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
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4529
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4479
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: 2024-10-14 02:07:11 -0400 (Mon, 14 Oct 2024)

EndedAt: 2024-10-14 02:12:50 -0400 (Mon, 14 Oct 2024)

EllapsedTime: 338.7 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 11.871  0.197  15.493
getDACtable  6.640  0.104   8.475
MSD          5.166  0.155   5.843
DiAutoCor    4.663  0.047   5.276
* 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 -- Mon Oct 14 02:12:26 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 
  6.203   0.555   7.422

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.001	0.018
CellMig-class	0.047	0.005	0.062
CellMigPCA	3.665	0.065	4.139
CellMigPCAclust	0.013	0.003	0.016
CellMigPCAclustALL	2.220	0.022	2.506
CellTracker	0.029	0.006	0.039
CellTrackerMainLoop	0.009	0.014	0.028
CentroidArray	0.030	0.005	0.036
CentroidValidation	1.612	0.032	1.793
ComputeTracksStats	0.050	0.006	0.058
DetectRadii	0.006	0.001	0.007
DiAutoCor	4.663	0.047	5.276
DiRatio	0.041	0.003	0.050
DiRatioPlot	0.063	0.021	0.092
EstimateDiameterRange	0.036	0.003	0.040
FMI	1.627	0.015	1.816
FianlizeOptiParams	0.001	0.000	0.002
FilterTrackedCells	0.007	0.002	0.008
FinRes	2.182	0.031	2.484
ForwardMigration	3.339	0.024	3.655
GenAllCombos	0.007	0.001	0.010
LinearConv2	0.056	0.003	0.069
LoadTiff	0.001	0.001	0.003
MSD	5.166	0.155	5.843
MakeHypercube	0.004	0.002	0.005
MigrationStats	0.002	0.002	0.005
NextOdd	0.000	0.001	0.001
NonParallel4OptimizeParams	0.002	0.001	0.002
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.023	0.004	0.033
OptimizeParamsMainLoop	0.006	0.011	0.020
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.696	0.041	0.858
PlotTracksSeparately	0.015	0.002	0.020
PostProcessTracking	0.001	0.001	0.001
Prep4OptimizeParams	0.233	0.007	0.274
ThreeConditions	0.018	0.004	0.025
TrackCellsDataset	0.023	0.005	0.033
TrajectoryDataset	0.035	0.004	0.052
ValidateTrackingArgs	0.000	0.000	0.001
VeAutoCor	3.609	0.044	4.174
VisualizeCntr	0.005	0.002	0.007
VisualizeImg	0.011	0.002	0.014
VisualizeStackCentroids	0.091	0.015	0.123
WSADataset	0.010	0.002	0.014
aggregateFR	2.124	0.023	2.461
aggregateTrackedCells	0.035	0.012	0.058
bpass	0.161	0.005	0.193
circshift	0.001	0.001	0.003
cntrd	2.503	0.039	2.887
fixDA	0.001	0.001	0.001
fixExpName	0.001	0.000	0.002
fixFM1	0.001	0.000	0.001
fixFM2	0.000	0.000	0.001
fixFM3	0.001	0.001	0.001
fixFM4	0.000	0.001	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.001	0.000	0.000
fixID1	0.001	0.000	0.002
fixMSD	0.000	0.000	0.002
fixPER1	0.001	0.001	0.001
fixPER2	0.000	0.001	0.002
fixPER3	0.001	0.000	0.001
getAvailableAggrMetrics	3.103	0.027	3.614
getCellImages	0.882	2.621	3.995
getCellMigSlot	0.896	1.705	2.968
getCellTrackMeta	0.022	0.004	0.031
getCellTrackStats	0.031	0.007	0.044
getCellTracks	0.023	0.006	0.032
getCellsMeta	0.023	0.003	0.031
getCellsStats	0.027	0.005	0.037
getDACtable	6.640	0.104	8.475
getDiRatio	0.062	0.007	0.103
getFMItable	1.586	0.030	2.075
getForMigtable	1.918	0.016	2.141
getImageCentroids	0.040	0.008	0.071
getImageStacks	0.090	0.018	0.187
getMSDtable	11.871	0.197	15.493
getOptimizedParameters	0.022	0.003	0.028
getOptimizedParams	0.026	0.006	0.034
getPerAndSpeed	0.676	0.042	0.790
getPopulationStats	0.026	0.006	0.035
getProcessedImages	0.923	3.580	4.971
getProcessingStatus	0.022	0.004	0.029
getResults	2.112	0.036	2.450
getTracks	0.025	0.004	0.032
getVACtable	3.605	0.036	4.124
initializeTrackParams	0.000	0.001	0.002
innerBondRaster	0.002	0.000	0.004
internalPermutation	0.003	0.001	0.004
matfix	0.002	0.000	0.004
nontrivialBondTracking	0.002	0.001	0.003
pkfnd	2.526	0.033	2.863
plot3DAllTracks	0.000	0.001	0.001
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.034	0.005	0.044
plotSampleTracks	0.026	0.006	0.036
preProcCellMig	0.011	0.002	0.016
rmPreProcessing	0.250	0.009	0.281
runTrackingPermutation	0.003	0.001	0.005
setAnalyticParams	0.023	0.003	0.030
setCellMigSlot	0.036	0.003	0.043
setCellTracks	0.023	0.003	0.029
setCellsMeta	0.023	0.004	0.027
setExpName	0.035	0.004	0.040
setOptimizedParams	0.024	0.004	0.031
setProcessedImages	0.023	0.005	0.034
setProcessingStatus	0.023	0.004	0.029
setTrackedCellsMeta	0.023	0.005	0.032
setTrackedCentroids	0.023	0.004	0.030
setTrackedPositions	0.042	0.006	0.054
setTrackingStats	0.023	0.004	0.028
sinkAway	0.001	0.001	0.003
subNetworkTracking	0.002	0.001	0.003
track	0.023	0.002	0.026
trackHypercubeBuild	0.001	0.000	0.002
trackSlideProcessing	0.002	0.000	0.002
trackSlideWrapUp	0.001	0.000	0.002
trivialBondRaster	0.004	0.001	0.005
trivialBondTracking	0.002	0.000	0.002
visualizeCellTracks	0.095	0.015	0.121
visualizeTrcks	0.045	0.003	0.052
warnMessage	0.001	0.001	0.003
wsaPreProcessing	0.157	0.005	0.191