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This page was generated on 2022-01-21 13:06:15 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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 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 550/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Dune 1.6.0  (landing page)
Hector Roux de Bezieux
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/Dune
git_branch: RELEASE_3_14
git_last_commit: e79ce4b
git_last_commit_date: 2021-10-26 12:58:07 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Dune.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Dune_1.6.0.tar.gz
StartedAt: 2022-01-20 19:11:24 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 19:18:41 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 437.0 seconds
RetCode: 0
Status:   OK  
CheckDir: Dune.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Dune.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Dune_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Dune.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.6.0'
* 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 6.02   0.02    6.05
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
     user system elapsed
Dune 7.04   0.02    7.07
* 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-3.14-bioc/meat/Dune.Rcheck/00check.log'
for details.



Installation output

Dune.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Dune_1.6.0.tar.gz && rm -rf Dune.buildbin-libdir && mkdir Dune.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Dune.buildbin-libdir Dune_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Dune_1.6.0.zip && rm Dune_1.6.0.tar.gz Dune_1.6.0.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
 28 3895k   28 1110k    0     0  2318k      0  0:00:01 --:--:--  0:00:01 2317k
100 3895k  100 3895k    0     0  3548k      0  0:00:01  0:00:01 --:--:-- 3551k

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_1.6.0.zip
* DONE (Dune)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Dune' successfully unpacked and MD5 sums checked

Tests output

Dune.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  75.29    1.23   76.51 

Dune.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  69.50    0.70   70.17 

Example timings

Dune.Rcheck/examples_i386/Dune-Ex.timings

nameusersystemelapsed
ARIImp3.550.193.75
ARIs0.000.020.02
ARItrend4.460.014.46
ConfusionEvolution000
ConfusionPlot0.180.000.19
Dune6.020.026.05
NMIImp3.020.003.01
NMIs0.010.000.02
NMItrend3.250.003.25
clusterConversion2.990.002.98
functionTracking3.200.003.21
intermediateMat3.090.003.09
plotARIs3.380.003.38
plotNMIs3.360.003.36
plotPrePost3.20.03.2
whenToStop3.500.193.69

Dune.Rcheck/examples_x64/Dune-Ex.timings

nameusersystemelapsed
ARIImp4.720.094.86
ARIs000
ARItrend4.750.004.75
ConfusionEvolution000
ConfusionPlot0.210.010.22
Dune7.040.027.07
NMIImp3.360.003.36
NMIs0.020.000.02
NMItrend3.720.003.72
clusterConversion3.430.003.44
functionTracking3.580.003.57
intermediateMat3.550.003.55
plotARIs3.690.003.69
plotNMIs3.930.003.94
plotPrePost4.300.004.29
whenToStop3.910.003.91