Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-18 12:07 -0400 (Sat, 18 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: 2025-10-17 13:45 -0400 (Fri, 17 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: cellmigRation
Version: 1.17.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cellmigRation_1.17.0.tar.gz
StartedAt: 2025-10-17 07:06:35 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 07:09:14 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 159.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cellmigRation_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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 5.765  0.004   5.789
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.


Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 17 07:09:07 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 
  4.163   0.222   4.385 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0260.0000.025
CellMigPCA2.5740.0642.645
CellMigPCAclust0.0070.0000.007
CellMigPCAclustALL1.0140.0521.070
CellTracker0.0160.0000.017
CellTrackerMainLoop0.0060.0030.007
CentroidArray0.0170.0000.018
CentroidValidation0.7290.0230.756
ComputeTracksStats0.0240.0040.028
DetectRadii0.0040.0000.004
DiAutoCor2.1210.0282.155
DiRatio0.0240.0000.024
DiRatioPlot0.0360.0080.050
EstimateDiameterRange0.0170.0040.021
FMI0.7430.0240.770
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0030.0000.004
FinRes0.9980.0001.002
ForwardMigration1.5400.0121.557
GenAllCombos0.0040.0000.004
LinearConv20.0280.0000.028
LoadTiff0.0000.0000.001
MSD2.2930.0122.316
MakeHypercube0.0020.0000.001
MigrationStats0.0010.0000.001
NextOdd0.0000.0000.001
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop000
OptimizeParams0.0130.0000.013
OptimizeParamsMainLoop0.0030.0030.006
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.000
PerAndSpeed0.4050.0080.419
PlotTracksSeparately0.0090.0000.010
PostProcessTracking000
Prep4OptimizeParams0.1170.0240.142
ThreeConditions0.010.000.01
TrackCellsDataset0.0120.0000.013
TrajectoryDataset0.0180.0000.018
ValidateTrackingArgs0.0010.0000.000
VeAutoCor1.7240.0201.749
VisualizeCntr0.0030.0000.002
VisualizeImg0.0070.0000.006
VisualizeStackCentroids0.0530.0000.053
WSADataset0.0020.0040.005
aggregateFR1.0210.0001.025
aggregateTrackedCells0.0160.0040.020
bpass0.0840.0040.088
circshift0.0000.0000.001
cntrd1.1380.0301.172
fixDA000
fixExpName000
fixFM1000
fixFM20.0000.0000.001
fixFM30.0010.0000.000
fixFM4000
fixFM5000
fixFM6000
fixID10.0000.0000.001
fixMSD0.0000.0000.001
fixPER10.0010.0000.001
fixPER2000
fixPER3000
getAvailableAggrMetrics1.4990.0041.507
getCellImages0.1660.1790.346
getCellMigSlot0.2420.0920.335
getCellTrackMeta0.0140.0000.014
getCellTrackStats0.0180.0000.017
getCellTracks0.0130.0000.013
getCellsMeta0.0130.0000.013
getCellsStats0.0130.0030.016
getDACtable3.1560.0163.183
getDiRatio0.0270.0000.027
getFMItable0.7710.0000.774
getForMigtable0.9180.0040.925
getImageCentroids0.0210.0000.021
getImageStacks0.0530.0000.054
getMSDtable5.7650.0045.789
getOptimizedParameters0.0130.0000.012
getOptimizedParams0.0110.0040.014
getPerAndSpeed0.4110.0080.420
getPopulationStats0.0100.0040.014
getProcessedImages0.1840.1390.325
getProcessingStatus0.0080.0040.012
getResults1.0210.0241.048
getTracks0.0140.0000.014
getVACtable1.7150.0001.721
initializeTrackParams0.0010.0000.001
innerBondRaster0.0020.0000.002
internalPermutation0.0010.0000.001
matfix0.0010.0000.001
nontrivialBondTracking0.0010.0000.001
pkfnd1.1480.0041.156
plot3DAllTracks0.0910.0200.113
plot3DTracks0.0070.0000.007
plotAllTracks0.0210.0000.021
plotSampleTracks0.0160.0000.016
preProcCellMig0.0030.0040.006
rmPreProcessing0.1200.0000.121
runTrackingPermutation0.0010.0000.002
setAnalyticParams0.0130.0000.012
setCellMigSlot0.0190.0000.019
setCellTracks0.0140.0000.014
setCellsMeta0.0130.0000.013
setExpName0.0180.0000.018
setOptimizedParams0.0450.0040.049
setProcessedImages0.0130.0000.013
setProcessingStatus0.0130.0000.012
setTrackedCellsMeta0.0130.0000.013
setTrackedCentroids0.0130.0000.013
setTrackedPositions0.0090.0040.014
setTrackingStats0.0130.0000.013
sinkAway0.0010.0000.001
subNetworkTracking0.0010.0000.002
track0.0120.0000.013
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0000.0000.001
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0560.0000.057
visualizeTrcks0.0320.0000.032
warnMessage000
wsaPreProcessing0.0730.0040.077