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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).

CHECK results for cellmigRation on machv2

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? here 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 264/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.0.0  (landing page)
Waldir Leoncio
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_13
git_last_commit: 5029a2f
git_last_commit_date: 2021-05-19 13:01:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellmigRation
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellmigRation_1.0.0.tar.gz
StartedAt: 2021-10-14 17:11:37 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 17:14:34 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 177.6 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellmigRation_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/cellmigRation.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.0.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
getMSDtable 6.892  0.025   6.928
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 -- Thu Oct 14 17:14:24 2021 
*********************************************** 
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 
  4.044   0.308   4.339 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0040.0020.005
CellMig-class0.0470.0050.052
CellMigPCA2.1430.0892.275
CellMigPCAclust0.0080.0010.010
CellMigPCAclustALL1.0070.0091.016
CellTracker0.0360.0030.040
CellTrackerMainLoop0.0050.0060.012
CentroidArray0.0370.0040.040
CentroidValidation0.9210.0140.934
ComputeTracksStats0.0480.0030.052
DetectRadii0.0060.0000.006
DiAutoCor2.8840.0172.905
DiRatio0.0320.0020.034
DiRatioPlot0.0450.0130.058
EstimateDiameterRange0.0240.0020.026
FMI0.9190.0050.924
FianlizeOptiParams000
FilterTrackedCells0.0070.0010.008
FinRes1.4710.0161.489
ForwardMigration1.6520.0071.660
GenAllCombos0.0060.0010.006
LinearConv20.0390.0020.041
LoadTiff0.0010.0000.002
MSD2.9180.0172.941
MakeHypercube0.0030.0010.004
MigrationStats0.0010.0010.003
NextOdd0.0010.0000.001
NonParallel4OptimizeParams0.0010.0000.002
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0260.0030.030
OptimizeParamsMainLoop0.0050.0050.011
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop000
PerAndSpeed0.5000.0300.532
PlotTracksSeparately0.0130.0020.016
PostProcessTracking0.0010.0010.001
Prep4OptimizeParams0.1570.0030.160
ThreeConditions0.0250.0030.028
TrackCellsDataset0.0250.0020.026
TrajectoryDataset0.0360.0020.038
ValidateTrackingArgs0.0000.0000.001
VeAutoCor2.0740.0182.093
VisualizeCntr0.0020.0000.003
VisualizeImg0.0050.0000.006
VisualizeStackCentroids0.0730.0080.081
WSADataset0.0110.0020.013
aggregateFR1.4950.0081.503
aggregateTrackedCells0.0380.0050.042
bpass0.1210.0030.125
circshift0.0000.0000.002
cntrd1.6820.0101.693
fixDA0.0010.0000.000
fixExpName0.0010.0000.001
fixFM10.0010.0000.000
fixFM2000
fixFM3000
fixFM40.0010.0010.001
fixFM50.0000.0000.001
fixFM60.0000.0010.000
fixID10.0000.0000.001
fixMSD0.0000.0010.001
fixPER10.0000.0000.001
fixPER20.0010.0000.001
fixPER30.0010.0000.001
getAvailableAggrMetrics1.8100.0081.819
getCellImages0.5221.2851.881
getCellMigSlot0.5500.8151.404
getCellTrackMeta0.0240.0020.025
getCellTrackStats0.0280.0030.031
getCellTracks0.0250.0040.028
getCellsMeta0.0260.0020.028
getCellsStats0.0300.0020.033
getDACtable3.8680.0253.922
getDiRatio0.0310.0030.035
getFMItable0.9820.0040.987
getForMigtable1.0850.0081.096
getImageCentroids0.0400.0060.045
getImageStacks0.0770.0090.086
getMSDtable6.8920.0256.928
getOptimizedParameters0.0280.0010.028
getOptimizedParams0.0300.0030.033
getPerAndSpeed0.4560.0240.481
getPopulationStats0.0270.0020.030
getProcessedImages0.6202.1332.805
getProcessingStatus0.0310.0020.034
getResults1.3710.0301.403
getTracks0.0320.0020.034
getVACtable2.1830.0062.190
initializeTrackParams0.0010.0010.001
innerBondRaster0.0020.0010.003
internalPermutation0.0020.0010.002
matfix0.0020.0010.002
nontrivialBondTracking0.0020.0000.002
pkfnd1.2030.0091.212
plot3DAllTracks0.0010.0010.000
plot3DTracks000
plotAllTracks0.0290.0030.033
plotSampleTracks0.0190.0030.022
preProcCellMig0.0110.0020.012
rmPreProcessing0.1830.0020.187
runTrackingPermutation0.0030.0000.003
setAnalyticParams0.0260.0020.029
setCellMigSlot0.0370.0020.039
setCellTracks0.0280.0020.029
setCellsMeta0.0250.0020.029
setExpName0.0380.0020.040
setOptimizedParams0.0250.0020.028
setProcessedImages0.0410.0040.046
setProcessingStatus0.0250.0010.026
setTrackedCellsMeta0.0220.0010.023
setTrackedCentroids0.0230.0020.024
setTrackedPositions0.0300.0020.032
setTrackingStats0.0260.0030.028
sinkAway0.0010.0010.001
subNetworkTracking0.0020.0000.001
track0.0140.0000.015
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0010.001
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0040.0000.004
trivialBondTracking0.0000.0000.001
visualizeCellTracks0.0750.0090.084
visualizeTrcks0.0310.0020.033
warnMessage0.0000.0010.001
wsaPreProcessing0.1100.0020.112