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This page was generated on 2025-09-06 12:03 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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 305/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.17.0  (landing page)
Waldir Leoncio
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 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: 2025-09-05 21:48:48 -0400 (Fri, 05 Sep 2025)
EndedAt: 2025-09-05 21:54:06 -0400 (Fri, 05 Sep 2025)
EllapsedTime: 318.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 (2025-06-13)
* 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 5.19  0.004   5.223
* 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 (2025-06-13) -- "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 -- Fri Sep  5 21:51:28 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 
  3.710   0.235   4.089 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0290.0030.048
CellMigPCA1.6030.0701.877
CellMigPCAclust0.0120.0000.011
CellMigPCAclustALL0.8990.0510.993
CellTracker0.0200.0030.023
CellTrackerMainLoop0.0010.0070.017
CentroidArray0.0200.0040.024
CentroidValidation0.5560.0080.575
ComputeTracksStats0.0290.0020.061
DetectRadii0.0030.0000.006
DiAutoCor2.3560.0192.486
DiRatio0.0280.0000.027
DiRatioPlot0.0430.0070.050
EstimateDiameterRange0.0220.0000.022
FMI0.7920.0040.837
FianlizeOptiParams0.0010.0000.000
FilterTrackedCells0.0030.0000.003
FinRes0.7800.0450.827
ForwardMigration1.4040.0031.421
GenAllCombos0.0030.0010.004
LinearConv20.0260.0030.029
LoadTiff0.0010.0000.001
MSD2.2800.0482.619
MakeHypercube0.0010.0000.001
MigrationStats0.0010.0000.001
NextOdd000
NonParallel4OptimizeParams0.0010.0010.001
NonParallelTrackLoop000
OptimizeParams0.0150.0050.020
OptimizeParamsMainLoop0.0030.0030.009
Parallel4OptimizeParams000
ParallelTrackLoop0.0000.0000.004
PerAndSpeed0.3410.0070.441
PlotTracksSeparately0.0110.0000.024
PostProcessTracking000
Prep4OptimizeParams0.1010.0030.108
ThreeConditions0.0130.0050.018
TrackCellsDataset0.0150.0050.021
TrajectoryDataset0.0250.0020.033
ValidateTrackingArgs0.0010.0000.000
VeAutoCor1.2250.0061.250
VisualizeCntr0.0020.0010.003
VisualizeImg0.0060.0000.006
VisualizeStackCentroids0.0680.0020.070
WSADataset0.0080.0000.008
aggregateFR0.8300.0000.936
aggregateTrackedCells0.0310.0020.032
bpass0.0820.0030.085
circshift0.0010.0000.000
cntrd1.1360.0171.157
fixDA0.0010.0000.001
fixExpName0.0010.0000.000
fixFM1000
fixFM2000
fixFM3000
fixFM40.0010.0000.000
fixFM50.0010.0000.001
fixFM60.0000.0010.000
fixID10.0010.0000.001
fixMSD0.0000.0000.001
fixPER10.0000.0000.001
fixPER2000
fixPER30.0000.0000.001
getAvailableAggrMetrics1.6780.0321.787
getCellImages0.2000.1420.343
getCellMigSlot0.3070.0810.390
getCellTrackMeta0.0210.0010.022
getCellTrackStats0.0220.0060.028
getCellTracks0.0210.0030.035
getCellsMeta0.0190.0040.024
getCellsStats0.0180.0080.026
getDACtable2.9100.0302.995
getDiRatio0.0280.0000.027
getFMItable0.7110.0020.713
getForMigtable0.8340.0000.837
getImageCentroids0.0390.0000.040
getImageStacks0.0670.0020.081
getMSDtable5.1900.0045.223
getOptimizedParameters0.0230.0010.024
getOptimizedParams0.0240.0030.027
getPerAndSpeed0.3990.0080.408
getPopulationStats0.0210.0070.028
getProcessedImages0.2310.1590.390
getProcessingStatus0.0200.0050.026
getResults1.0780.0021.081
getTracks0.0250.0000.026
getVACtable1.8720.0011.874
initializeTrackParams0.0010.0000.000
innerBondRaster0.0020.0000.002
internalPermutation0.0010.0000.001
matfix0.0010.0000.001
nontrivialBondTracking0.0010.0000.001
pkfnd1.0870.0061.097
plot3DAllTracks0.0940.0190.148
plot3DTracks0.0090.0010.009
plotAllTracks0.0200.0010.021
plotSampleTracks0.0170.0000.017
preProcCellMig0.0080.0000.009
rmPreProcessing0.0960.0020.098
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0170.0020.019
setCellMigSlot0.0260.0010.027
setCellTracks0.0150.0040.019
setCellsMeta0.0140.0050.019
setExpName0.0240.0030.027
setOptimizedParams0.0170.0020.019
setProcessedImages0.0170.0020.019
setProcessingStatus0.0140.0050.019
setTrackedCellsMeta0.0140.0060.020
setTrackedCentroids0.0150.0050.021
setTrackedPositions0.0330.0010.034
setTrackingStats0.0180.0010.020
sinkAway0.0010.0000.000
subNetworkTracking0.0020.0000.002
track0.0110.0000.011
trackHypercubeBuild0.0000.0000.001
trackSlideProcessing000
trackSlideWrapUp000
trivialBondRaster0.0020.0000.001
trivialBondTracking0.0010.0000.000
visualizeCellTracks0.0690.0030.071
visualizeTrcks0.0260.0010.027
warnMessage0.0000.0000.001
wsaPreProcessing0.0570.0020.059