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This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 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 1.18.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_22
git_last_commit: 995cd43
git_last_commit_date: 2025-10-29 11:08:05 -0400 (Wed, 29 Oct 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: 1.18.0
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_1.18.0.tar.gz
StartedAt: 2025-10-30 02:49:08 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 02:51:31 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 143.6 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_1.18.0.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 ‘1.18.0’
* 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 ‘1.18.0’
** 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 -- Thu Oct 30 02:51:19 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 
  3.530   0.348   3.917 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0010.0010.001
CellMig-class0.0190.0020.021
CellMigPCA1.9730.0662.044
CellMigPCAclust0.0060.0020.007
CellMigPCAclustALL0.6300.0110.641
CellTracker0.0140.0030.017
CellTrackerMainLoop0.0050.0070.024
CentroidArray0.0130.0010.015
CentroidValidation0.4350.0170.453
ComputeTracksStats0.0270.0040.030
DetectRadii0.0030.0000.003
DiAutoCor1.3170.0151.338
DiRatio0.0110.0010.012
DiRatioPlot0.0360.0160.055
EstimateDiameterRange0.0150.0020.017
FMI0.4260.0070.432
FianlizeOptiParams0.0010.0000.000
FilterTrackedCells0.0020.0000.003
FinRes0.5440.0130.560
ForwardMigration0.9450.0090.954
GenAllCombos0.0030.0000.004
LinearConv20.0190.0010.021
LoadTiff0.0000.0000.001
MSD1.6840.0381.727
MakeHypercube0.0010.0010.001
MigrationStats0.0000.0000.001
NextOdd000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0000.0010.001
OptimizeParams0.0120.0020.014
OptimizeParamsMainLoop0.0050.0070.023
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.3190.0260.356
PlotTracksSeparately0.0080.0010.010
PostProcessTracking0.0000.0000.001
Prep4OptimizeParams0.0950.0030.098
ThreeConditions0.0110.0030.015
TrackCellsDataset0.0090.0010.011
TrajectoryDataset0.0190.0020.022
ValidateTrackingArgs0.0010.0000.001
VeAutoCor1.2010.0091.213
VisualizeCntr0.0010.0010.003
VisualizeImg0.0050.0010.007
VisualizeStackCentroids0.0510.0100.066
WSADataset0.0040.0010.006
aggregateFR0.7330.0060.740
aggregateTrackedCells0.0200.0050.025
bpass0.0630.0020.067
circshift0.0010.0000.001
cntrd0.7740.0120.787
fixDA0.0000.0000.001
fixExpName0.0010.0000.000
fixFM10.0010.0000.000
fixFM20.0000.0000.001
fixFM30.0000.0010.000
fixFM40.0000.0000.001
fixFM5000
fixFM60.0010.0000.001
fixID10.0010.0000.000
fixMSD0.0010.0010.001
fixPER10.0000.0000.001
fixPER20.0000.0010.001
fixPER30.0010.0000.000
getAvailableAggrMetrics1.0330.0091.043
getCellImages0.2740.9221.202
getCellMigSlot0.3690.5740.946
getCellTrackMeta0.0080.0010.009
getCellTrackStats0.0110.0020.013
getCellTracks0.0090.0020.012
getCellsMeta0.0130.0020.016
getCellsStats0.0160.0030.019
getDACtable1.8220.0141.838
getDiRatio0.0170.0020.020
getFMItable0.4400.0040.445
getForMigtable0.5560.0060.563
getImageCentroids0.0180.0060.025
getImageStacks0.0540.0090.064
getMSDtable4.0200.0364.067
getOptimizedParameters0.0090.0020.010
getOptimizedParams0.0110.0040.014
getPerAndSpeed0.2760.0280.315
getPopulationStats0.0090.0020.012
getProcessedImages0.2591.6051.889
getProcessingStatus0.0120.0020.015
getResults0.6660.0160.687
getTracks0.0110.0020.012
getVACtable1.0910.0081.099
initializeTrackParams000
innerBondRaster0.0020.0000.002
internalPermutation0.0010.0000.002
matfix0.0010.0010.002
nontrivialBondTracking0.0010.0010.001
pkfnd0.7160.0090.726
plot3DAllTracks0.0000.0000.001
plot3DTracks000
plotAllTracks0.0180.0030.022
plotSampleTracks0.0140.0030.018
preProcCellMig0.0060.0010.007
rmPreProcessing0.0770.0020.080
runTrackingPermutation0.0010.0000.001
setAnalyticParams0.0090.0020.010
setCellMigSlot0.0150.0020.016
setCellTracks0.0090.0020.011
setCellsMeta0.0090.0020.010
setExpName0.0180.0010.020
setOptimizedParams0.0110.0010.012
setProcessedImages0.0110.0010.013
setProcessingStatus0.0220.0060.028
setTrackedCellsMeta0.0100.0020.011
setTrackedCentroids0.0120.0020.014
setTrackedPositions0.0120.0030.014
setTrackingStats0.0120.0020.013
sinkAway0.0000.0000.001
subNetworkTracking0.0010.0010.001
track0.0100.0010.010
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0000.0000.001
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0560.0080.065
visualizeTrcks0.0300.0020.033
warnMessage0.0010.0000.000
wsaPreProcessing0.0590.0020.061