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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:geva.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings geva_1.3.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/geva.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geva/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geva' version '1.3.0'
* 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 'geva' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
geva.quick    30.67   0.23   30.91
top.genes     15.11   0.03   15.14
geva.finalize 13.34   0.14   13.49
geva.hcluster  5.08   0.03    5.11
* 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: OK

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL geva
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'geva' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geva'
    finding HTML links ... done
    GEVACluster-class                       html  
    GEVAGroupSet-class                      html  
    GEVAGroupedSummary-class                html  
    GEVAInput-class                         html  
    GEVAQuantiles-class                     html  
    GEVAQuantilesAdjusted-class             html  
    GEVAResults-class                       html  
    GEVASummary-class                       html  
    SVAttribute-class                       html  
    SVTable-class                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-geva/00new/geva/help/svtable.html
    TypedList-class                         html  
    generics                                html  
    geva-package                            html  
    geva.cluster                            html  
    geva.dcluster                           html  
    geva.finalize                           html  
    geva.hcluster                           html  
    geva.ideal.example                      html  
    geva.input.correct                      html  
    geva.merge.input                        html  
    geva.quantiles                          html  
    geva.quick                              html  
    geva.summarize                          html  
    top.genes                               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
* DONE (geva)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(geva)
> 
> test_check("geva")
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 54 significant genes:
similar: 33
factor-specific: 7
factor-dependent: 14
Input summarized
Calculating hierarchical clustering...
Found 6 clusters
Merging scores...
Searching for dependent factors...
Searching for specific factors...
Found 60 significant genes:
factor-specific: 18
factor-dependent: 39
similar: 3
Testing plot with GEVAResults
Testing with cluster.method = 'hierarchical'
Calculating hierarchical clustering...
Found 6 clusters
Testing with cluster.method = 'density'
Calculating density clustering...
Found 3 clusters
Testing quantiles grouping
Testing with quantile.method = 'range.slice'
Testing with quantile.method = 'proportional'
Testing with quantile.method = 'density'
Testing with quantile.method = 'k.max.sd'
Testing with quantile.method = 'custom'
Testing plot with GEVACluster and GEVAQuantiles
Reading 'gevainput25485f9542e.txt' ...
Reading 'gevainput25484b9d3481.txt' ...
Reading 'gevainput2548796712d9.txt' ...
Reading 'gevainput254857062b2b.txt' ...
Reading 'gevainput254811f77baf.txt' ...
Reading 'gevainput25484df0b8c.txt' ...
Reading 'gevainput254849efc07.txt' ...
Reading 'gevainput2548467a4fe1.txt' ...
Reading 'gevainput25487f083314.txt' ...
Read 9 columns with 10000 probes
Testing with summary.method = 'mean'
Testing with summary.method = 'median'
Testing with variation.method = 'sd'
Testing with variation.method = 'var'
Testing with variation.method = 'mad'
Testing plot with GEVASummary
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  38.76    0.65   39.45