Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:36:22 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 303/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.12.0  (landing page)
Waldir Leoncio
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_19
git_last_commit: 38ab506
git_last_commit_date: 2024-04-30 11:33:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for cellmigRation on nebbiolo1


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: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cellmigRation_1.12.0.tar.gz
StartedAt: 2024-05-03 21:34:20 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:38:04 -0400 (Fri, 03 May 2024)
EllapsedTime: 224.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cellmigRation_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cellmigRation.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.12.0’
* 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
* 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-3.19-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.


Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘cellmigRation’ ...
** 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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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 May  3 21:36:04 2024 
*********************************************** 
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 
  2.706   0.210   2.905 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0240.0040.029
CellMigPCA1.1120.0641.177
CellMigPCAclust0.0070.0000.007
CellMigPCAclustALL0.5870.0040.591
CellTracker0.0180.0000.018
CellTrackerMainLoop0.0070.0000.023
CentroidArray0.0190.0000.019
CentroidValidation0.4300.0040.435
ComputeTracksStats0.0220.0040.026
DetectRadii0.0030.0000.002
DiAutoCor1.2380.0361.275
DiRatio0.0180.0000.018
DiRatioPlot0.0350.0000.034
EstimateDiameterRange0.0120.0040.016
FMI0.4310.0040.435
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0030.0000.003
FinRes0.5680.0040.573
ForwardMigration0.8620.0080.870
GenAllCombos0.0030.0000.003
LinearConv20.0180.0000.018
LoadTiff0.0010.0000.001
MSD1.4240.0121.437
MakeHypercube0.0010.0010.002
MigrationStats0.0000.0010.001
NextOdd000
NonParallel4OptimizeParams0.0000.0010.001
NonParallelTrackLoop0.0000.0010.000
OptimizeParams0.0160.0020.017
OptimizeParamsMainLoop0.0070.0000.023
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.2830.0280.312
PlotTracksSeparately0.010.000.01
PostProcessTracking000
Prep4OptimizeParams0.1200.0040.123
ThreeConditions0.0020.0120.014
TrackCellsDataset0.0170.0000.017
TrajectoryDataset0.0220.0000.022
ValidateTrackingArgs0.0000.0000.001
VeAutoCor1.0270.0471.073
VisualizeCntr0.0010.0020.003
VisualizeImg0.0040.0020.006
VisualizeStackCentroids0.0630.0040.067
WSADataset0.0070.0000.007
aggregateFR0.5830.0280.612
aggregateTrackedCells0.0200.0040.024
bpass0.0600.0000.059
circshift0.0000.0000.001
cntrd0.6900.0160.706
fixDA0.0000.0000.001
fixExpName0.0000.0000.001
fixFM1000
fixFM20.0000.0000.001
fixFM3000
fixFM40.0010.0000.000
fixFM5000
fixFM6000
fixID10.0000.0000.001
fixMSD0.0000.0000.001
fixPER10.0000.0000.001
fixPER20.0000.0010.000
fixPER30.0000.0010.000
getAvailableAggrMetrics0.8610.0330.894
getCellImages0.2840.9641.248
getCellMigSlot0.3030.6080.910
getCellTrackMeta0.0140.0040.018
getCellTrackStats0.0100.0110.021
getCellTracks0.0150.0040.018
getCellsMeta0.0140.0040.018
getCellsStats0.0370.0080.045
getDACtable2.0770.0442.122
getDiRatio0.0170.0000.018
getFMItable0.3940.0040.397
getForMigtable0.4850.0200.505
getImageCentroids0.0230.0000.023
getImageStacks0.0580.0080.066
getMSDtable3.2020.0443.246
getOptimizedParameters0.0120.0030.017
getOptimizedParams0.0160.0020.018
getPerAndSpeed0.2670.0020.268
getPopulationStats0.0120.0050.019
getProcessedImages0.3050.9541.259
getProcessingStatus0.0180.0000.018
getResults0.5860.0040.590
getTracks0.0180.0000.018
getVACtable0.9740.0601.034
initializeTrackParams000
innerBondRaster0.0010.0000.001
internalPermutation0.0010.0000.001
matfix0.0010.0000.001
nontrivialBondTracking0.0000.0010.001
pkfnd0.6460.0140.659
plot3DAllTracks0.0750.0250.101
plot3DTracks0.0010.0070.008
plotAllTracks0.0180.0000.018
plotSampleTracks0.0110.0040.015
preProcCellMig0.0040.0040.008
rmPreProcessing0.0780.0000.078
runTrackingPermutation0.0020.0000.001
setAnalyticParams0.0160.0000.017
setCellMigSlot0.0230.0000.023
setCellTracks0.0180.0000.017
setCellsMeta0.0100.0080.017
setExpName0.0230.0000.022
setOptimizedParams0.0000.0170.017
setProcessedImages0.0160.0010.017
setProcessingStatus0.0130.0040.017
setTrackedCellsMeta0.0170.0000.017
setTrackedCentroids0.0140.0040.017
setTrackedPositions0.0170.0000.017
setTrackingStats0.0170.0000.017
sinkAway0.0010.0000.001
subNetworkTracking0.0020.0000.002
track0.0160.0040.020
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0020.0000.002
trivialBondTracking000
visualizeCellTracks0.0680.0000.068
visualizeTrcks0.0250.0000.025
warnMessage0.0010.0000.001
wsaPreProcessing0.0470.0000.047