Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 306/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.16.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_21
git_last_commit: 526a2a8
git_last_commit_date: 2025-04-15 12:26:19 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2025-10-14 01:12:38 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 01:17:38 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 299.9 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘1.16.0’
* 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 10.565  0.053  10.644
getDACtable  6.069  0.042   6.326
* 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-3.21-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 ‘1.16.0’
** 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 RC (2025-06-05 r88288) -- "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 14 01:17:19 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 
  6.610   0.570   7.168 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0020.004
CellMig-class0.0420.0070.050
CellMigPCA4.3110.1744.698
CellMigPCAclust0.0110.0060.019
CellMigPCAclustALL2.0050.0232.195
CellTracker0.0240.0100.037
CellTrackerMainLoop0.0070.0110.019
CentroidArray0.0250.0090.035
CentroidValidation1.4720.0411.550
ComputeTracksStats0.0440.0100.056
DetectRadii0.0050.0010.008
DiAutoCor4.1600.0464.410
DiRatio0.0340.0080.043
DiRatioPlot0.0610.0300.097
EstimateDiameterRange0.0310.0030.035
FMI1.4520.0151.529
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0060.0010.007
FinRes1.9700.0282.087
ForwardMigration2.9460.0213.105
GenAllCombos0.0060.0010.009
LinearConv20.0510.0030.056
LoadTiff0.0010.0010.003
MSD4.4030.0414.621
MakeHypercube0.0030.0010.006
MigrationStats0.0020.0020.004
NextOdd0.0010.0010.001
NonParallel4OptimizeParams0.0020.0010.002
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0190.0080.029
OptimizeParamsMainLoop0.0060.0090.018
Parallel4OptimizeParams0.0010.0010.001
ParallelTrackLoop0.0010.0010.001
PerAndSpeed0.6610.0450.741
PlotTracksSeparately0.0140.0070.023
PostProcessTracking0.0000.0010.001
Prep4OptimizeParams0.2190.0090.237
ThreeConditions0.0180.0100.028
TrackCellsDataset0.0180.0070.028
TrajectoryDataset0.0450.0090.057
ValidateTrackingArgs0.0000.0010.001
VeAutoCor3.3540.0503.528
VisualizeCntr0.0030.0010.004
VisualizeImg0.0090.0010.011
VisualizeStackCentroids0.0890.0180.108
WSADataset0.0090.0060.015
aggregateFR1.9800.0192.015
aggregateTrackedCells0.0320.0150.048
bpass0.1710.0050.184
circshift0.0010.0000.001
cntrd2.3510.0322.404
fixDA0.0010.0010.002
fixExpName0.0010.0000.001
fixFM10.0010.0000.001
fixFM2000
fixFM30.0000.0000.001
fixFM40.0010.0000.001
fixFM50.0010.0000.001
fixFM60.0000.0010.001
fixID10.0010.0010.001
fixMSD0.0010.0010.001
fixPER10.0000.0000.001
fixPER20.0010.0000.001
fixPER30.0010.0000.001
getAvailableAggrMetrics2.8000.0192.826
getCellImages0.8222.5063.392
getCellMigSlot0.8111.5912.438
getCellTrackMeta0.0190.0080.027
getCellTrackStats0.0260.0100.039
getCellTracks0.0200.0100.037
getCellsMeta0.0190.0090.033
getCellsStats0.0240.0090.042
getDACtable6.0690.0426.326
getDiRatio0.0370.0080.044
getFMItable1.4100.0181.432
getForMigtable1.6950.0121.710
getImageCentroids0.0340.0100.045
getImageStacks0.0860.0170.104
getMSDtable10.565 0.05310.644
getOptimizedParameters0.0190.0070.026
getOptimizedParams0.0230.0080.031
getPerAndSpeed0.6240.0430.669
getPopulationStats0.0210.0090.030
getProcessedImages0.8072.8963.762
getProcessingStatus0.0190.0080.027
getResults1.8150.0281.848
getTracks0.0220.0070.030
getVACtable3.1280.0173.148
initializeTrackParams0.0000.0010.001
innerBondRaster0.0030.0010.004
internalPermutation0.0020.0010.003
matfix0.0030.0010.004
nontrivialBondTracking0.0020.0010.002
pkfnd2.1960.0222.223
plot3DAllTracks0.0000.0010.001
plot3DTracks0.0010.0000.001
plotAllTracks0.0320.0090.041
plotSampleTracks0.0230.0090.031
preProcCellMig0.0080.0060.014
rmPreProcessing0.2390.0100.250
runTrackingPermutation0.0030.0000.003
setAnalyticParams0.0190.0070.026
setCellMigSlot0.0320.0070.039
setCellTracks0.0190.0070.027
setCellsMeta0.0180.0080.025
setExpName0.0310.0070.038
setOptimizedParams0.0190.0080.028
setProcessedImages0.0190.0070.027
setProcessingStatus0.0190.0080.026
setTrackedCellsMeta0.0190.0080.027
setTrackedCentroids0.0190.0090.027
setTrackedPositions0.0190.0090.029
setTrackingStats0.0200.0080.027
sinkAway0.0010.0010.002
subNetworkTracking0.0020.0010.003
track0.0190.0020.022
trackHypercubeBuild0.0020.0010.002
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0010.0000.002
trivialBondRaster0.0030.0010.003
trivialBondTracking0.0010.0010.002
visualizeCellTracks0.0870.0180.104
visualizeTrcks0.0440.0040.048
warnMessage0.0010.0000.001
wsaPreProcessing0.1400.0080.148