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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).

CHECK results for Dune on machv2

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? 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 540/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Dune 1.4.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Dune
git_branch: RELEASE_3_13
git_last_commit: b65b866
git_last_commit_date: 2021-05-19 12:50:32 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Dune
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Dune.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Dune_1.4.0.tar.gz
StartedAt: 2021-10-14 18:37:37 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:44:01 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 383.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Dune.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Dune.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Dune_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Dune.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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              11.382  0.024  11.417
intermediateMat    7.159  0.014   7.178
ARIImp             6.966  0.097   7.069
plotNMIs           6.759  0.018   6.783
ARItrend           6.662  0.042   6.709
plotPrePost        6.525  0.011   6.541
NMItrend           6.498  0.009   6.511
whenToStop         6.236  0.008   6.248
NMIImp             6.234  0.009   6.246
clusterConversion  6.158  0.024   6.190
plotARIs           6.166  0.009   6.177
functionTracking   6.096  0.012   6.114
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/Dune.Rcheck/00check.log’
for details.



Installation output

Dune.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Dune
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 ]
> 
> proc.time()
   user  system elapsed 
124.197   0.889 125.225 

Example timings

Dune.Rcheck/Dune-Ex.timings

nameusersystemelapsed
ARIImp6.9660.0977.069
ARIs0.0100.0020.011
ARItrend6.6620.0426.709
ConfusionEvolution0.0000.0010.000
ConfusionPlot0.2870.0020.289
Dune11.382 0.02411.417
NMIImp6.2340.0096.246
NMIs0.0120.0010.013
NMItrend6.4980.0096.511
clusterConversion6.1580.0246.190
functionTracking6.0960.0126.114
intermediateMat7.1590.0147.178
plotARIs6.1660.0096.177
plotNMIs6.7590.0186.783
plotPrePost6.5250.0116.541
whenToStop6.2360.0086.248