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This page was generated on 2025-10-17 12:06 -0400 (Fri, 17 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 311/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.17.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-10-16 13:45 -0400 (Thu, 16 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cellmigRation on kjohnson3

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: 2025-10-16 18:52:12 -0400 (Thu, 16 Oct 2025)
EndedAt: 2025-10-16 18:53:00 -0400 (Thu, 16 Oct 2025)
EllapsedTime: 47.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* 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-arm64/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: aarch64-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 16 18:52:55 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 
  1.202   0.094   1.294 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0010.0010.001
CellMig-class0.0130.0010.014
CellMigPCA0.6240.0170.642
CellMigPCAclust0.0030.0010.004
CellMigPCAclustALL0.2120.0030.215
CellTracker0.0070.0010.009
CellTrackerMainLoop0.0010.0030.006
CentroidArray0.0070.0000.008
CentroidValidation0.1510.0050.156
ComputeTracksStats0.0090.0010.010
DetectRadii0.0010.0000.001
DiAutoCor0.4220.0050.434
DiRatio0.0060.0000.007
DiRatioPlot0.0120.0050.018
EstimateDiameterRange0.0050.0010.005
FMI0.1530.0020.155
FianlizeOptiParams0.0010.0010.000
FilterTrackedCells0.0010.0000.001
FinRes0.2120.0050.219
ForwardMigration0.2990.0030.302
GenAllCombos0.0010.0000.001
LinearConv20.0060.0000.007
LoadTiff0.0010.0000.001
MSD0.4540.0080.463
MakeHypercube0.0010.0000.000
MigrationStats000
NextOdd000
NonParallel4OptimizeParams0.0010.0010.000
NonParallelTrackLoop000
OptimizeParams0.0060.0000.008
OptimizeParamsMainLoop0.0010.0030.010
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop000
PerAndSpeed0.0870.0080.096
PlotTracksSeparately0.0040.0010.005
PostProcessTracking000
Prep4OptimizeParams0.0290.0020.031
ThreeConditions0.0040.0010.006
TrackCellsDataset0.0060.0010.007
TrajectoryDataset0.0150.0020.017
ValidateTrackingArgs0.0000.0000.001
VeAutoCor0.3640.0120.376
VisualizeCntr0.0010.0000.001
VisualizeImg0.0010.0000.002
VisualizeStackCentroids0.0190.0020.022
WSADataset0.0030.0010.003
aggregateFR0.2030.0030.206
aggregateTrackedCells0.0080.0010.010
bpass0.0300.0020.031
circshift000
cntrd0.2280.0050.234
fixDA0.0010.0000.000
fixExpName0.0000.0000.001
fixFM1000
fixFM2000
fixFM3000
fixFM4000
fixFM5000
fixFM6000
fixID10.0000.0000.001
fixMSD000
fixPER1000
fixPER2000
fixPER3000
getAvailableAggrMetrics0.2950.0030.298
getCellImages0.0790.2520.334
getCellMigSlot0.1220.1790.301
getCellTrackMeta0.0070.0010.008
getCellTrackStats0.0080.0020.009
getCellTracks0.0060.0010.008
getCellsMeta0.0060.0010.007
getCellsStats0.0070.0010.008
getDACtable0.6370.0110.655
getDiRatio0.0070.0010.007
getFMItable0.1550.0030.162
getForMigtable0.1860.0020.189
getImageCentroids0.0090.0020.009
getImageStacks0.0200.0030.023
getMSDtable1.1880.0191.207
getOptimizedParameters0.0070.0010.008
getOptimizedParams0.0070.0010.008
getPerAndSpeed0.0900.0110.101
getPopulationStats0.0070.0010.008
getProcessedImages0.0760.3280.412
getProcessingStatus0.0070.0010.007
getResults0.2000.0070.207
getTracks0.0070.0010.008
getVACtable0.3390.0040.342
initializeTrackParams000
innerBondRaster0.0000.0000.001
internalPermutation000
matfix0.0000.0000.001
nontrivialBondTracking0.0010.0000.000
pkfnd0.2200.0070.227
plot3DAllTracks000
plot3DTracks000
plotAllTracks0.0070.0020.008
plotSampleTracks0.0060.0010.007
preProcCellMig0.0030.0010.004
rmPreProcessing0.0360.0020.037
runTrackingPermutation0.0000.0000.001
setAnalyticParams0.0060.0010.008
setCellMigSlot0.0110.0010.012
setCellTracks0.0070.0010.008
setCellsMeta0.0070.0010.008
setExpName0.0110.0010.011
setOptimizedParams0.0060.0010.007
setProcessedImages0.0060.0010.007
setProcessingStatus0.0070.0010.008
setTrackedCellsMeta0.0060.0010.008
setTrackedCentroids0.0060.0010.007
setTrackedPositions0.0070.0010.007
setTrackingStats0.0060.0010.007
sinkAway000
subNetworkTracking0.0010.0000.001
track0.0130.0070.019
trackHypercubeBuild000
trackSlideProcessing000
trackSlideWrapUp000
trivialBondRaster000
trivialBondTracking0.0010.0000.000
visualizeCellTracks0.0200.0030.024
visualizeTrcks0.0160.0010.016
warnMessage000
wsaPreProcessing0.0180.0010.019