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This page was generated on 2025-10-04 12:04 -0400 (Sat, 04 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 309/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.17.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 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 12.7.1 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 2025-10-03 20:22:54 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 20:25:29 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 155.7 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_1.17.0.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 -- Fri Oct  3 20:25:17 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 
  3.745   0.382   4.147 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.001
CellMig-class0.0270.0040.032
CellMigPCA2.1320.0822.225
CellMigPCAclust0.0060.0020.008
CellMigPCAclustALL0.7880.0090.800
CellTracker0.0170.0030.020
CellTrackerMainLoop0.0040.0090.024
CentroidArray0.0150.0030.017
CentroidValidation0.5300.0200.554
ComputeTracksStats0.0200.0030.024
DetectRadii0.0030.0000.004
DiAutoCor1.5760.0191.604
DiRatio0.0180.0020.019
DiRatioPlot0.0360.0160.056
EstimateDiameterRange0.0170.0020.020
FMI0.5600.0060.568
FianlizeOptiParams0.0000.0010.001
FilterTrackedCells0.0030.0010.004
FinRes0.7660.0150.786
ForwardMigration1.0840.0071.096
GenAllCombos0.0030.0010.003
LinearConv20.0190.0010.021
LoadTiff0.0010.0000.001
MSD1.7660.0191.794
MakeHypercube0.0010.0010.001
MigrationStats0.0010.0010.002
NextOdd0.0000.0000.001
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0130.0030.016
OptimizeParamsMainLoop0.0050.0080.023
Parallel4OptimizeParams000
ParallelTrackLoop0.0000.0010.001
PerAndSpeed0.3150.0280.354
PlotTracksSeparately0.0070.0020.008
PostProcessTracking000
Prep4OptimizeParams0.0960.0040.100
ThreeConditions0.0090.0040.013
TrackCellsDataset0.0090.0010.011
TrajectoryDataset0.0300.0030.034
ValidateTrackingArgs0.0000.0000.001
VeAutoCor1.2950.0241.325
VisualizeCntr0.0020.0010.003
VisualizeImg0.0040.0010.006
VisualizeStackCentroids0.0510.0080.060
WSADataset0.0050.0020.006
aggregateFR0.7470.0070.756
aggregateTrackedCells0.0150.0050.020
bpass0.0820.0030.084
circshift0.0010.0010.001
cntrd0.8300.0140.846
fixDA0.0010.0010.001
fixExpName0.0010.0000.001
fixFM10.0010.0000.000
fixFM2000
fixFM30.0000.0000.001
fixFM40.0000.0010.000
fixFM50.0000.0000.001
fixFM60.0010.0000.001
fixID10.0010.0000.001
fixMSD0.0010.0000.001
fixPER10.0010.0000.000
fixPER20.0000.0010.000
fixPER30.0000.0010.000
getAvailableAggrMetrics1.1450.0081.158
getCellImages0.2850.9161.209
getCellMigSlot0.3750.5610.940
getCellTrackMeta0.0130.0030.015
getCellTrackStats0.0140.0030.017
getCellTracks0.0120.0030.015
getCellsMeta0.0130.0030.016
getCellsStats0.0130.0030.017
getDACtable2.2270.0172.252
getDiRatio0.0170.0010.019
getFMItable0.5330.0040.537
getForMigtable0.6470.0040.653
getImageCentroids0.0210.0030.024
getImageStacks0.0560.0080.064
getMSDtable4.3640.0434.433
getOptimizedParameters0.0110.0020.013
getOptimizedParams0.0130.0030.014
getPerAndSpeed0.2970.0290.336
getPopulationStats0.0120.0020.014
getProcessedImages0.2601.1191.397
getProcessingStatus0.0090.0020.011
getResults0.6820.0160.703
getTracks0.0120.0020.015
getVACtable1.0650.0081.075
initializeTrackParams0.0000.0010.001
innerBondRaster0.0010.0000.002
internalPermutation0.0010.0000.001
matfix0.0000.0000.001
nontrivialBondTracking0.0010.0010.002
pkfnd0.6540.0100.666
plot3DAllTracks0.0000.0000.001
plot3DTracks000
plotAllTracks0.0160.0040.020
plotSampleTracks0.0100.0030.014
preProcCellMig0.0040.0010.006
rmPreProcessing0.1070.0030.110
runTrackingPermutation0.0020.0010.002
setAnalyticParams0.0110.0020.012
setCellMigSlot0.0210.0020.023
setCellTracks0.0120.0020.013
setCellsMeta0.0110.0020.014
setExpName0.0210.0020.028
setOptimizedParams0.0120.0030.017
setProcessedImages0.0110.0020.012
setProcessingStatus0.0090.0010.010
setTrackedCellsMeta0.0120.0010.013
setTrackedCentroids0.0120.0020.014
setTrackedPositions0.0110.0020.014
setTrackingStats0.0120.0030.014
sinkAway0.0010.0010.001
subNetworkTracking0.0230.0030.026
track0.0110.0000.011
trackHypercubeBuild0.0010.0000.002
trackSlideProcessing0.0010.0000.000
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0520.0070.059
visualizeTrcks0.0260.0010.028
warnMessage000
wsaPreProcessing0.0510.0020.053