Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:02 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for cellmigRation on lconway


To the developers/maintainers of the cellmigRation package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 280/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.6.0  (landing page)
Waldir Leoncio
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_16
git_last_commit: f639003
git_last_commit_date: 2022-11-01 11:24:36 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellmigRation
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.6.0.tar.gz
StartedAt: 2023-04-10 19:17:13 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 19:19:12 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 118.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/cellmigRation.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.6.0’
* 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 R 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 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 ... OK
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 Apr 10 19:19:02 2023 
*********************************************** 
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 
  2.866   0.281   3.163 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0010.003
CellMig-class0.0220.0020.025
CellMigPCA1.3850.0261.416
CellMigPCAclust0.0060.0010.007
CellMigPCAclustALL0.5620.0410.605
CellTracker0.0180.0040.022
CellTrackerMainLoop0.0050.0060.020
CentroidArray0.0160.0020.019
CentroidValidation0.3660.0130.379
ComputeTracksStats0.0230.0020.026
DetectRadii0.0020.0000.004
DiAutoCor1.1720.0161.195
DiRatio0.0130.0010.014
DiRatioPlot0.0330.0130.049
EstimateDiameterRange0.0130.0020.015
FMI0.3860.0060.393
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0010.0010.002
FinRes0.4800.0110.494
ForwardMigration0.7690.0090.781
GenAllCombos0.0030.0000.003
LinearConv20.0160.0010.018
LoadTiff0.0010.0000.001
MSD1.1960.0251.227
MakeHypercube0.0010.0000.001
MigrationStats0.0010.0010.001
NextOdd000
NonParallel4OptimizeParams0.0000.0010.001
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0140.0020.015
OptimizeParamsMainLoop0.0040.0050.022
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0000.0000.001
PerAndSpeed0.2480.0230.277
PlotTracksSeparately0.0080.0010.010
PostProcessTracking0.0010.0010.000
Prep4OptimizeParams0.0740.0050.079
ThreeConditions0.0100.0030.012
TrackCellsDataset0.0130.0020.015
TrajectoryDataset0.0280.0040.033
ValidateTrackingArgs000
VeAutoCor0.8290.0130.843
VisualizeCntr0.0020.0010.002
VisualizeImg0.0050.0010.006
VisualizeStackCentroids0.0430.0060.048
WSADataset0.0070.0010.009
aggregateFR0.6250.0060.633
aggregateTrackedCells0.0190.0040.022
bpass0.0630.0020.066
circshift0.0010.0000.001
cntrd0.6080.0130.624
fixDA0.0010.0000.001
fixExpName0.0010.0000.001
fixFM10.0000.0010.000
fixFM2000
fixFM30.0010.0010.001
fixFM4000
fixFM50.0000.0010.000
fixFM6000
fixID1000
fixMSD0.0000.0000.001
fixPER1000
fixPER20.0010.0010.000
fixPER3000
getAvailableAggrMetrics0.7770.0080.786
getCellImages0.2440.8421.095
getCellMigSlot0.3130.4920.811
getCellTrackMeta0.0120.0020.014
getCellTrackStats0.0170.0030.020
getCellTracks0.0280.0040.032
getCellsMeta0.0140.0020.016
getCellsStats0.0140.0020.016
getDACtable1.5430.0131.558
getDiRatio0.0130.0010.015
getFMItable0.3930.0040.398
getForMigtable0.6850.0060.692
getImageCentroids0.0190.0030.021
getImageStacks0.0410.0070.049
getMSDtable2.9480.0302.990
getOptimizedParameters0.0120.0020.014
getOptimizedParams0.0140.0010.015
getPerAndSpeed0.2630.0250.295
getPopulationStats0.0160.0010.018
getProcessedImages0.2230.7921.022
getProcessingStatus0.0120.0010.013
getResults0.5100.0150.530
getTracks0.0160.0020.019
getVACtable0.8650.0070.875
initializeTrackParams0.0000.0000.001
innerBondRaster0.0010.0000.002
internalPermutation0.0000.0000.001
matfix0.0000.0000.001
nontrivialBondTracking0.0010.0000.001
pkfnd0.5900.0130.607
plot3DAllTracks0.0010.0000.001
plot3DTracks000
plotAllTracks0.0170.0030.020
plotSampleTracks0.0140.0030.017
preProcCellMig0.0080.0010.009
rmPreProcessing0.0910.0040.095
runTrackingPermutation0.0010.0000.001
setAnalyticParams0.0110.0010.013
setCellMigSlot0.0170.0010.018
setCellTracks0.0120.0020.015
setCellsMeta0.0120.0010.014
setExpName0.0180.0010.019
setOptimizedParams0.0120.0020.014
setProcessedImages0.0120.0020.014
setProcessingStatus0.0130.0020.014
setTrackedCellsMeta0.0120.0020.014
setTrackedCentroids0.0120.0020.014
setTrackedPositions0.0120.0020.014
setTrackingStats0.0120.0020.014
sinkAway0.0000.0000.001
subNetworkTracking0.0010.0000.001
track0.0080.0010.007
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.000
trackSlideWrapUp0.0000.0000.001
trivialBondRaster0.0010.0010.002
trivialBondTracking0.0010.0000.000
visualizeCellTracks0.0540.0150.069
visualizeTrcks0.0240.0020.027
warnMessage0.0010.0000.001
wsaPreProcessing0.0490.0010.050