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This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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

Package 1499/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
optimalFlow 1.20.0  (landing page)
Hristo Inouzhe
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/optimalFlow
git_branch: RELEASE_3_21
git_last_commit: 62702a7
git_last_commit_date: 2025-04-15 11:58:40 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for optimalFlow on lconway

To the developers/maintainers of the optimalFlow package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: optimalFlow
Version: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2025-04-21 22:24:58 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 22:31:25 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 387.0 seconds
RetCode: 0
Status:   OK  
CheckDir: optimalFlow.Rcheck
Warnings: 0

Command output

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### Running 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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/optimalFlow.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘optimalFlow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘optimalFlow’ version ‘1.20.0’
* 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 code 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             8.347 16.067  40.280
cytoPlotDatabase3d        5.387  9.245  31.623
optimalFlowClassification 7.444  6.558  37.372
cytoPlotDatabase          5.289  8.056  25.373
cytoPlot                  5.380  1.545  17.710
wasserCostFunction        5.033  1.665  27.757
cytoPlot3d                4.153  1.315  15.482
optimalFlowTemplates      3.978  1.275  27.446
tclustWithInitialization  2.388  2.083  10.005
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘optimalFlow’ ...
** this is package ‘optimalFlow’ version ‘1.20.0’
** 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
costWasserMatchingEllipse0.1680.0920.262
cytoPlot 5.380 1.54517.710
cytoPlot3d 4.153 1.31515.482
cytoPlotDatabase 5.289 8.05625.373
cytoPlotDatabase3d 5.387 9.24531.623
estimCovCellGeneral0.0190.0060.026
estimationCellBarycenter0.0050.0090.014
f1Score0.1860.0210.208
f1ScoreVoting 8.34716.06740.280
labelTransfer0.0010.0000.000
labelTransferEllipse0.0100.0120.019
optimalFlowClassification 7.444 6.55837.372
optimalFlowTemplates 3.978 1.27527.446
qdaClassification0.0010.0010.001
tclustWithInitialization 2.388 2.08310.005
tclust_H2.8050.6044.664
trimmedKBarycenter0.1290.0520.185
voteLabelTransfer0.0010.0000.000
w2dist0.0020.0010.003
wasserCostFunction 5.033 1.66527.757