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This page was generated on 2025-08-14 11:43 -0400 (Thu, 14 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4566
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-11 13:40 -0400 (Mon, 11 Aug 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 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: 2025-08-12 01:05:07 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 01:09:58 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 291.2 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 10.512  0.079  10.807
getDACtable  5.899  0.032   6.027
* 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 Aug 12 01:09:38 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 
  6.355   0.560   7.092 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0030.0020.005
CellMig-class0.0410.0070.048
CellMigPCA3.6600.0553.747
CellMigPCAclust0.0110.0050.016
CellMigPCAclustALL2.0080.1202.148
CellTracker0.0230.0080.032
CellTrackerMainLoop0.0070.0090.026
CentroidArray0.0250.0070.032
CentroidValidation1.4540.0431.525
ComputeTracksStats0.0440.0080.051
DetectRadii0.0060.0000.006
DiAutoCor4.1220.0454.195
DiRatio0.0330.0050.038
DiRatioPlot0.0610.0260.089
EstimateDiameterRange0.0300.0020.032
FMI1.4290.0141.472
FianlizeOptiParams0.0010.0010.001
FilterTrackedCells0.0060.0010.007
FinRes1.9080.0261.946
ForwardMigration2.8900.0232.934
GenAllCombos0.0060.0010.008
LinearConv20.0530.0030.057
LoadTiff0.0010.0000.002
MSD4.3810.0424.461
MakeHypercube0.0030.0020.005
MigrationStats0.0010.0020.004
NextOdd0.0010.0010.001
NonParallel4OptimizeParams0.0020.0000.003
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0200.0070.027
OptimizeParamsMainLoop0.0050.0100.017
Parallel4OptimizeParams0.0010.0010.002
ParallelTrackLoop0.0010.0000.002
PerAndSpeed0.6510.0420.725
PlotTracksSeparately0.0120.0050.017
PostProcessTracking0.0010.0010.001
Prep4OptimizeParams0.2500.0140.264
ThreeConditions0.0180.0080.026
TrackCellsDataset0.0190.0070.025
TrajectoryDataset0.0310.0060.038
ValidateTrackingArgs0.0010.0010.001
VeAutoCor3.2930.0463.368
VisualizeCntr0.0040.0010.005
VisualizeImg0.0100.0020.012
VisualizeStackCentroids0.0880.0180.106
WSADataset0.0090.0050.015
aggregateFR1.9380.0151.967
aggregateTrackedCells0.0310.0140.046
bpass0.1540.0040.159
circshift0.0010.0000.002
cntrd2.3200.0392.369
fixDA0.0000.0000.001
fixExpName0.0010.0010.001
fixFM10.0000.0010.000
fixFM20.0010.0000.001
fixFM30.0000.0000.001
fixFM40.0010.0000.001
fixFM50.0000.0010.001
fixFM60.0000.0010.001
fixID10.0010.0010.002
fixMSD0.0010.0000.001
fixPER10.0000.0000.001
fixPER20.0010.0010.001
fixPER30.0010.0010.002
getAvailableAggrMetrics2.8480.0182.881
getCellImages0.8652.6053.543
getCellMigSlot0.8681.6672.571
getCellTrackMeta0.0190.0060.026
getCellTrackStats0.0270.0070.034
getCellTracks0.0190.0090.029
getCellsMeta0.0190.0050.024
getCellsStats0.0240.0070.030
getDACtable5.8990.0326.027
getDiRatio0.0400.0070.048
getFMItable1.4010.0121.431
getForMigtable1.6690.0121.684
getImageCentroids0.0350.0130.049
getImageStacks0.0870.0180.107
getMSDtable10.512 0.07910.807
getOptimizedParameters0.0190.0060.026
getOptimizedParams0.0220.0080.030
getPerAndSpeed0.6470.0420.702
getPopulationStats0.0220.0070.029
getProcessedImages0.8662.7603.768
getProcessingStatus0.0200.0070.027
getResults1.8580.0261.901
getTracks0.0210.0060.028
getVACtable3.1810.0233.237
initializeTrackParams0.0010.0010.001
innerBondRaster0.0020.0010.003
internalPermutation0.0020.0000.003
matfix0.0020.0010.003
nontrivialBondTracking0.0020.0000.002
pkfnd2.2610.0212.302
plot3DAllTracks0.0010.0010.001
plot3DTracks0.0000.0010.001
plotAllTracks0.0310.0080.039
plotSampleTracks0.0220.0080.031
preProcCellMig0.0090.0050.014
rmPreProcessing0.2450.0100.258
runTrackingPermutation0.0030.0010.003
setAnalyticParams0.0190.0050.025
setCellMigSlot0.0320.0060.038
setCellTracks0.0200.0080.028
setCellsMeta0.0190.0070.026
setExpName0.0320.0060.038
setOptimizedParams0.0190.0070.026
setProcessedImages0.0190.0060.025
setProcessingStatus0.0200.0080.028
setTrackedCellsMeta0.0190.0070.026
setTrackedCentroids0.0200.0080.028
setTrackedPositions0.0190.0050.025
setTrackingStats0.0200.0060.026
sinkAway0.0010.0010.002
subNetworkTracking0.0020.0000.002
track0.0190.0020.021
trackHypercubeBuild0.0010.0010.002
trackSlideProcessing0.0020.0000.002
trackSlideWrapUp0.0010.0000.002
trivialBondRaster0.0030.0010.004
trivialBondTracking0.0010.0010.002
visualizeCellTracks0.1020.0230.126
visualizeTrcks0.0450.0030.048
warnMessage0.0010.0000.001
wsaPreProcessing0.1450.0060.152