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This page was generated on 2025-10-13 12:07 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4864
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4652
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4597
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 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 309/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.17.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-10-12 13:45 -0400 (Sun, 12 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 12.7.1 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 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: 2025-10-10 07:00:32 -0000 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 07:03:10 -0000 (Fri, 10 Oct 2025)
EllapsedTime: 158.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 5.68  0.004   5.705
* 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 10 07:03:03 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 
  3.943   0.187   4.130 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.001
CellMig-class0.0250.0000.026
CellMigPCA2.5540.0602.622
CellMigPCAclust0.0070.0000.007
CellMigPCAclustALL0.9910.0681.062
CellTracker0.0090.0080.016
CellTrackerMainLoop0.0060.0020.007
CentroidArray0.0180.0000.019
CentroidValidation0.7060.0240.731
ComputeTracksStats0.0190.0080.027
DetectRadii0.0000.0030.003
DiAutoCor2.0950.0352.137
DiRatio0.0210.0000.021
DiRatioPlot0.0310.0120.049
EstimateDiameterRange0.0180.0000.019
FMI0.7650.0190.787
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0010.0020.004
FinRes1.0100.0001.014
ForwardMigration1.5010.0161.521
GenAllCombos0.0050.0000.004
LinearConv20.0310.0000.031
LoadTiff0.0010.0000.001
MSD2.2840.0122.306
MakeHypercube0.0010.0000.002
MigrationStats0.0010.0000.001
NextOdd0.0010.0000.000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop000
OptimizeParams0.0130.0000.013
OptimizeParamsMainLoop0.0030.0030.006
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop0.0000.0000.001
PerAndSpeed0.4040.0040.413
PlotTracksSeparately0.0090.0000.009
PostProcessTracking0.0000.0000.001
Prep4OptimizeParams0.1230.0000.123
ThreeConditions0.0090.0000.010
TrackCellsDataset0.0130.0000.013
TrajectoryDataset0.0180.0000.017
ValidateTrackingArgs0.0010.0000.000
VeAutoCor1.7450.0481.798
VisualizeCntr0.0020.0000.003
VisualizeImg0.0060.0000.006
VisualizeStackCentroids0.0530.0000.053
WSADataset0.0060.0000.005
aggregateFR1.0280.0001.031
aggregateTrackedCells0.0190.0000.019
bpass0.0830.0040.088
circshift000
cntrd1.1330.0281.164
fixDA0.0010.0000.001
fixExpName0.0010.0000.001
fixFM10.0000.0000.001
fixFM2000
fixFM3000
fixFM40.0010.0000.000
fixFM50.0000.0000.001
fixFM6000
fixID1000
fixMSD0.0010.0000.000
fixPER10.0010.0000.000
fixPER20.0000.0000.001
fixPER30.0000.0000.001
getAvailableAggrMetrics1.5060.0001.512
getCellImages0.1870.1550.344
getCellMigSlot0.1880.1470.336
getCellTrackMeta0.0100.0040.013
getCellTrackStats0.0160.0000.017
getCellTracks0.0060.0080.014
getCellsMeta0.0130.0000.014
getCellsStats0.0110.0040.016
getDACtable3.0810.0243.115
getDiRatio0.0230.0000.023
getFMItable0.7670.0040.773
getForMigtable0.9040.0000.907
getImageCentroids0.0130.0070.020
getImageStacks0.0530.0000.053
getMSDtable5.6800.0045.705
getOptimizedParameters0.0080.0040.012
getOptimizedParams0.0110.0040.014
getPerAndSpeed0.4110.0040.417
getPopulationStats0.0090.0040.014
getProcessedImages0.1440.1760.320
getProcessingStatus0.0120.0000.012
getResults1.0360.0311.072
getTracks0.0100.0030.014
getVACtable1.7170.0001.721
initializeTrackParams000
innerBondRaster0.0020.0000.002
internalPermutation0.0020.0000.002
matfix0.0020.0000.002
nontrivialBondTracking0.0020.0000.001
pkfnd1.1400.0001.144
plot3DAllTracks0.0940.0200.114
plot3DTracks0.0080.0000.007
plotAllTracks0.0210.0000.021
plotSampleTracks0.0120.0040.016
preProcCellMig0.0070.0000.006
rmPreProcessing0.1140.0080.122
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0120.0010.012
setCellMigSlot0.0150.0030.018
setCellTracks0.0130.0000.013
setCellsMeta0.0130.0000.013
setExpName0.0180.0000.018
setOptimizedParams0.0460.0000.047
setProcessedImages0.0120.0000.013
setProcessingStatus0.0120.0000.013
setTrackedCellsMeta0.0080.0040.012
setTrackedCentroids0.0120.0000.013
setTrackedPositions0.0120.0000.013
setTrackingStats0.0120.0000.013
sinkAway0.0010.0000.001
subNetworkTracking0.0010.0000.002
track0.0110.0000.012
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp000
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0000.0000.001
visualizeCellTracks0.0550.0000.055
visualizeTrcks0.0320.0000.032
warnMessage000
wsaPreProcessing0.0770.0000.077