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This page was generated on 2025-10-29 12:06 -0400 (Wed, 29 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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

Package 313/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.17.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-10-28 13:45 -0400 (Tue, 28 Oct 2025)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: devel
git_last_commit: 2938d5a
git_last_commit_date: 2025-04-15 12:26:19 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2025-10-28 20:01:21 -0400 (Tue, 28 Oct 2025)
EndedAt: 2025-10-28 20:03:52 -0400 (Tue, 28 Oct 2025)
EllapsedTime: 151.5 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.17.0’
* 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-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.17.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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 Oct 28 20:03:40 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 
  3.599   0.351   3.976 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0010.0000.002
CellMig-class0.0240.0030.027
CellMigPCA2.0070.0732.093
CellMigPCAclust0.0060.0020.008
CellMigPCAclustALL0.7340.0100.748
CellTracker0.0110.0020.013
CellTrackerMainLoop0.0060.0070.026
CentroidArray0.0130.0020.015
CentroidValidation0.5030.0180.525
ComputeTracksStats0.0200.0020.023
DetectRadii0.0020.0000.003
DiAutoCor1.3940.0131.412
DiRatio0.0190.0010.020
DiRatioPlot0.0370.0150.055
EstimateDiameterRange0.0160.0020.018
FMI0.5160.0050.522
FianlizeOptiParams000
FilterTrackedCells0.0020.0000.003
FinRes0.6870.0140.706
ForwardMigration1.0630.0081.076
GenAllCombos0.0020.0000.003
LinearConv20.0180.0010.020
LoadTiff0.0010.0010.002
MSD1.5970.0191.624
MakeHypercube0.0010.0010.002
MigrationStats0.0000.0010.001
NextOdd000
NonParallel4OptimizeParams0.0010.0010.001
NonParallelTrackLoop000
OptimizeParams0.0110.0020.013
OptimizeParamsMainLoop0.0040.0080.023
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.2990.0270.337
PlotTracksSeparately0.0060.0010.008
PostProcessTracking000
Prep4OptimizeParams0.1010.0030.105
ThreeConditions0.0090.0020.012
TrackCellsDataset0.0110.0020.013
TrajectoryDataset0.0320.0030.035
ValidateTrackingArgs0.0010.0000.001
VeAutoCor1.2170.0221.246
VisualizeCntr0.0020.0010.003
VisualizeImg0.0040.0010.005
VisualizeStackCentroids0.0440.0080.051
WSADataset0.0050.0020.007
aggregateFR0.6610.0060.670
aggregateTrackedCells0.0170.0040.021
bpass0.0780.0030.081
circshift000
cntrd0.7110.0130.726
fixDA0.0010.0010.000
fixExpName000
fixFM10.0000.0010.001
fixFM2000
fixFM3000
fixFM4000
fixFM50.0010.0010.000
fixFM60.0000.0000.001
fixID10.0000.0000.001
fixMSD000
fixPER1000
fixPER20.0000.0000.001
fixPER30.0010.0000.001
getAvailableAggrMetrics1.0010.0081.012
getCellImages0.2640.8401.119
getCellMigSlot0.3550.5310.893
getCellTrackMeta0.0090.0020.011
getCellTrackStats0.0130.0030.016
getCellTracks0.0120.0030.015
getCellsMeta0.0100.0020.011
getCellsStats0.0140.0020.016
getDACtable2.1640.0232.202
getDiRatio0.0180.0020.020
getFMItable0.4830.0040.488
getForMigtable0.5630.0050.569
getImageCentroids0.0150.0030.019
getImageStacks0.0390.0060.045
getMSDtable3.9110.0373.968
getOptimizedParameters0.0100.0020.012
getOptimizedParams0.0110.0030.014
getPerAndSpeed0.3030.0290.342
getPopulationStats0.0110.0020.014
getProcessedImages0.2581.3711.641
getProcessingStatus0.0110.0020.013
getResults0.7040.0170.727
getTracks0.0140.0030.016
getVACtable1.1780.0131.197
initializeTrackParams0.0000.0000.001
innerBondRaster0.0010.0000.002
internalPermutation0.0000.0000.001
matfix0.0010.0000.002
nontrivialBondTracking0.0010.0010.001
pkfnd0.6760.0080.688
plot3DAllTracks000
plot3DTracks0.0000.0010.000
plotAllTracks0.0150.0030.019
plotSampleTracks0.0130.0020.016
preProcCellMig0.0050.0010.007
rmPreProcessing0.0980.0030.101
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0110.0020.014
setCellMigSlot0.0170.0020.018
setCellTracks0.0110.0020.014
setCellsMeta0.0100.0010.013
setExpName0.0180.0020.019
setOptimizedParams0.0110.0020.012
setProcessedImages0.0090.0010.011
setProcessingStatus0.0110.0020.013
setTrackedCellsMeta0.0100.0020.012
setTrackedCentroids0.0110.0020.014
setTrackedPositions0.0110.0010.014
setTrackingStats0.0090.0010.011
sinkAway0.0000.0000.001
subNetworkTracking0.0230.0070.031
track0.0090.0000.009
trackHypercubeBuild0.0010.0010.002
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0010.0000.000
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0460.0070.053
visualizeTrcks0.0270.0020.029
warnMessage0.0010.0010.000
wsaPreProcessing0.0420.0010.043