Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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 nebbiolo1


To the developers/maintainers of the cellmigRation package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 292/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellmigRation 1.7.0  (landing page)
Waldir Leoncio
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/cellmigRation
git_branch: devel
git_last_commit: 0323749
git_last_commit_date: 2022-11-01 11:24:36 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: cellmigRation
Version: 1.7.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings cellmigRation_1.7.0.tar.gz
StartedAt: 2023-04-11 19:10:27 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 19:14:16 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 229.8 seconds
RetCode: 0
Status:   OK  
CheckDir: cellmigRation.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings cellmigRation_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/cellmigRation.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.7.0’
* 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 loading without being on the library search path ... 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
* 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 ...
  ‘cellmigRation.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

cellmigRation.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 11 19:12:17 2023 
*********************************************** 
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 
  2.746   0.222   2.956 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0280.0000.028
CellMigPCA1.2570.0681.326
CellMigPCAclust0.0110.0000.011
CellMigPCAclustALL0.6400.0000.639
CellTracker0.0200.0000.019
CellTrackerMainLoop0.0050.0030.030
CentroidArray0.0100.0090.020
CentroidValidation0.4260.0410.468
ComputeTracksStats0.0450.0040.048
DetectRadii0.0000.0030.003
DiAutoCor1.3170.0361.354
DiRatio0.0170.0000.017
DiRatioPlot0.0320.0040.036
EstimateDiameterRange0.0170.0000.017
FMI0.4650.0000.465
FianlizeOptiParams000
FilterTrackedCells0.0030.0000.003
FinRes0.6180.0000.618
ForwardMigration0.9050.0240.929
GenAllCombos0.0030.0000.003
LinearConv20.0210.0000.021
LoadTiff0.0010.0000.001
MSD1.4320.0521.485
MakeHypercube0.0010.0000.001
MigrationStats0.0000.0010.001
NextOdd000
NonParallel4OptimizeParams0.0000.0010.002
NonParallelTrackLoop000
OptimizeParams0.0180.0000.018
OptimizeParamsMainLoop0.0060.0000.028
Parallel4OptimizeParams0.0000.0000.001
ParallelTrackLoop0.0010.0000.000
PerAndSpeed0.3250.0200.346
PlotTracksSeparately0.0090.0000.009
PostProcessTracking0.0010.0000.000
Prep4OptimizeParams0.0910.0040.094
ThreeConditions0.0100.0040.014
TrackCellsDataset0.0160.0000.016
TrajectoryDataset0.0140.0080.022
ValidateTrackingArgs0.0000.0000.001
VeAutoCor1.0150.0281.043
VisualizeCntr0.0020.0000.002
VisualizeImg0.0050.0000.005
VisualizeStackCentroids0.0660.0000.066
WSADataset0.0070.0000.007
aggregateFR0.6030.0360.639
aggregateTrackedCells0.0200.0040.024
bpass0.0540.0040.058
circshift0.0000.0000.001
cntrd0.6530.0120.665
fixDA000
fixExpName000
fixFM1000
fixFM20.0010.0000.000
fixFM30.0000.0000.001
fixFM4000
fixFM5000
fixFM60.0010.0000.000
fixID10.0010.0000.001
fixMSD0.0000.0000.001
fixPER10.0000.0000.001
fixPER2000
fixPER3000
getAvailableAggrMetrics0.8790.0220.901
getCellImages0.2510.9961.248
getCellMigSlot0.2630.6360.898
getCellTrackMeta0.0100.0080.018
getCellTrackStats0.0220.0000.022
getCellTracks0.0110.0080.019
getCellsMeta0.0140.0040.017
getCellsStats0.0280.0240.052
getDACtable1.8760.0241.899
getDiRatio0.0190.0000.020
getFMItable0.7100.0160.726
getForMigtable0.5090.0000.509
getImageCentroids0.0190.0040.023
getImageStacks0.0610.0040.064
getMSDtable3.3850.0343.419
getOptimizedParameters0.0120.0050.016
getOptimizedParams0.0140.0040.019
getPerAndSpeed0.2600.0080.269
getPopulationStats0.0180.0000.018
getProcessedImages0.2890.9521.241
getProcessingStatus0.0170.0000.018
getResults0.5850.0040.589
getTracks0.0140.0040.018
getVACtable0.9750.0160.992
initializeTrackParams0.0000.0000.001
innerBondRaster0.0010.0000.002
internalPermutation0.0010.0000.001
matfix0.0020.0000.001
nontrivialBondTracking0.0010.0000.001
pkfnd0.6650.0040.669
plot3DAllTracks0.0780.0310.111
plot3DTracks0.0080.0000.009
plotAllTracks0.0190.0000.019
plotSampleTracks0.0120.0040.016
preProcCellMig0.0040.0030.008
rmPreProcessing0.0890.0010.088
runTrackingPermutation0.0040.0000.004
setAnalyticParams0.0210.0000.021
setCellMigSlot0.0200.0030.023
setCellTracks0.0160.0000.017
setCellsMeta0.0130.0040.016
setExpName0.0230.0000.023
setOptimizedParams0.0170.0000.018
setProcessedImages0.0030.0140.018
setProcessingStatus0.0170.0000.017
setTrackedCellsMeta0.0180.0000.017
setTrackedCentroids0.0140.0030.018
setTrackedPositions0.0290.0010.029
setTrackingStats0.0050.0110.017
sinkAway0.0000.0000.001
subNetworkTracking0.0020.0000.001
track0.010.000.01
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.000
trackSlideWrapUp0.0010.0000.001
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0660.0000.067
visualizeTrcks0.0250.0000.024
warnMessage0.0010.0000.001
wsaPreProcessing0.0510.0000.050