Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:41 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 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 20.04.5 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: 2022-10-19 00:19:10 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 00:23:15 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 245.6 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 4.2.1 (2022-06-23)
* 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 9.101  0.030   9.157
getDACtable 4.992  0.015   5.015
* 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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 -- Wed Oct 19 00:23:03 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 
  6.422   0.429   7.113 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0040.0000.004
CellMig-class0.0460.0060.052
CellMigPCA3.1270.0253.168
CellMigPCAclust0.0130.0010.014
CellMigPCAclustALL1.6670.0821.753
CellTracker0.0310.0030.033
CellTrackerMainLoop0.0060.0050.012
CentroidArray0.0360.0040.040
CentroidValidation1.2200.0221.243
ComputeTracksStats0.0500.0030.053
DetectRadii0.0040.0000.005
DiAutoCor3.4460.0123.462
DiRatio0.0340.0010.035
DiRatioPlot0.0560.0120.069
EstimateDiameterRange0.0240.0020.026
FMI1.2070.0061.214
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0030.0000.004
FinRes1.6020.0121.615
ForwardMigration2.4180.0092.429
GenAllCombos0.0040.0010.005
LinearConv20.0440.0010.045
LoadTiff0.0010.0010.002
MSD3.6680.0383.712
MakeHypercube0.0020.0000.003
MigrationStats0.0010.0000.002
NextOdd0.0010.0000.000
NonParallel4OptimizeParams0.0020.0000.002
NonParallelTrackLoop000
OptimizeParams0.0320.0030.035
OptimizeParamsMainLoop0.0050.0050.010
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.5860.0280.617
PlotTracksSeparately0.0160.0020.017
PostProcessTracking0.0000.0000.001
Prep4OptimizeParams0.2040.0030.209
ThreeConditions0.0310.0030.034
TrackCellsDataset0.0310.0030.035
TrajectoryDataset0.0340.0020.036
ValidateTrackingArgs0.0010.0000.000
VeAutoCor2.7820.0122.796
VisualizeCntr0.0030.0000.004
VisualizeImg0.0080.0000.009
VisualizeStackCentroids0.0890.0070.096
WSADataset0.0110.0020.012
aggregateFR1.5890.0071.598
aggregateTrackedCells0.0400.0030.044
bpass0.1270.0030.131
circshift0.0000.0000.001
cntrd1.9200.0131.934
fixDA0.0010.0010.001
fixExpName0.0010.0000.001
fixFM10.0010.0010.000
fixFM2000
fixFM30.0000.0000.001
fixFM4000
fixFM50.0010.0000.000
fixFM60.0000.0000.001
fixID10.0010.0000.001
fixMSD0.0010.0000.001
fixPER10.0000.0000.001
fixPER2000
fixPER30.0010.0000.001
getAvailableAggrMetrics2.4020.0072.412
getCellImages0.5060.6831.190
getCellMigSlot0.5810.4291.011
getCellTrackMeta0.0290.0020.030
getCellTrackStats0.0390.0030.042
getCellTracks0.0310.0030.033
getCellsMeta0.0510.0030.055
getCellsStats0.0330.0020.035
getDACtable4.9920.0155.015
getDiRatio0.0390.0020.042
getFMItable1.2160.0061.227
getForMigtable1.7600.0091.773
getImageCentroids0.0440.0030.046
getImageStacks0.0860.0050.091
getMSDtable9.1010.0309.157
getOptimizedParameters0.0330.0020.035
getOptimizedParams0.0340.0040.037
getPerAndSpeed0.5760.0210.598
getPopulationStats0.0330.0020.034
getProcessedImages0.5010.7341.239
getProcessingStatus0.0300.0020.032
getResults1.6360.0121.661
getTracks0.0320.0020.035
getVACtable2.7490.0082.762
initializeTrackParams0.0000.0010.001
innerBondRaster0.0020.0000.002
internalPermutation0.0020.0010.002
matfix0.0010.0000.001
nontrivialBondTracking0.0010.0000.002
pkfnd1.8840.0081.895
plot3DAllTracks000
plot3DTracks0.0010.0010.000
plotAllTracks0.0330.0030.037
plotSampleTracks0.0260.0030.028
preProcCellMig0.0100.0020.013
rmPreProcessing0.2080.0020.210
runTrackingPermutation0.0030.0000.002
setAnalyticParams0.0320.0030.034
setCellMigSlot0.0350.0020.036
setCellTracks0.0310.0020.032
setCellsMeta0.0300.0020.033
setExpName0.0370.0020.040
setOptimizedParams0.0330.0020.035
setProcessedImages0.0320.0040.036
setProcessingStatus0.0320.0030.036
setTrackedCellsMeta0.0510.0030.054
setTrackedCentroids0.0310.0020.033
setTrackedPositions0.0290.0020.030
setTrackingStats0.0310.0020.034
sinkAway0.0010.0000.001
subNetworkTracking0.0030.0010.002
track0.0190.0000.019
trackHypercubeBuild0.0020.0000.001
trackSlideProcessing0.0010.0000.002
trackSlideWrapUp0.0000.0000.001
trivialBondRaster0.0030.0000.004
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.1010.0080.110
visualizeTrcks0.0370.0020.040
warnMessage0.0010.0010.001
wsaPreProcessing0.1130.0030.117