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This page was generated on 2025-10-14 12:03 -0400 (Tue, 14 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" 4610
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: 2025-10-13 13:45 -0400 (Mon, 13 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cellmigRation_1.17.0.tar.gz
StartedAt: 2025-10-13 22:09:31 -0400 (Mon, 13 Oct 2025)
EndedAt: 2025-10-13 22:15:23 -0400 (Mon, 13 Oct 2025)
EllapsedTime: 351.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings cellmigRation_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 6.428  0.011   6.641
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.22-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 -- Mon Oct 13 22:12:35 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 
  4.257   0.365   5.335 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.005
CellMig-class0.0400.0030.043
CellMigPCA3.1540.0733.328
CellMigPCAclust0.0090.0020.012
CellMigPCAclustALL1.1180.0831.206
CellTracker0.0220.0060.030
CellTrackerMainLoop0.0020.0090.015
CentroidArray0.0230.0050.041
CentroidValidation0.7050.0170.756
ComputeTracksStats0.0380.0010.038
DetectRadii0.0040.0000.004
DiAutoCor1.7470.0481.911
DiRatio0.0200.0010.043
DiRatioPlot0.0330.0070.041
EstimateDiameterRange0.0170.0000.017
FMI0.6030.0000.880
FianlizeOptiParams000
FilterTrackedCells0.0030.0000.007
FinRes0.7830.0051.017
ForwardMigration1.1720.0291.464
GenAllCombos0.0040.0000.003
LinearConv20.0250.0000.025
LoadTiff0.0010.0000.001
MSD2.3140.0062.477
MakeHypercube0.0010.0000.001
MigrationStats0.0000.0010.001
NextOdd0.0010.0000.000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0190.0030.022
OptimizeParamsMainLoop0.0020.0060.014
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.4800.0070.490
PlotTracksSeparately0.0130.0010.013
PostProcessTracking0.0010.0000.001
Prep4OptimizeParams0.1550.0020.157
ThreeConditions0.0150.0060.020
TrackCellsDataset0.0240.0010.025
TrajectoryDataset0.0300.0040.035
ValidateTrackingArgs0.0000.0010.001
VeAutoCor1.8080.0461.858
VisualizeCntr0.0020.0010.003
VisualizeImg0.0070.0000.007
VisualizeStackCentroids0.0830.0020.085
WSADataset0.0080.0010.009
aggregateFR1.0530.0011.054
aggregateTrackedCells0.0300.0010.030
bpass0.0910.0010.092
circshift0.0000.0000.001
cntrd1.1970.0051.204
fixDA0.0010.0000.000
fixExpName0.0010.0000.001
fixFM1000
fixFM2000
fixFM30.0000.0010.001
fixFM40.0000.0010.000
fixFM50.0010.0000.000
fixFM60.0010.0000.000
fixID10.0010.0000.000
fixMSD0.0010.0000.000
fixPER1000
fixPER2000
fixPER30.0000.0000.001
getAvailableAggrMetrics1.4570.0341.567
getCellImages0.2450.1810.426
getCellMigSlot0.3700.1070.477
getCellTrackMeta0.0250.0020.027
getCellTrackStats0.0260.0060.031
getCellTracks0.0210.0050.026
getCellsMeta0.0220.0040.026
getCellsStats0.0260.0030.029
getDACtable2.9200.0083.184
getDiRatio0.0210.0010.022
getFMItable0.7480.0020.776
getForMigtable0.7380.0010.739
getImageCentroids0.0270.0050.032
getImageStacks0.0860.0060.092
getMSDtable6.4280.0116.641
getOptimizedParameters0.0240.0000.025
getOptimizedParams0.0220.0040.027
getPerAndSpeed0.4200.0060.497
getPopulationStats0.0200.0040.028
getProcessedImages0.1710.1200.339
getProcessingStatus0.0180.0020.019
getResults0.8370.0041.121
getTracks0.0230.0020.050
getVACtable1.5550.0011.580
initializeTrackParams0.0000.0000.001
innerBondRaster0.0020.0000.002
internalPermutation0.0010.0000.002
matfix0.0010.0000.001
nontrivialBondTracking0.0020.0000.001
pkfnd0.8980.0010.908
plot3DAllTracks0.1140.0210.218
plot3DTracks0.0090.0000.009
plotAllTracks0.0210.0000.022
plotSampleTracks0.0180.0000.018
preProcCellMig0.0090.0000.009
rmPreProcessing0.1090.0000.108
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0190.0000.020
setCellMigSlot0.0260.0010.028
setCellTracks0.0170.0030.020
setCellsMeta0.0140.0060.020
setExpName0.0260.0010.027
setOptimizedParams0.0590.0020.062
setProcessedImages0.0180.0010.018
setProcessingStatus0.0190.0000.019
setTrackedCellsMeta0.0170.0030.020
setTrackedCentroids0.0190.0000.020
setTrackedPositions0.0170.0030.020
setTrackingStats0.0190.0010.019
sinkAway0.0010.0000.001
subNetworkTracking0.0020.0000.002
track0.0120.0000.011
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.000
trackSlideWrapUp000
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0680.0040.073
visualizeTrcks0.0280.0010.028
warnMessage000
wsaPreProcessing0.0600.0010.062