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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1463/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
optimalFlow 1.19.0  (landing page)
Hristo Inouzhe
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/optimalFlow
git_branch: devel
git_last_commit: 3518f15
git_last_commit_date: 2024-10-29 10:46:57 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  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: 1.19.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings optimalFlow_1.19.0.tar.gz
StartedAt: 2024-12-24 09:33:26 -0000 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 09:38:01 -0000 (Tue, 24 Dec 2024)
EllapsedTime: 275.5 seconds
RetCode: 0
Status:   OK  
CheckDir: optimalFlow.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:optimalFlow.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings optimalFlow_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/optimalFlow.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘optimalFlow/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘optimalFlow’ version ‘1.19.0’
* 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 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             10.085  1.199  22.035
optimalFlowClassification  9.534  0.712  19.500
cytoPlot                   7.780  0.980  18.595
cytoPlot3d                 6.353  0.793  17.539
cytoPlotDatabase           6.055  0.935  17.417
wasserCostFunction         6.095  0.769  16.724
cytoPlotDatabase3d         6.130  0.675  16.117
optimalFlowTemplates       5.930  0.741  15.968
* 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-3.21-bioc/meat/optimalFlow.Rcheck/00check.log’
for details.


Installation output

optimalFlow.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL optimalFlow
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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
costWasserMatchingEllipse0.1540.0320.187
cytoPlot 7.780 0.98018.595
cytoPlot3d 6.353 0.79317.539
cytoPlotDatabase 6.055 0.93517.417
cytoPlotDatabase3d 6.130 0.67516.117
estimCovCellGeneral0.0410.0000.050
estimationCellBarycenter0.0040.0000.005
f1Score0.1980.0000.198
f1ScoreVoting10.085 1.19922.035
labelTransfer000
labelTransferEllipse0.0050.0040.008
optimalFlowClassification 9.534 0.71219.500
optimalFlowTemplates 5.930 0.74115.968
qdaClassification0.0010.0000.001
tclustWithInitialization2.6590.2152.881
tclust_H2.5860.2952.890
trimmedKBarycenter0.1070.0320.138
voteLabelTransfer000
w2dist0.0020.0000.002
wasserCostFunction 6.095 0.76916.724