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This page was generated on 2022-01-21 13:08:13 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 optimalFlow on machv2


To the developers/maintainers of the optimalFlow package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/optimalFlow.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 1345/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
optimalFlow 1.6.0  (landing page)
Hristo Inouzhe
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/optimalFlow
git_branch: RELEASE_3_14
git_last_commit: ea8a7af
git_last_commit_date: 2021-10-26 12:59:43 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: optimalFlow
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings optimalFlow_1.6.0.tar.gz
StartedAt: 2022-01-20 16:01:00 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 16:06:38 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 338.4 seconds
RetCode: 0
Status:   OK  
CheckDir: optimalFlow.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings optimalFlow_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/optimalFlow.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.0’
* 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
optimalFlowClassification 11.059  1.361  25.271
f1ScoreVoting             10.372  1.359  22.856
cytoPlot                   8.042  1.119  21.033
optimalFlowTemplates       6.214  0.939  20.779
cytoPlotDatabase           5.809  0.901  18.760
wasserCostFunction         5.707  0.900  19.462
cytoPlot3d                 5.693  0.873  18.210
cytoPlotDatabase3d         5.646  0.911  18.279
tclustWithInitialization   4.182  0.686   5.132
tclust_H                   4.119  0.697   5.021
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/optimalFlow.Rcheck/00check.log’
for details.



Installation output

optimalFlow.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL optimalFlow
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
costWasserMatchingEllipse0.1870.0240.210
cytoPlot 8.042 1.11921.033
cytoPlot3d 5.693 0.87318.210
cytoPlotDatabase 5.809 0.90118.760
cytoPlotDatabase3d 5.646 0.91118.279
estimCovCellGeneral0.3390.0130.353
estimationCellBarycenter0.0060.0010.007
f1Score0.2000.0130.214
f1ScoreVoting10.372 1.35922.856
labelTransfer0.0010.0000.000
labelTransferEllipse0.0110.0020.013
optimalFlowClassification11.059 1.36125.271
optimalFlowTemplates 6.214 0.93920.779
qdaClassification0.0010.0010.002
tclustWithInitialization4.1820.6865.132
tclust_H4.1190.6975.021
trimmedKBarycenter0.1510.0310.187
voteLabelTransfer000
w2dist0.0020.0010.003
wasserCostFunction 5.707 0.90019.462