Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:03 -0400 (Fri, 15 Oct 2021).

CHECK results for Dune on tokay2

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: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Dune.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Dune_1.4.0.tar.gz
StartedAt: 2021-10-14 22:34:52 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:42:26 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 454.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Dune.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Dune.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Dune_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Dune.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
Dune 6.59   0.02    6.61
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
Dune 6.67      0    6.68
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/Dune.Rcheck/00check.log'
for details.



Installation output

Dune.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Dune_1.4.0.tar.gz && rm -rf Dune.buildbin-libdir && mkdir Dune.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Dune.buildbin-libdir Dune_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Dune_1.4.0.zip && rm Dune_1.4.0.tar.gz Dune_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 68 3900k   68 2686k    0     0  2823k      0  0:00:01 --:--:--  0:00:01 2822k
100 3900k  100 3900k    0     0  3206k      0  0:00:01  0:00:01 --:--:-- 3207k

install for i386

* 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
  converting help for package 'Dune'
    finding HTML links ... done
    ARIImp                                  html  
    ARIs                                    html  
    ARItrend                                html  
    finding level-2 HTML links ... done

    ConfusionEvolution                      html  
    ConfusionPlot                           html  
    Dune                                    html  
    NMIImp                                  html  
    NMIs                                    html  
    NMItrend                                html  
    clusMat                                 html  
    clusterConversion                       html  
    dot-adjustedRandIndex                   html  
    functionTracking                        html  
    intermediateMat                         html  
    nuclei                                  html  
    plotARIs                                html  
    plotNMIs                                html  
    plotPrePost                             html  
    whenToStop                              html  
** 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

install for x64

* installing *source* package 'Dune' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Dune' as Dune_1.4.0.zip
* DONE (Dune)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Dune' successfully unpacked and MD5 sums checked

Tests output

Dune.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  68.79    0.60   69.40 

Dune.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  76.71    0.43   77.14 

Example timings

Dune.Rcheck/examples_i386/Dune-Ex.timings

nameusersystemelapsed
ARIImp3.660.063.75
ARIs0.020.000.02
ARItrend4.030.004.03
ConfusionEvolution000
ConfusionPlot0.220.000.22
Dune6.590.026.61
NMIImp3.160.223.37
NMIs000
NMItrend3.400.003.41
clusterConversion3.130.013.14
functionTracking3.400.023.42
intermediateMat3.380.013.39
plotARIs3.440.003.43
plotNMIs3.470.003.47
plotPrePost3.510.003.51
whenToStop3.340.003.35

Dune.Rcheck/examples_x64/Dune-Ex.timings

nameusersystemelapsed
ARIImp4.160.044.20
ARIs000
ARItrend4.600.024.61
ConfusionEvolution000
ConfusionPlot0.250.000.25
Dune6.670.006.68
NMIImp3.390.003.39
NMIs000
NMItrend3.440.003.43
clusterConversion3.230.003.24
functionTracking3.410.003.40
intermediateMat3.360.013.38
plotARIs3.560.003.56
plotNMIs3.700.003.71
plotPrePost3.910.003.90
whenToStop4.720.054.77