Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-16 11:07:23 -0400 (Mon, 16 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4153
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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 merida1


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 277/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.4.0  (landing page)
Waldir Leoncio
Snapshot Date: 2022-05-15 13:55:12 -0400 (Sun, 15 May 2022)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: RELEASE_3_15
git_last_commit: c95600f
git_last_commit_date: 2022-04-26 12:14:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cellmigRation
Version: 1.4.0
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_1.4.0.tar.gz
StartedAt: 2022-05-16 00:10:51 -0400 (Mon, 16 May 2022)
EndedAt: 2022-05-16 00:14:54 -0400 (Mon, 16 May 2022)
EllapsedTime: 243.7 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cellmigRation.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.4.0’
* 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 9.158  0.027   9.198
getDACtable 5.208  0.039   5.253
* 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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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 -- Mon May 16 00:14:42 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 
  6.044   0.399   6.428 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0040.0010.004
CellMig-class0.0510.0030.054
CellMigPCA2.9590.1193.083
CellMigPCAclust0.0130.0020.014
CellMigPCAclustALL1.7270.0101.739
CellTracker0.0360.0030.039
CellTrackerMainLoop0.0060.0050.013
CentroidArray0.0370.0020.038
CentroidValidation1.2770.0171.302
ComputeTracksStats0.0550.0020.058
DetectRadii0.0060.0010.005
DiAutoCor3.6710.0143.695
DiRatio0.0310.0010.031
DiRatioPlot0.0580.0140.072
EstimateDiameterRange0.0290.0020.031
FMI1.2530.0061.261
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0060.0000.006
FinRes1.7290.0141.748
ForwardMigration2.5560.0072.566
GenAllCombos0.0050.0000.006
LinearConv20.0420.0010.043
LoadTiff0.0010.0010.002
MSD3.9960.0164.020
MakeHypercube0.0020.0000.003
MigrationStats0.0010.0000.002
NextOdd0.0010.0000.000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0010.0000.000
OptimizeParams0.0310.0030.034
OptimizeParamsMainLoop0.0060.0050.010
Parallel4OptimizeParams0.0010.0010.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.5700.0220.594
PlotTracksSeparately0.0150.0010.017
PostProcessTracking0.0010.0000.000
Prep4OptimizeParams0.1990.0040.203
ThreeConditions0.0330.0030.036
TrackCellsDataset0.0320.0020.034
TrajectoryDataset0.0370.0020.039
ValidateTrackingArgs0.0000.0000.001
VeAutoCor2.8070.0102.820
VisualizeCntr0.0030.0010.004
VisualizeImg0.0090.0010.010
VisualizeStackCentroids0.0990.0070.105
WSADataset0.0110.0010.013
aggregateFR1.6120.0091.627
aggregateTrackedCells0.0430.0050.048
bpass0.1320.0040.138
circshift0.0000.0000.001
cntrd1.9540.0111.970
fixDA0.0000.0000.001
fixExpName000
fixFM1000
fixFM2000
fixFM3000
fixFM40.0000.0000.001
fixFM50.0000.0000.001
fixFM60.0010.0000.000
fixID10.0010.0000.000
fixMSD000
fixPER10.0000.0000.001
fixPER20.0010.0000.001
fixPER30.0010.0000.001
getAvailableAggrMetrics2.3660.0122.383
getCellImages0.5160.6941.211
getCellMigSlot0.6040.4381.042
getCellTrackMeta0.0310.0020.034
getCellTrackStats0.0380.0020.040
getCellTracks0.0300.0040.033
getCellsMeta0.0340.0030.037
getCellsStats0.0340.0030.036
getDACtable5.2080.0395.253
getDiRatio0.0390.0020.042
getFMItable1.2250.0051.232
getForMigtable1.4920.0041.498
getImageCentroids0.0450.0030.048
getImageStacks0.1000.0080.108
getMSDtable9.1580.0279.198
getOptimizedParameters0.0320.0020.035
getOptimizedParams0.0310.0030.033
getPerAndSpeed0.5580.0210.581
getPopulationStats0.0320.0030.034
getProcessedImages0.5120.7451.300
getProcessingStatus0.0330.0030.036
getResults1.7090.0171.769
getTracks0.0330.0030.036
getVACtable2.8200.0092.833
initializeTrackParams0.0010.0000.000
innerBondRaster0.0030.0000.003
internalPermutation0.0020.0000.002
matfix0.0020.0010.002
nontrivialBondTracking0.0020.0000.003
pkfnd1.9820.0071.991
plot3DAllTracks0.0010.0010.000
plot3DTracks0.0010.0000.001
plotAllTracks0.0300.0030.033
plotSampleTracks0.0240.0030.027
preProcCellMig0.0110.0020.014
rmPreProcessing0.2370.0040.240
runTrackingPermutation0.0030.0000.004
setAnalyticParams0.0320.0020.034
setCellMigSlot0.0400.0030.042
setCellTracks0.0290.0010.032
setCellsMeta0.0310.0020.033
setExpName0.0390.0020.041
setOptimizedParams0.0330.0020.035
setProcessedImages0.0300.0010.032
setProcessingStatus0.0300.0020.032
setTrackedCellsMeta0.0430.0040.047
setTrackedCentroids0.0300.0020.032
setTrackedPositions0.0320.0030.034
setTrackingStats0.0320.0020.034
sinkAway0.0010.0000.001
subNetworkTracking0.0030.0010.002
track0.0170.0000.018
trackHypercubeBuild0.0010.0010.001
trackSlideProcessing0.0010.0000.002
trackSlideWrapUp0.0010.0010.000
trivialBondRaster0.0040.0000.004
trivialBondTracking0.0010.0010.001
visualizeCellTracks0.1030.0100.113
visualizeTrcks0.0370.0020.040
warnMessage0.0000.0000.001
wsaPreProcessing0.1350.0020.137