Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2022-01-27 11:06:11 -0500 (Thu, 27 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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 nebbiolo1


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 1343/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
optimalFlow 1.7.0  (landing page)
Hristo Inouzhe
Snapshot Date: 2022-01-26 13:55:18 -0500 (Wed, 26 Jan 2022)
git_url: https://git.bioconductor.org/packages/optimalFlow
git_branch: master
git_last_commit: 3e7c594
git_last_commit_date: 2021-10-26 12:59:43 -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    NA  
palomino3Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: optimalFlow
Version: 1.7.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings optimalFlow_1.7.0.tar.gz
StartedAt: 2022-01-26 20:23:35 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 20:26:29 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 173.8 seconds
RetCode: 0
Status:   OK  
CheckDir: optimalFlow.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings optimalFlow_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/optimalFlow.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.7.0’
* 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 ‘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 5.209  0.434  11.393
cytoPlot                  4.731  0.508  11.579
f1ScoreVoting             4.743  0.450  11.270
cytoPlotDatabase          3.144  0.328   9.479
cytoPlot3d                3.072  0.379   9.641
optimalFlowTemplates      3.057  0.372  10.975
wasserCostFunction        2.662  0.325   8.908
cytoPlotDatabase3d        2.707  0.269   8.962
* 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-3.15-bioc/meat/optimalFlow.Rcheck/00check.log’
for details.



Installation output

optimalFlow.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL optimalFlow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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
costWasserMatchingEllipse0.0890.0000.088
cytoPlot 4.731 0.50811.579
cytoPlot3d3.0720.3799.641
cytoPlotDatabase3.1440.3289.479
cytoPlotDatabase3d2.7070.2698.962
estimCovCellGeneral0.0380.0000.039
estimationCellBarycenter0.0010.0030.003
f1Score0.1270.0000.127
f1ScoreVoting 4.743 0.45011.270
labelTransfer0.0000.0000.001
labelTransferEllipse0.0060.0000.006
optimalFlowClassification 5.209 0.43411.393
optimalFlowTemplates 3.057 0.37210.975
qdaClassification0.0020.0000.002
tclustWithInitialization1.6640.2311.840
tclust_H1.8160.1461.892
trimmedKBarycenter0.0770.0040.080
voteLabelTransfer0.0000.0000.001
w2dist0.0010.0000.002
wasserCostFunction2.6620.3258.908