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This page was generated on 2024-02-18 02:30:06 -0500 (Sun, 18 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4424
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4400
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 1449/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
optimalFlow 1.15.0  (landing page)
Hristo Inouzhe
Snapshot Date: 2024-02-16 14:10:20 -0500 (Fri, 16 Feb 2024)
git_url: https://git.bioconductor.org/packages/optimalFlow
git_branch: devel
git_last_commit: afbf581
git_last_commit_date: 2023-10-24 11:22:22 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for optimalFlow on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: optimalFlow
Version: 1.15.0
Command: /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings optimalFlow_1.15.0.tar.gz
StartedAt: 2024-02-17 08:28:30 -0000 (Sat, 17 Feb 2024)
EndedAt: 2024-02-17 08:32:43 -0000 (Sat, 17 Feb 2024)
EllapsedTime: 252.5 seconds
RetCode: 0
Status:   OK  
CheckDir: optimalFlow.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/R/R-devel_2024-01-16_r85812/site-library --no-vignettes --timings optimalFlow_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/optimalFlow.Rcheck’
* using R Under development (unstable) (2024-01-16 r85812)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘optimalFlow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘optimalFlow’ version ‘1.15.0’
* 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 loading without being on the library search path ... 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             9.959  0.308  18.922
optimalFlowClassification 9.869  0.371  18.756
cytoPlot                  8.002  0.677  17.340
cytoPlotDatabase3d        6.122  0.426  15.491
cytoPlotDatabase          6.053  0.412  15.325
cytoPlot3d                6.019  0.345  15.208
optimalFlowTemplates      5.975  0.344  14.826
wasserCostFunction        5.994  0.281  15.287
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/optimalFlow.Rcheck/00check.log’
for details.



Installation output

optimalFlow.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-devel_2024-01-16_r85812/bin/R CMD INSTALL optimalFlow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2024-01-16_r85812/site-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
costWasserMatchingEllipse0.1410.0080.152
cytoPlot 8.002 0.67717.340
cytoPlot3d 6.019 0.34515.208
cytoPlotDatabase 6.053 0.41215.325
cytoPlotDatabase3d 6.122 0.42615.491
estimCovCellGeneral0.0330.0040.046
estimationCellBarycenter0.0040.0000.003
f1Score0.1580.0320.191
f1ScoreVoting 9.959 0.30818.922
labelTransfer000
labelTransferEllipse0.0080.0000.007
optimalFlowClassification 9.869 0.37118.756
optimalFlowTemplates 5.975 0.34414.826
qdaClassification0.0000.0010.001
tclustWithInitialization2.5400.1332.680
tclust_H2.8600.0962.963
trimmedKBarycenter0.0980.0040.103
voteLabelTransfer000
w2dist0.0020.0000.002
wasserCostFunction 5.994 0.28115.287