Multiple platform build/check report for BioC 3.20 - CHECK results for cellmigRation on merida1

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"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
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: 1.14.0

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: 2025-01-21 00:55:04 -0500 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 00:59:54 -0500 (Tue, 21 Jan 2025)

EllapsedTime: 289.9 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: 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 ‘1.14.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getMSDtable 11.389  0.069  11.555
getDACtable  6.292  0.038   6.378
MSD          5.095  0.143   5.497
* 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-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 -- Tue Jan 21 00:59:33 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 
  6.173   0.566   6.746

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.003	0.001	0.004
CellMig-class	0.047	0.005	0.052
CellMigPCA	3.609	0.059	3.830
CellMigPCAclust	0.013	0.003	0.015
CellMigPCAclustALL	2.170	0.016	2.254
CellTracker	0.027	0.005	0.035
CellTrackerMainLoop	0.007	0.013	0.024
CentroidArray	0.028	0.005	0.033
CentroidValidation	1.583	0.028	1.685
ComputeTracksStats	0.049	0.005	0.055
DetectRadii	0.007	0.001	0.007
DiAutoCor	4.583	0.031	4.716
DiRatio	0.038	0.002	0.040
DiRatioPlot	0.059	0.021	0.096
EstimateDiameterRange	0.032	0.003	0.035
FMI	1.596	0.010	1.643
FianlizeOptiParams	0.001	0.001	0.002
FilterTrackedCells	0.007	0.001	0.009
FinRes	2.143	0.027	2.206
ForwardMigration	3.211	0.017	3.335
GenAllCombos	0.007	0.001	0.007
LinearConv2	0.052	0.003	0.056
LoadTiff	0.002	0.000	0.003
MSD	5.095	0.143	5.497
MakeHypercube	0.003	0.002	0.005
MigrationStats	0.002	0.002	0.004
NextOdd	0.001	0.000	0.001
NonParallel4OptimizeParams	0.001	0.000	0.003
NonParallelTrackLoop	0.000	0.001	0.001
OptimizeParams	0.023	0.004	0.028
OptimizeParamsMainLoop	0.006	0.010	0.018
Parallel4OptimizeParams	0.001	0.000	0.002
ParallelTrackLoop	0.001	0.000	0.001
PerAndSpeed	0.681	0.040	0.726
PlotTracksSeparately	0.014	0.003	0.016
PostProcessTracking	0.001	0.000	0.002
Prep4OptimizeParams	0.234	0.008	0.243
ThreeConditions	0.019	0.005	0.025
TrackCellsDataset	0.022	0.004	0.026
TrajectoryDataset	0.034	0.003	0.037
ValidateTrackingArgs	0.001	0.000	0.001
VeAutoCor	3.579	0.040	3.644
VisualizeCntr	0.004	0.002	0.006
VisualizeImg	0.010	0.002	0.012
VisualizeStackCentroids	0.090	0.015	0.106
WSADataset	0.010	0.002	0.012
aggregateFR	2.071	0.016	2.154
aggregateTrackedCells	0.036	0.012	0.048
bpass	0.158	0.004	0.165
circshift	0.001	0.001	0.001
cntrd	2.435	0.039	2.524
fixDA	0.000	0.001	0.001
fixExpName	0.001	0.000	0.001
fixFM1	0.001	0.000	0.001
fixFM2	0	0	0
fixFM3	0.001	0.001	0.002
fixFM4	0.000	0.000	0.001
fixFM5	0.001	0.000	0.001
fixFM6	0.001	0.000	0.001
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	3.071	0.020	3.153
getCellImages	0.890	2.613	3.599
getCellMigSlot	0.855	1.617	2.537
getCellTrackMeta	0.023	0.002	0.025
getCellTrackStats	0.031	0.006	0.039
getCellTracks	0.023	0.006	0.029
getCellsMeta	0.022	0.003	0.025
getCellsStats	0.027	0.005	0.033
getDACtable	6.292	0.038	6.378
getDiRatio	0.041	0.004	0.046
getFMItable	1.499	0.012	1.515
getForMigtable	1.843	0.014	1.866
getImageCentroids	0.039	0.008	0.046
getImageStacks	0.090	0.016	0.108
getMSDtable	11.389	0.069	11.555
getOptimizedParameters	0.022	0.005	0.027
getOptimizedParams	0.026	0.006	0.035
getPerAndSpeed	0.694	0.044	0.745
getPopulationStats	0.025	0.004	0.029
getProcessedImages	0.840	2.722	3.590
getProcessingStatus	0.022	0.004	0.027
getResults	2.042	0.026	2.076
getTracks	0.026	0.004	0.029
getVACtable	3.466	0.017	3.498
initializeTrackParams	0.000	0.001	0.001
innerBondRaster	0.003	0.001	0.004
internalPermutation	0.002	0.000	0.003
matfix	0.002	0.001	0.003
nontrivialBondTracking	0.003	0.000	0.002
pkfnd	2.486	0.034	2.541
plot3DAllTracks	0.000	0.001	0.001
plot3DTracks	0.001	0.000	0.001
plotAllTracks	0.034	0.005	0.040
plotSampleTracks	0.025	0.005	0.030
preProcCellMig	0.011	0.002	0.014
rmPreProcessing	0.248	0.006	0.257
runTrackingPermutation	0.003	0.000	0.003
setAnalyticParams	0.022	0.003	0.026
setCellMigSlot	0.036	0.003	0.040
setCellTracks	0.022	0.003	0.026
setCellsMeta	0.022	0.003	0.025
setExpName	0.036	0.003	0.039
setOptimizedParams	0.022	0.003	0.026
setProcessedImages	0.023	0.005	0.028
setProcessingStatus	0.023	0.005	0.028
setTrackedCellsMeta	0.022	0.004	0.027
setTrackedCentroids	0.022	0.004	0.026
setTrackedPositions	0.021	0.004	0.026
setTrackingStats	0.023	0.004	0.027
sinkAway	0.001	0.001	0.002
subNetworkTracking	0.002	0.001	0.003
track	0.038	0.004	0.044
trackHypercubeBuild	0.002	0.000	0.002
trackSlideProcessing	0.002	0.001	0.002
trackSlideWrapUp	0.001	0.000	0.002
trivialBondRaster	0.004	0.000	0.004
trivialBondTracking	0.001	0.001	0.002
visualizeCellTracks	0.090	0.015	0.106
visualizeTrcks	0.045	0.003	0.048
warnMessage	0.001	0.000	0.002
wsaPreProcessing	0.155	0.004	0.162