Multiple platform build/check report for BioC 3.21 - CHECK results for cellmigRation on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4756
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4475
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4435
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4390
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4383
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 nebbiolo1

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: 1.15.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cellmigRation_1.15.0.tar.gz

StartedAt: 2025-01-03 20:30:03 -0500 (Fri, 03 Jan 2025)

EndedAt: 2025-01-03 20:33:52 -0500 (Fri, 03 Jan 2025)

EllapsedTime: 229.3 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings cellmigRation_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 Jan  3 20:31:48 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 
  2.469   0.240   2.695

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.001	0.001
CellMig-class	0.024	0.002	0.027
CellMigPCA	1.360	0.073	1.433
CellMigPCAclust	0.008	0.000	0.007
CellMigPCAclustALL	0.623	0.002	0.625
CellTracker	0.017	0.002	0.019
CellTrackerMainLoop	0.003	0.007	0.007
CentroidArray	0.018	0.002	0.020
CentroidValidation	0.453	0.003	0.458
ComputeTracksStats	0.025	0.002	0.027
DetectRadii	0.003	0.000	0.003
DiAutoCor	1.384	0.248	1.632
DiRatio	0.017	0.001	0.018
DiRatioPlot	0.028	0.010	0.039
EstimateDiameterRange	0.013	0.004	0.016
FMI	0.470	0.014	0.485
FianlizeOptiParams	0.000	0.001	0.001
FilterTrackedCells	0.003	0.001	0.005
FinRes	0.665	0.056	0.722
ForwardMigration	0.943	0.023	0.968
GenAllCombos	0.002	0.001	0.003
LinearConv2	0.019	0.001	0.021
LoadTiff	0.000	0.000	0.001
MSD	1.781	0.187	1.969
MakeHypercube	0.001	0.000	0.002
MigrationStats	0.000	0.001	0.001
NextOdd	0.000	0.001	0.000
NonParallel4OptimizeParams	0.001	0.001	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.015	0.005	0.019
OptimizeParamsMainLoop	0.003	0.006	0.008
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.001	0.001
PerAndSpeed	0.347	0.009	0.356
PlotTracksSeparately	0.01	0.00	0.01
PostProcessTracking	0.001	0.000	0.001
Prep4OptimizeParams	0.087	0.004	0.092
ThreeConditions	0.011	0.005	0.015
TrackCellsDataset	0.015	0.003	0.017
TrajectoryDataset	0.021	0.000	0.022
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	1.006	0.004	1.009
VisualizeCntr	0.001	0.001	0.002
VisualizeImg	0.005	0.000	0.005
VisualizeStackCentroids	0.055	0.004	0.058
WSADataset	0.006	0.000	0.007
aggregateFR	0.583	0.018	0.601
aggregateTrackedCells	0.017	0.008	0.025
bpass	0.065	0.001	0.066
circshift	0.001	0.000	0.001
cntrd	0.647	0.019	0.667
fixDA	0.001	0.000	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0	0	0
fixFM2	0.001	0.000	0.001
fixFM3	0.001	0.000	0.001
fixFM4	0	0	0
fixFM5	0	0	0
fixFM6	0.000	0.001	0.000
fixID1	0.000	0.000	0.001
fixMSD	0	0	0
fixPER1	0.000	0.001	0.001
fixPER2	0.000	0.001	0.001
fixPER3	0.000	0.001	0.001
getAvailableAggrMetrics	0.875	0.022	0.897
getCellImages	0.249	0.973	1.223
getCellMigSlot	0.262	0.643	0.906
getCellTrackMeta	0.016	0.002	0.017
getCellTrackStats	0.019	0.003	0.023
getCellTracks	0.015	0.003	0.019
getCellsMeta	0.016	0.002	0.018
getCellsStats	0.016	0.005	0.020
getDACtable	1.882	0.052	1.936
getDiRatio	0.018	0.002	0.019
getFMItable	0.446	0.005	0.452
getForMigtable	0.559	0.006	0.566
getImageCentroids	0.017	0.007	0.025
getImageStacks	0.056	0.003	0.059
getMSDtable	3.521	0.033	3.555
getOptimizedParameters	0.014	0.002	0.016
getOptimizedParams	0.017	0.002	0.019
getPerAndSpeed	0.295	0.022	0.318
getPopulationStats	0.013	0.005	0.019
getProcessedImages	0.204	1.028	1.232
getProcessingStatus	0.016	0.002	0.018
getResults	0.607	0.004	0.611
getTracks	0.016	0.002	0.018
getVACtable	1.027	0.001	1.029
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.001	0.001	0.002
internalPermutation	0.001	0.000	0.002
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.002	0.000	0.001
pkfnd	0.689	0.003	0.692
plot3DAllTracks	0.105	0.034	0.139
plot3DTracks	0.007	0.002	0.009
plotAllTracks	0.017	0.002	0.019
plotSampleTracks	0.013	0.003	0.016
preProcCellMig	0.007	0.000	0.008
rmPreProcessing	0.083	0.006	0.089
runTrackingPermutation	0.001	0.000	0.002
setAnalyticParams	0.012	0.006	0.017
setCellMigSlot	0.020	0.002	0.022
setCellTracks	0.012	0.005	0.017
setCellsMeta	0.016	0.001	0.017
setExpName	0.018	0.004	0.022
setOptimizedParams	0.015	0.003	0.017
setProcessedImages	0.016	0.001	0.016
setProcessingStatus	0.016	0.001	0.017
setTrackedCellsMeta	0.014	0.003	0.016
setTrackedCentroids	0.016	0.002	0.018
setTrackedPositions	0.030	0.005	0.035
setTrackingStats	0.014	0.003	0.018
sinkAway	0.000	0.001	0.001
subNetworkTracking	0.001	0.000	0.002
track	0.010	0.001	0.010
trackHypercubeBuild	0.000	0.000	0.001
trackSlideProcessing	0.000	0.001	0.000
trackSlideWrapUp	0.001	0.000	0.001
trivialBondRaster	0.001	0.001	0.002
trivialBondTracking	0.001	0.000	0.001
visualizeCellTracks	0.057	0.003	0.060
visualizeTrcks	0.024	0.001	0.025
warnMessage	0.001	0.000	0.001
wsaPreProcessing	0.049	0.001	0.050