Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:34 -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 nebbiolo2


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: 2023-04-12 05:13:01 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 05:16:53 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 232.2 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 Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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
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Type 'q()' to quit R.

> BiocGenerics:::testPackage("cellmigRation")


RUNIT TEST PROTOCOL -- Wed Apr 12 05:14:55 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 
  2.985   0.255   3.245 

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

nameusersystemelapsed
AddDimension0.0020.0000.002
CellMig-class0.0280.0000.028
CellMigPCA1.1740.0591.234
CellMigPCAclust0.0070.0000.008
CellMigPCAclustALL0.60.00.6
CellTracker0.0110.0080.019
CellTrackerMainLoop0.0040.0110.012
CentroidArray0.0180.0040.022
CentroidValidation0.4440.0040.449
ComputeTracksStats0.0280.0000.027
DetectRadii0.0030.0000.002
DiAutoCor1.5210.0201.541
DiRatio0.0190.0000.019
DiRatioPlot0.0400.0000.039
EstimateDiameterRange0.0180.0000.018
FMI0.5070.0000.507
FianlizeOptiParams0.0000.0000.001
FilterTrackedCells0.0000.0030.003
FinRes0.7190.0170.734
ForwardMigration0.940.040.98
GenAllCombos0.0030.0000.004
LinearConv20.0180.0040.023
LoadTiff0.0000.0010.001
MSD1.4060.0221.428
MakeHypercube0.0020.0010.001
MigrationStats0.0010.0000.001
NextOdd0.0010.0000.000
NonParallel4OptimizeParams0.0010.0000.001
NonParallelTrackLoop0.0010.0000.000
OptimizeParams0.0140.0030.018
OptimizeParamsMainLoop0.0080.0000.027
Parallel4OptimizeParams0.0010.0000.001
ParallelTrackLoop0.0010.0000.001
PerAndSpeed0.3410.0110.354
PlotTracksSeparately0.0090.0000.009
PostProcessTracking0.0010.0000.000
Prep4OptimizeParams0.0980.0000.097
ThreeConditions0.0100.0030.015
TrackCellsDataset0.0180.0000.018
TrajectoryDataset0.0220.0000.023
ValidateTrackingArgs0.0010.0000.001
VeAutoCor1.1060.0201.125
VisualizeCntr0.0030.0000.002
VisualizeImg0.0050.0000.005
VisualizeStackCentroids0.0680.0000.068
WSADataset0.0070.0000.007
aggregateFR0.6230.0040.627
aggregateTrackedCells0.0200.0040.025
bpass0.0590.0000.060
circshift0.0010.0000.000
cntrd0.6740.0200.694
fixDA0.0000.0000.001
fixExpName0.0000.0000.001
fixFM10.0000.0000.001
fixFM20.0010.0000.000
fixFM3000
fixFM40.0010.0000.000
fixFM5000
fixFM60.0000.0000.001
fixID10.0010.0000.000
fixMSD000
fixPER10.0000.0000.001
fixPER2000
fixPER30.0000.0000.001
getAvailableAggrMetrics0.8900.0040.895
getCellImages0.2280.3470.576
getCellMigSlot0.2370.2560.494
getCellTrackMeta0.0170.0000.017
getCellTrackStats0.0210.0000.021
getCellTracks0.0190.0000.019
getCellsMeta0.0140.0030.019
getCellsStats0.0350.0000.036
getDACtable1.810.001.81
getDiRatio0.0150.0040.019
getFMItable0.7030.0650.769
getForMigtable0.5190.0140.532
getImageCentroids0.0220.0000.022
getImageStacks0.0640.0000.064
getMSDtable3.2990.0163.315
getOptimizedParameters0.0130.0040.017
getOptimizedParams0.0180.0000.018
getPerAndSpeed0.2910.0000.291
getPopulationStats0.0110.0080.019
getProcessedImages0.2170.3160.533
getProcessingStatus0.0180.0000.018
getResults0.5880.0110.600
getTracks0.0150.0040.019
getVACtable0.9780.0000.977
initializeTrackParams000
innerBondRaster0.0010.0000.002
internalPermutation0.0010.0000.001
matfix0.0010.0000.001
nontrivialBondTracking0.0010.0000.001
pkfnd0.6920.0040.696
plot3DAllTracks0.0870.0130.101
plot3DTracks0.0080.0000.009
plotAllTracks0.0190.0000.019
plotSampleTracks0.0160.0000.015
preProcCellMig0.0070.0000.008
rmPreProcessing0.0820.0030.086
runTrackingPermutation0.0020.0000.002
setAnalyticParams0.0170.0000.018
setCellMigSlot0.0220.0000.023
setCellTracks0.0180.0000.019
setCellsMeta0.0190.0000.019
setExpName0.0230.0000.023
setOptimizedParams0.0150.0040.019
setProcessedImages0.0190.0040.023
setProcessingStatus0.0150.0040.018
setTrackedCellsMeta0.0190.0000.019
setTrackedCentroids0.0180.0000.018
setTrackedPositions0.0310.0040.034
setTrackingStats0.0190.0000.019
sinkAway0.0010.0000.001
subNetworkTracking0.0020.0000.002
track0.0120.0000.012
trackHypercubeBuild0.0010.0000.001
trackSlideProcessing0.0010.0000.001
trackSlideWrapUp000
trivialBondRaster0.0020.0000.002
trivialBondTracking0.0010.0000.001
visualizeCellTracks0.0710.0000.071
visualizeTrcks0.0260.0000.026
warnMessage0.0010.0000.001
wsaPreProcessing0.0500.0000.049