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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:npGSEA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings npGSEA_1.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/npGSEA.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 'npGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'npGSEA' version '1.31.0'
* 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 'npGSEA' 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 ... NOTE
.prepXYZ: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
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 files in 'vignettes' ... OK
* checking examples ... 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/npGSEA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL npGSEA
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'npGSEA' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
** help
*** installing help indices
  converting help for package 'npGSEA'
    finding HTML links ... done
    DF-methods                              html  
    alphaValue-methods                      html  
    betaHats-methods                        html  
    betaStat-methods                        html  
    betaValue-methods                       html  
    chiSqStat-methods                       html  
    geneSetName-methods                     html  
    getIncidence                            html  
    npGSEA                                  html  
    npGSEAPlot-methods                      html  
    npGSEAResultBeta-class                  html  
    npGSEAResultBetaCollection-class        html  
    npGSEAResultChiSq-class                 html  
    npGSEAResultChiSqCollection-class       html  
    npGSEAResultNorm-class                  html  
    npGSEAResultNormCollection-class        html  
    pLeft-methods                           html  
    pRight-methods                          html  
    pTwoSided-methods                       html  
    pValues-methods                         html  
    show-methods                            html  
    sigmaSq-methods                         html  
    stat-methods                            html  
    xSet-methods                            html  
    zStat-methods                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
** testing if installed package can be loaded from final location
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
** testing if installed package keeps a record of temporary installation path
* DONE (npGSEA)
Making 'packages.html' ... done