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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gep2pep.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gep2pep_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/gep2pep.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 'gep2pep/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gep2pep' version '1.15.0'
* 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 'gep2pep' 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 files in 'vignettes' ... OK
* checking examples ... OK
* 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:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL gep2pep
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'gep2pep' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gep2pep'
    finding HTML links ... done
    CategorizedCollection-class             html  
    CategorizedCollection                   html  
    CondSEA                                 html  
    PathSEA                                 html  
    addSingleGeneSets                       html  
    as.CategorizedCollection                html  
    buildPEPs                               html  
    checkRepository                         html  
    clearCache                              html  
    createMergedRepository                  html  
    createRepository                        html  
    exportSEA                               html  
    gene2pathways                           html  
    gep2pep-package                         html  
    getCollections                          html  
    getDetails                              html  
    getResults                              html  
    importFromRawMode                       html  
    importMSigDB.xml                        html  
    loadCollection                          html  
    loadESmatrix                            html  
    loadPVmatrix                            html  
    loadSampleGEP                           html  
    loadSamplePWS                           html  
    makeCollectionIDs                       html  
    openRepository                          html  
    setId2setName                           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 (gep2pep)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'proBatch' is missing or broken
 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(gep2pep)
> 
> test_check("gep2pep")
Chunk 1 of 2, 519 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 664 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 538 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 690 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 548 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 684 bytes (current file size: 16.3 Kb)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 154 ]

== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 154 ]
> 
> proc.time()
   user  system elapsed 
   9.50    1.48   15.00