Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:52 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 Dune on merida1


To the developers/maintainers of the Dune package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Dune.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 570/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Dune 1.8.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Dune
git_branch: RELEASE_3_15
git_last_commit: 9bc5007
git_last_commit_date: 2022-04-26 12:03:32 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Dune
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Dune.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Dune_1.8.0.tar.gz
StartedAt: 2022-10-19 01:55:38 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:04:56 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 557.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Dune.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Dune.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Dune_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/Dune.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Dune/DESCRIPTION’ ... OK
* this is package ‘Dune’ version ‘1.8.0’
* 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 ‘Dune’ 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.metricTrend: no visible binding for global variable ‘.’
.metricTrend: no visible binding for global variable ‘step’
.metricTrend: no visible binding for global variable ‘change’
.metricTrend: no visible binding for global variable ‘value’
.plotMetric: no visible binding for global variable ‘label2’
.plotMetric: no visible binding for global variable ‘metric’
.plotMetric: no visible binding for global variable ‘label1’
ARIImp : f: no visible binding for global variable ‘cells’
ConfusionEvolution : <anonymous>: no visible binding for global
  variable ‘Freq’
ConfusionEvolution : <anonymous>: no visible binding for global
  variable ‘total_x’
ConfusionEvolution : <anonymous>: no visible binding for global
  variable ‘total_y’
ConfusionEvolution: no visible binding for global variable ‘overlap’
ConfusionEvolution: no visible binding for global variable ‘Freq’
ConfusionEvolution: no visible binding for global variable ‘step’
ConfusionPlot: no visible binding for global variable ‘Freq’
ConfusionPlot: no visible binding for global variable ‘total_x’
ConfusionPlot: no visible binding for global variable ‘total_y’
ConfusionPlot: no visible binding for global variable ‘overlap’
NMIImp : f: no visible binding for global variable ‘cells’
intermediateMat: no visible binding for global variable ‘cells’
plotPrePost: no visible binding for global variable ‘Nb’
Undefined global functions or variables:
  . Freq Nb cells change label1 label2 metric overlap step total_x
  total_y value
Consider adding
  importFrom("stats", "step")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Dune              16.780  0.053  16.893
ARItrend          10.465  0.036  10.541
ARIImp             9.664  0.116   9.826
NMItrend           9.532  0.024   9.577
plotPrePost        9.386  0.024   9.423
plotNMIs           9.333  0.023   9.372
plotARIs           9.319  0.017   9.348
functionTracking   9.166  0.021   9.199
clusterConversion  9.109  0.016   9.147
NMIImp             8.735  0.016   8.764
intermediateMat    8.700  0.018   8.729
whenToStop         8.489  0.015   8.517
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.15-bioc/meat/Dune.Rcheck/00check.log’
for details.



Installation output

Dune.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Dune
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘Dune’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** 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 (Dune)

Tests output

Dune.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Dune)
Dune now uses the Normalized Mutual Informationinstead of the adjusted Rand Index. You can restore the old option bysetting metric'ARI' in the Dune function.
> 
> test_check("Dune")
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 452 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 452 ]
> 
> proc.time()
   user  system elapsed 
177.068   1.177 178.619 

Example timings

Dune.Rcheck/Dune-Ex.timings

nameusersystemelapsed
ARIImp9.6640.1169.826
ARIs0.0120.0010.013
ARItrend10.465 0.03610.541
ConfusionEvolution000
ConfusionPlot0.4960.0040.501
Dune16.780 0.05316.893
NMIImp8.7350.0168.764
NMIs0.0120.0010.013
NMItrend9.5320.0249.577
clusterConversion9.1090.0169.147
functionTracking9.1660.0219.199
intermediateMat8.7000.0188.729
plotARIs9.3190.0179.348
plotNMIs9.3330.0239.372
plotPrePost9.3860.0249.423
whenToStop8.4890.0158.517