Multiple platform build/check report for BioC 3.13 - CHECK results for Dune on tokay2

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

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### Running command:
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###   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
###
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* 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.

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###
### 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
###
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  % 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


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


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

name	user	system	elapsed
ARIImp	3.66	0.06	3.75
ARIs	0.02	0.00	0.02
ARItrend	4.03	0.00	4.03
ConfusionEvolution	0	0	0
ConfusionPlot	0.22	0.00	0.22
Dune	6.59	0.02	6.61
NMIImp	3.16	0.22	3.37
NMIs	0	0	0
NMItrend	3.40	0.00	3.41
clusterConversion	3.13	0.01	3.14
functionTracking	3.40	0.02	3.42
intermediateMat	3.38	0.01	3.39
plotARIs	3.44	0.00	3.43
plotNMIs	3.47	0.00	3.47
plotPrePost	3.51	0.00	3.51
whenToStop	3.34	0.00	3.35

name	user	system	elapsed
ARIImp	4.16	0.04	4.20
ARIs	0	0	0
ARItrend	4.60	0.02	4.61
ConfusionEvolution	0	0	0
ConfusionPlot	0.25	0.00	0.25
Dune	6.67	0.00	6.68
NMIImp	3.39	0.00	3.39
NMIs	0	0	0
NMItrend	3.44	0.00	3.43
clusterConversion	3.23	0.00	3.24
functionTracking	3.41	0.00	3.40
intermediateMat	3.36	0.01	3.38
plotARIs	3.56	0.00	3.56
plotNMIs	3.70	0.00	3.71
plotPrePost	3.91	0.00	3.90
whenToStop	4.72	0.05	4.77

CHECK results for Dune on tokay2

Summary

Command output

Installation output

Tests output

Example timings