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CHECK report for optimalFlow on malbec1

This page was generated on 2021-05-06 12:28:28 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the optimalFlow package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1275/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
optimalFlow 1.2.0  (landing page)
Hristo Inouzhe
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/optimalFlow
Branch: RELEASE_3_12
Last Commit: e837f61
Last Changed Date: 2020-10-27 11:57:10 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  ERROR    ERROR  skippedskipped

Summary

Package: optimalFlow
Version: 1.2.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings optimalFlow_1.2.0.tar.gz
StartedAt: 2021-05-06 04:13:20 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:17:33 -0400 (Thu, 06 May 2021)
EllapsedTime: 253.5 seconds
RetCode: 0
Status:   OK  
CheckDir: optimalFlow.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings optimalFlow_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/optimalFlow.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘optimalFlow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘optimalFlow’ version ‘1.2.0’
* 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 ‘optimalFlow’ 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘GaussianBarycenters’ ‘distGaussianCov’ ‘distGaussianMean’
  ‘wassersteinKBarycenter’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
voteLabelTransfer: no visible binding for global variable ‘cell’
voteLabelTransfer: no visible binding for global variable
  ‘compound.proportion’
voteLabelTransfer: no visible binding for global variable
  ‘vote.proportion’
voteTransformation : <anonymous>: no visible binding for global
  variable ‘cell’
voteTransformation : <anonymous>: no visible binding for global
  variable ‘simple.proportion’
voteTransformation : <anonymous>: no visible binding for global
  variable ‘compound.proportion’
Undefined global functions or variables:
  cell compound.proportion simple.proportion vote.proportion
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
f1ScoreVoting             8.288  0.784  19.568
optimalFlowClassification 6.680  0.604  16.741
cytoPlot                  6.332  0.656  16.512
cytoPlotDatabase          5.296  0.484  15.115
cytoPlot3d                4.636  0.568  13.935
cytoPlotDatabase3d        4.592  0.556  16.108
wasserCostFunction        4.480  0.496  15.046
optimalFlowTemplates      4.124  0.512  14.158
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/optimalFlow.Rcheck/00check.log’
for details.



Installation output

optimalFlow.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL optimalFlow
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘optimalFlow’ ...
** using staged installation
** R
** 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 (optimalFlow)

Tests output


Example timings

optimalFlow.Rcheck/optimalFlow-Ex.timings

nameusersystemelapsed
costWasserMatchingEllipse0.1160.0040.131
cytoPlot 6.332 0.65616.512
cytoPlot3d 4.636 0.56813.935
cytoPlotDatabase 5.296 0.48415.115
cytoPlotDatabase3d 4.592 0.55616.108
estimCovCellGeneral0.0400.0080.117
estimationCellBarycenter0.0040.0000.006
f1Score0.2200.0080.228
f1ScoreVoting 8.288 0.78419.568
labelTransfer000
labelTransferEllipse0.0080.0000.007
optimalFlowClassification 6.680 0.60416.741
optimalFlowTemplates 4.124 0.51214.158
qdaClassification0.0000.0000.001
tclustWithInitialization2.6920.2922.974
tclust_H2.8600.2683.174
trimmedKBarycenter0.1200.0080.135
voteLabelTransfer0.0000.0000.001
w2dist0.0040.0000.002
wasserCostFunction 4.480 0.49615.046