0.709	0.014	0.724
fixDA	0.001	0.000	0.001
fixExpName	0.000	0.000	0.001
fixFM1	0.000	0.000	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0.001	0.000	0.000
fixPER1	0	0	0
fixPER2	0.001	0.000	0.000
fixPER3	0.000	0.001	0.000
getAvailableAggrMetrics	1.015	0.010	1.028
getCellImages	0.268	0.840	1.115
getCellMigSlot	0.350	0.532	0.886
getCellTrackMeta	0.012	0.002	0.014
getCellTrackStats	0.020	0.003	0.023
getCellTracks	0.016	0.003	0.019
getCellsMeta	0.017	0.002	0.020
getCellsStats	0.017	0.003	0.020
getDACtable	1.993	0.019	2.016
getDiRatio	0.024	0.002	0.026
getFMItable	0.436	0.005	0.440
getForMigtable	0.573	0.006	0.580
getImageCentroids	0.024	0.004	0.027
getImageStacks	0.055	0.010	0.066
getMSDtable	4.114	0.033	4.163
getOptimizedParameters	0.012	0.002	0.014
getOptimizedParams	0.013	0.003	0.016
getPerAndSpeed	0.315	0.025	0.348
getPopulationStats	0.014	0.002	0.015
getProcessedImages	0.273	1.648	1.941
getProcessingStatus	0.015	0.001	0.017
getResults	0.703	0.014	0.721
getTracks	0.013	0.002	0.015
getVACtable	1.264	0.011	1.279
initializeTrackParams	0	0	0
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.001	0.002
matfix	0.001	0.000	0.002
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.783	0.019	0.805
plot3DAllTracks	0	0	0
plot3DTracks	0	0	0
plotAllTracks	0.017	0.003	0.021
plotSampleTracks	0.016	0.003	0.020
preProcCellMig	0.008	0.002	0.009
rmPreProcessing	0.097	0.008	0.105
runTrackingPermutation	0.001	0.001	0.002
setAnalyticParams	0.016	0.002	0.018
setCellMigSlot	0.025	0.002	0.027
setCellTracks	0.016	0.002	0.018
setCellsMeta	0.016	0.001	0.018
setExpName	0.021	0.001	0.024
setOptimizedParams	0.014	0.003	0.017
setProcessedImages	0.017	0.003	0.019
setProcessingStatus	0.015	0.002	0.017
setTrackedCellsMeta	0.015	0.003	0.018
setTrackedCentroids	0.015	0.002	0.017
setTrackedPositions	0.030	0.005	0.035
setTrackingStats	0.013	0.001	0.014
sinkAway	0.001	0.000	0.001
subNetworkTracking	0.001	0.000	0.002
track	0.007	0.001	0.008
trackHypercubeBuild	0.000	0.000	0.001
trackSlideProcessing	0	0	0
trackSlideWrapUp	0.000	0.000	0.001
trivialBondRaster	0.002	0.000	0.001
trivialBondTracking	0	0	0
visualizeCellTracks	0.048	0.007	0.056
visualizeTrcks	0.027	0.001	0.029
warnMessage	0.000	0.001	0.001
wsaPreProcessing	0.056	0.002	0.059