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This page was generated on 2024-07-19 17:37 -0400 (Fri, 19 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 617/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Dune 1.16.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/Dune
git_branch: RELEASE_3_19
git_last_commit: 91192ae
git_last_commit_date: 2024-04-30 11:22:00 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for Dune on nebbiolo1

To the developers/maintainers of the Dune package:
- 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 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: Dune
Version: 1.16.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Dune.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Dune_1.16.0.tar.gz
StartedAt: 2024-07-17 23:12:05 -0400 (Wed, 17 Jul 2024)
EndedAt: 2024-07-17 23:17:01 -0400 (Wed, 17 Jul 2024)
EllapsedTime: 295.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Dune.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Dune.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Dune_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Dune.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Dune/DESCRIPTION’ ... OK
* this is package ‘Dune’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... NOTE
Found export directive that requires package ‘methods’:
  ‘exportMethods’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* 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 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 whether startup messages can be suppressed ... 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 5.695  0.054   5.749
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Dune.Rcheck/00check.log’
for details.


Installation output

Dune.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Dune
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 2 | SKIP 0 | PASS 452 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 452 ]
> 
> proc.time()
   user  system elapsed 
 66.234   1.991  68.217 

Example timings

Dune.Rcheck/Dune-Ex.timings

nameusersystemelapsed
ARIImp3.1810.1643.345
ARIs0.0040.0000.004
ARItrend3.5430.0243.567
ConfusionEvolution0.0000.0000.001
ConfusionPlot0.3570.0120.369
Dune5.6950.0545.749
NMIImp2.9800.0052.986
NMIs0.0010.0040.006
NMItrend3.2440.0163.261
clusterConversion3.0530.0163.069
functionTracking3.2640.0323.295
intermediateMat3.0640.0043.067
plotARIs3.3290.0163.345
plotNMIs3.2720.0003.272
plotPrePost3.2120.0163.229
whenToStop3.0590.0443.103