Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-26 11:11:09 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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? 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 267/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.3.0  (landing page)
Waldir Leoncio
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: master
git_last_commit: 71dc596
git_last_commit_date: 2021-10-26 13:08:41 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
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: 1.3.0
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_1.3.0.tar.gz
StartedAt: 2022-01-25 23:05:05 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 23:08:46 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 221.2 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_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cellmigRation.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.3.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 8.855  0.029   8.900
getDACtable 5.241  0.019   5.267
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.



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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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 Jan 25 23:08:33 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 
  5.144   0.356   5.483 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0040.0010.004
CellMig-class0.0460.0040.049
CellMigPCA2.9790.1043.089
CellMigPCAclust0.0110.0020.012
CellMigPCAclustALL1.6980.0101.709
CellTracker0.0350.0040.040
CellTrackerMainLoop0.0070.0060.012
CentroidArray0.0380.0030.040
CentroidValidation1.2440.0151.260
ComputeTracksStats0.0520.0040.055
DetectRadii0.0050.0000.005
DiAutoCor3.5540.0133.575
DiRatio0.0330.0010.033
DiRatioPlot0.0580.0140.072
EstimateDiameterRange0.0300.0020.032
FMI1.2750.0041.281
FianlizeOptiParams0.0010.0000.001
FilterTrackedCells0.0040.0000.005
FinRes1.6730.0121.689
ForwardMigration2.5430.0102.560
GenAllCombos0.0060.0010.006
LinearConv20.0440.0010.046
LoadTiff0.0010.0000.002
MSD3.8610.0273.899
MakeHypercube0.0030.0010.003
MigrationStats0.0010.0010.002
NextOdd0.0010.0000.001
NonParallel4OptimizeParams0.0010.0000.002
NonParallelTrackLoop000
OptimizeParams0.0330.0020.035
OptimizeParamsMainLoop0.0040.0050.010
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0010.001
PerAndSpeed0.6000.0360.649
PlotTracksSeparately0.0140.0020.016
PostProcessTracking0.0000.0000.001
Prep4OptimizeParams0.2060.0050.210
ThreeConditions0.0320.0020.034
TrackCellsDataset0.0310.0030.033
TrajectoryDataset0.0370.0020.039
ValidateTrackingArgs0.0010.0010.001
VeAutoCor2.9310.0132.951
VisualizeCntr0.0040.0000.004
VisualizeImg0.0090.0000.010
VisualizeStackCentroids0.0980.0070.106
WSADataset0.0120.0020.013
aggregateFR1.7550.0071.765
aggregateTrackedCells0.0430.0060.049
bpass0.1320.0020.135
circshift0.0010.0000.001
cntrd2.0580.0132.075
fixDA0.0010.0000.000
fixExpName0.0010.0000.001
fixFM10.0000.0000.001
fixFM2000
fixFM30.0000.0010.000
fixFM40.0000.0000.001
fixFM50.0010.0000.000
fixFM60.0010.0000.001
fixID10.0010.0000.000
fixMSD0.0010.0000.001
fixPER1000
fixPER20.0000.0000.001
fixPER30.0010.0010.001
getAvailableAggrMetrics2.4110.0082.423
getCellImages0.5230.7041.231
getCellMigSlot0.5920.4371.030
getCellTrackMeta0.0310.0030.034
getCellTrackStats0.0390.0020.042
getCellTracks0.0320.0030.035
getCellsMeta0.0320.0020.034
getCellsStats0.0360.0040.039
getDACtable5.2410.0195.267
getDiRatio0.0310.0010.033
getFMItable1.1610.0041.167
getForMigtable1.3880.0051.394
getImageCentroids0.0450.0030.047
getImageStacks0.0880.0100.099
getMSDtable8.8550.0298.900
getOptimizedParameters0.0270.0030.029
getOptimizedParams0.0340.0020.036
getPerAndSpeed0.5580.0220.582
getPopulationStats0.0340.0020.036
getProcessedImages0.4790.6891.169
getProcessingStatus0.0310.0020.034
getResults1.5920.0271.622
getTracks0.0330.0020.036
getVACtable2.7990.0082.810
initializeTrackParams0.0000.0000.001
innerBondRaster0.0020.0000.002
internalPermutation0.0020.0000.003
matfix0.0020.0000.002
nontrivialBondTracking0.0020.0000.002
pkfnd1.9490.0091.960
plot3DAllTracks0.0000.0000.001
plot3DTracks0.0000.0000.001
plotAllTracks0.0310.0030.034
plotSampleTracks0.0220.0030.025
preProcCellMig0.0110.0020.013
rmPreProcessing0.2080.0030.210
runTrackingPermutation0.0030.0000.003
setAnalyticParams0.0300.0030.032
setCellMigSlot0.0390.0020.042
setCellTracks0.0300.0020.031
setCellsMeta0.0310.0010.033
setExpName0.0390.0020.041
setOptimizedParams0.0320.0020.034
setProcessedImages0.0330.0030.035
setProcessingStatus0.0320.0030.035
setTrackedCellsMeta0.0420.0050.047
setTrackedCentroids0.0320.0020.033
setTrackedPositions0.0300.0020.032
setTrackingStats0.0290.0020.031
sinkAway0.0010.0000.001
subNetworkTracking0.0020.0000.002
track0.0180.0010.018
trackHypercubeBuild0.0020.0010.002
trackSlideProcessing0.0010.0000.002
trackSlideWrapUp0.0010.0010.001
trivialBondRaster0.0040.0000.004
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0850.0050.090
visualizeTrcks0.0360.0010.039
warnMessage0.0010.0000.001
wsaPreProcessing0.1300.0020.132