Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:45 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 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? 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 270/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.2.0  (landing page)
Waldir Leoncio
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_14
git_last_commit: 18f748f
git_last_commit_date: 2021-10-26 13:08:41 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2022-04-12 11:18:30 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 11:22:01 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 210.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/cellmigRation.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.2.0’
* 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 7.944  0.027   7.981
* 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/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 11:21:49 2022 
*********************************************** 
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 
  5.233   0.361   5.572 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0040.0010.004
CellMig-class0.0420.0030.045
CellMigPCA2.5470.1042.654
CellMigPCAclust0.0110.0020.013
CellMigPCAclustALL1.4910.0241.516
CellTracker0.0340.0040.038
CellTrackerMainLoop0.0050.0050.011
CentroidArray0.0360.0030.039
CentroidValidation0.9330.0140.947
ComputeTracksStats0.0490.0030.053
DetectRadii0.0050.0000.005
DiAutoCor2.9910.0133.007
DiRatio0.0350.0020.037
DiRatioPlot0.0510.0140.065
EstimateDiameterRange0.0260.0010.027
FMI1.0170.0051.023
FianlizeOptiParams0.0010.0000.000
FilterTrackedCells0.0050.0000.006
FinRes1.3770.0141.393
ForwardMigration2.3030.0152.323
GenAllCombos0.0060.0010.006
LinearConv20.0430.0010.046
LoadTiff0.0010.0010.003
MSD3.5520.0153.717
MakeHypercube0.0020.0020.004
MigrationStats0.0020.0020.003
NextOdd0.0010.0010.001
NonParallel4OptimizeParams0.0010.0010.002
NonParallelTrackLoop0.0000.0000.001
OptimizeParams0.0310.0020.034
OptimizeParamsMainLoop0.0040.0060.011
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0010.001
PerAndSpeed0.5290.0250.597
PlotTracksSeparately0.0130.0010.015
PostProcessTracking0.0010.0010.001
Prep4OptimizeParams0.2130.0050.218
ThreeConditions0.0320.0030.035
TrackCellsDataset0.0280.0020.031
TrajectoryDataset0.0320.0010.033
ValidateTrackingArgs0.0010.0000.001
VeAutoCor2.5570.0082.567
VisualizeCntr0.0030.0010.004
VisualizeImg0.0080.0010.009
VisualizeStackCentroids0.0890.0110.099
WSADataset0.0100.0010.012
aggregateFR1.3240.0051.330
aggregateTrackedCells0.0340.0050.040
bpass0.1110.0020.115
circshift0.0010.0000.001
cntrd1.7870.0101.798
fixDA0.0010.0000.000
fixExpName0.0000.0010.001
fixFM1000
fixFM20.0000.0010.000
fixFM30.0010.0000.001
fixFM40.0010.0010.001
fixFM5000
fixFM60.0000.0010.000
fixID10.0000.0000.001
fixMSD0.0000.0010.000
fixPER10.0000.0000.001
fixPER2000
fixPER3000
getAvailableAggrMetrics2.1690.0072.178
getCellImages0.6351.5192.237
getCellMigSlot0.6571.0281.714
getCellTrackMeta0.0310.0020.033
getCellTrackStats0.0370.0040.042
getCellTracks0.0330.0050.037
getCellsMeta0.0450.0030.048
getCellsStats0.0310.0020.034
getDACtable4.4360.0434.481
getDiRatio0.0300.0030.032
getFMItable1.2050.0061.212
getForMigtable1.4210.0061.428
getImageCentroids0.0370.0060.042
getImageStacks0.0940.0100.104
getMSDtable7.9440.0277.981
getOptimizedParameters0.0330.0020.035
getOptimizedParams0.0350.0050.040
getPerAndSpeed0.5320.0270.561
getPopulationStats0.0320.0030.034
getProcessedImages0.5501.9212.528
getProcessingStatus0.0310.0020.034
getResults1.5950.0141.611
getTracks0.0330.0030.035
getVACtable2.4020.0092.415
initializeTrackParams0.0010.0010.001
innerBondRaster0.0030.0000.003
internalPermutation0.0010.0000.003
matfix0.0020.0000.002
nontrivialBondTracking0.0020.0000.002
pkfnd1.6720.0111.684
plot3DAllTracks0.0000.0010.001
plot3DTracks0.0010.0000.001
plotAllTracks0.0310.0030.034
plotSampleTracks0.0200.0030.022
preProcCellMig0.0100.0010.012
rmPreProcessing0.2080.0030.211
runTrackingPermutation0.0030.0010.003
setAnalyticParams0.0320.0020.034
setCellMigSlot0.0280.0020.030
setCellTracks0.0270.0020.029
setCellsMeta0.0270.0030.030
setExpName0.0400.0030.042
setOptimizedParams0.0260.0020.028
setProcessedImages0.0310.0030.034
setProcessingStatus0.0390.0030.042
setTrackedCellsMeta0.0300.0010.031
setTrackedCentroids0.0310.0020.033
setTrackedPositions0.0310.0030.033
setTrackingStats0.0290.0040.033
sinkAway0.0010.0010.001
subNetworkTracking0.0020.0010.002
track0.0170.0010.018
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0030.0000.004
trivialBondTracking0.0010.0000.002
visualizeCellTracks0.1010.0110.111
visualizeTrcks0.0320.0010.035
warnMessage0.0010.0000.001
wsaPreProcessing0.1270.0030.130