Multiple platform build/check report for BioC 3.19 - CHECK results for cellmigRation on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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: 1.12.0

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: 2024-10-17 02:27:54 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 02:33:26 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 332.2 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.12.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
getMSDtable        11.818  0.148  14.519
getDACtable         6.566  0.073   8.153
MSD                 5.178  0.165   6.316
DiAutoCor           4.617  0.047   5.305
getProcessedImages  0.950  3.677   5.479
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 -- Thu Oct 17 02:33:02 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 
  6.276   0.564   7.811

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.002	0.006
CellMig-class	0.047	0.006	0.063
CellMigPCA	3.677	0.069	4.361
CellMigPCAclust	0.012	0.003	0.018
CellMigPCAclustALL	2.218	0.028	2.671
CellTracker	0.027	0.005	0.038
CellTrackerMainLoop	0.008	0.012	0.031
CentroidArray	0.030	0.005	0.036
CentroidValidation	1.635	0.036	1.944
ComputeTracksStats	0.050	0.005	0.066
DetectRadii	0.006	0.001	0.007
DiAutoCor	4.617	0.047	5.305
DiRatio	0.040	0.003	0.047
DiRatioPlot	0.067	0.024	0.129
EstimateDiameterRange	0.033	0.004	0.041
FMI	1.631	0.016	1.861
FianlizeOptiParams	0.001	0.001	0.002
FilterTrackedCells	0.007	0.001	0.009
FinRes	2.227	0.036	2.625
ForwardMigration	3.297	0.034	3.852
GenAllCombos	0.006	0.000	0.007
LinearConv2	0.055	0.003	0.066
LoadTiff	0.001	0.001	0.008
MSD	5.178	0.165	6.316
MakeHypercube	0.004	0.002	0.006
MigrationStats	0.001	0.002	0.006
NextOdd	0.001	0.001	0.001
NonParallel4OptimizeParams	0.002	0.000	0.002
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.024	0.004	0.033
OptimizeParamsMainLoop	0.005	0.010	0.021
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.695	0.044	0.916
PlotTracksSeparately	0.016	0.003	0.021
PostProcessTracking	0.001	0.000	0.002
Prep4OptimizeParams	0.238	0.007	0.284
ThreeConditions	0.019	0.005	0.030
TrackCellsDataset	0.023	0.004	0.032
TrajectoryDataset	0.035	0.004	0.047
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	3.609	0.050	4.267
VisualizeCntr	0.004	0.002	0.008
VisualizeImg	0.010	0.002	0.013
VisualizeStackCentroids	0.095	0.018	0.176
WSADataset	0.011	0.003	0.017
aggregateFR	2.117	0.025	2.511
aggregateTrackedCells	0.035	0.012	0.055
bpass	0.161	0.005	0.197
circshift	0.000	0.001	0.001
cntrd	2.519	0.044	3.004
fixDA	0.001	0.001	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0.000	0.000	0.001
fixFM2	0.001	0.000	0.003
fixFM3	0.000	0.001	0.002
fixFM4	0.001	0.001	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.001	0.000	0.002
fixID1	0.001	0.001	0.001
fixMSD	0.001	0.001	0.001
fixPER1	0.001	0.001	0.001
fixPER2	0.000	0.000	0.001
fixPER3	0.001	0.000	0.002
getAvailableAggrMetrics	3.138	0.035	3.672
getCellImages	0.909	2.655	4.224
getCellMigSlot	0.873	1.714	3.078
getCellTrackMeta	0.023	0.004	0.038
getCellTrackStats	0.030	0.007	0.044
getCellTracks	0.024	0.007	0.039
getCellsMeta	0.023	0.003	0.033
getCellsStats	0.028	0.005	0.041
getDACtable	6.566	0.073	8.153
getDiRatio	0.059	0.007	0.082
getFMItable	1.556	0.018	1.901
getForMigtable	1.904	0.020	2.343
getImageCentroids	0.040	0.010	0.065
getImageStacks	0.093	0.016	0.126
getMSDtable	11.818	0.148	14.519
getOptimizedParameters	0.022	0.003	0.031
getOptimizedParams	0.026	0.006	0.038
getPerAndSpeed	0.696	0.045	0.949
getPopulationStats	0.025	0.005	0.035
getProcessedImages	0.950	3.677	5.479
getProcessingStatus	0.023	0.003	0.027
getResults	2.093	0.036	2.484
getTracks	0.026	0.004	0.033
getVACtable	3.642	0.037	4.289
initializeTrackParams	0.000	0.001	0.002
innerBondRaster	0.003	0.000	0.003
internalPermutation	0.002	0.000	0.003
matfix	0.003	0.001	0.005
nontrivialBondTracking	0.002	0.000	0.002
pkfnd	2.564	0.032	3.015
plot3DAllTracks	0.001	0.001	0.001
plot3DTracks	0.000	0.000	0.001
plotAllTracks	0.035	0.006	0.045
plotSampleTracks	0.026	0.006	0.034
preProcCellMig	0.011	0.003	0.014
rmPreProcessing	0.246	0.008	0.279
runTrackingPermutation	0.003	0.000	0.003
setAnalyticParams	0.023	0.003	0.028
setCellMigSlot	0.036	0.003	0.044
setCellTracks	0.023	0.004	0.030
setCellsMeta	0.022	0.003	0.027
setExpName	0.036	0.003	0.042
setOptimizedParams	0.022	0.003	0.029
setProcessedImages	0.022	0.003	0.028
setProcessingStatus	0.023	0.003	0.029
setTrackedCellsMeta	0.023	0.004	0.031
setTrackedCentroids	0.023	0.004	0.030
setTrackedPositions	0.044	0.006	0.060
setTrackingStats	0.023	0.003	0.030
sinkAway	0.001	0.001	0.001
subNetworkTracking	0.002	0.001	0.003
track	0.020	0.001	0.021
trackHypercubeBuild	0.002	0.000	0.003
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.001	0.001	0.002
trivialBondRaster	0.004	0.000	0.004
trivialBondTracking	0.001	0.000	0.002
visualizeCellTracks	0.098	0.015	0.130
visualizeTrcks	0.045	0.002	0.057
warnMessage	0.001	0.001	0.004
wsaPreProcessing	0.160	0.004	0.194