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This page was generated on 2025-08-27 12:06 -0400 (Wed, 27 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4612
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 305/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.17.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-08-26 13:45 -0400 (Tue, 26 Aug 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 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: 2025-08-26 18:31:55 -0400 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 18:32:44 -0400 (Tue, 26 Aug 2025)
EllapsedTime: 48.6 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 (2025-06-14 r88325)
* 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 (2025-06-14 r88325) -- "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 -- Tue Aug 26 18:32:38 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 
  1.126   0.109   1.257 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0000.0010.001
CellMig-class0.0130.0010.015
CellMigPCA0.5690.0080.611
CellMigPCAclust0.0040.0010.004
CellMigPCAclustALL0.2040.0160.220
CellTracker0.0070.0010.008
CellTrackerMainLoop0.0020.0050.007
CentroidArray0.0080.0010.008
CentroidValidation0.1480.0050.154
ComputeTracksStats0.0100.0010.010
DetectRadii0.0010.0000.000
DiAutoCor0.4250.0070.432
DiRatio0.0060.0010.007
DiRatioPlot0.0110.0040.016
EstimateDiameterRange0.0040.0010.005
FMI0.1510.0030.156
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0010.0000.001
FinRes0.2050.0070.214
ForwardMigration0.2990.0050.306
GenAllCombos0.0010.0000.001
LinearConv20.0060.0000.006
LoadTiff000
MSD0.4490.0070.458
MakeHypercube0.0010.0000.001
MigrationStats0.0000.0010.001
NextOdd000
NonParallel4OptimizeParams0.0010.0000.000
NonParallelTrackLoop000
OptimizeParams0.0070.0010.010
OptimizeParamsMainLoop0.0020.0040.014
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop000
PerAndSpeed0.0890.0090.099
PlotTracksSeparately0.0040.0000.004
PostProcessTracking0.0000.0000.001
Prep4OptimizeParams0.0440.0090.053
ThreeConditions0.0050.0010.006
TrackCellsDataset0.0060.0010.007
TrajectoryDataset0.0110.0010.012
ValidateTrackingArgs0.0000.0000.001
VeAutoCor0.3470.0140.368
VisualizeCntr0.0010.0000.001
VisualizeImg0.0020.0010.002
VisualizeStackCentroids0.0200.0030.024
WSADataset0.0040.0000.004
aggregateFR0.2050.0030.210
aggregateTrackedCells0.0080.0020.010
bpass0.0260.0010.027
circshift0.0000.0000.001
cntrd0.2380.0080.249
fixDA0.0000.0000.001
fixExpName000
fixFM10.0000.0010.000
fixFM20.0010.0000.000
fixFM3000
fixFM4000
fixFM50.0000.0000.001
fixFM6000
fixID1000
fixMSD0.0000.0000.001
fixPER1000
fixPER2000
fixPER30.0000.0000.001
getAvailableAggrMetrics0.2990.0040.310
getCellImages0.0790.2460.331
getCellMigSlot0.1190.1580.279
getCellTrackMeta0.0060.0010.007
getCellTrackStats0.0100.0010.011
getCellTracks0.0060.0010.008
getCellsMeta0.0070.0010.008
getCellsStats0.0070.0010.008
getDACtable0.6170.0100.643
getDiRatio0.0070.0010.008
getFMItable0.1450.0020.147
getForMigtable0.1850.0030.189
getImageCentroids0.0080.0010.010
getImageStacks0.0190.0020.027
getMSDtable1.1870.0171.247
getOptimizedParameters0.0070.0010.007
getOptimizedParams0.0070.0010.008
getPerAndSpeed0.0870.0090.097
getPopulationStats0.0070.0010.008
getProcessedImages0.0820.6040.690
getProcessingStatus0.0060.0020.008
getResults0.2130.0080.222
getTracks0.0080.0010.009
getVACtable0.3460.0060.364
initializeTrackParams000
innerBondRaster0.0010.0000.000
internalPermutation0.0000.0000.001
matfix0.0010.0000.000
nontrivialBondTracking000
pkfnd0.2240.0060.242
plot3DAllTracks000
plot3DTracks000
plotAllTracks0.0070.0010.009
plotSampleTracks0.0060.0020.008
preProcCellMig0.0040.0010.004
rmPreProcessing0.0360.0020.038
runTrackingPermutation000
setAnalyticParams0.0060.0010.008
setCellMigSlot0.0110.0010.012
setCellTracks0.0070.0010.007
setCellsMeta0.0060.0010.007
setExpName0.0110.0010.012
setOptimizedParams0.0060.0010.007
setProcessedImages0.0060.0010.008
setProcessingStatus0.0070.0010.008
setTrackedCellsMeta0.0060.0010.007
setTrackedCentroids0.0070.0010.008
setTrackedPositions0.0060.0010.007
setTrackingStats0.0070.0010.008
sinkAway000
subNetworkTracking0.0010.0000.001
track0.0030.0000.003
trackHypercubeBuild000
trackSlideProcessing000
trackSlideWrapUp0.0010.0000.000
trivialBondRaster0.0000.0010.001
trivialBondTracking000
visualizeCellTracks0.0240.0040.030
visualizeTrcks0.0160.0000.016
warnMessage000
wsaPreProcessing0.0170.0010.018