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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RcisTarget.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RcisTarget_1.15.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/RcisTarget.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 'RcisTarget/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RcisTarget' version '1.15.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'RcisTarget' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'feather'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
convertToTargetRegions: no visible global function definition for
  'isClass'
convertToTargetRegions: no visible global function definition for
  'findOverlaps'
convertToTargetRegions: no visible global function definition for
  'pintersect'
convertToTargetRegions: no visible global function definition for
  'subjectHits'
convertToTargetRegions: no visible global function definition for
  'width'
convertToTargetRegions: no visible global function definition for
  'elementMetadata'
Undefined global functions or variables:
  elementMetadata findOverlaps isClass pintersect subjectHits width
Consider adding
  importFrom("methods", "isClass")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in documentation object 'getDbRegionsLoc'
  'indexCol'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
addSignificantGenes     14.06   3.08   17.17
addMotifAnnotation      13.44   0.75   14.19
aucScores-class          8.59   1.00    9.60
getMotifAnnotation       7.44   1.12    8.54
reRank                   7.02   0.73    7.75
rankingRcisTarget-class  6.90   0.77    7.67
* 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: 1 WARNING, 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/RcisTarget.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RcisTarget
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RcisTarget' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RcisTarget'
    finding HTML links ... done
    RcisTarget                              html  
    finding level-2 HTML links ... done

    addLogo                                 html  
    addMotifAnnotation                      html  
    addSignificantGenes                     html  
    aucScores-class                         html  
    calcAUC                                 html  
    convertToTargetRegions                  html  
    dbRegionsLoc                            html  
    getDbRegionsLoc                         html  
    getMotifAnnotation                      html  
    importAnnotations                       html  
    importRankings                          html  
    motifAnnotations                        html  
    rankingRcisTarget-class                 html  
    reRank                                  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 (RcisTarget)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'DMCHMM' 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(RcisTarget)
> 
> test_check("RcisTarget")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
  32.60    6.45   52.03