Package: staRank

Version: 1.20.0

Command: rm -rf staRank.buildbin-libdir staRank.Rcheck && mkdir staRank.buildbin-libdir staRank.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=staRank.buildbin-libdir staRank_1.20.0.tar.gz >staRank.Rcheck\00install.out 2>&1 && cp staRank.Rcheck\00install.out staRank-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=staRank.buildbin-libdir --install="check:staRank-install.out" --force-multiarch --no-vignettes --timings staRank_1.20.0.tar.gz

StartedAt: 2018-04-12 03:25:48 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:29:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 224.8 seconds

RetCode: 0

Status:  OK

CheckDir: staRank.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf staRank.buildbin-libdir staRank.Rcheck && mkdir staRank.buildbin-libdir staRank.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=staRank.buildbin-libdir staRank_1.20.0.tar.gz >staRank.Rcheck\00install.out 2>&1 && cp staRank.Rcheck\00install.out staRank-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=staRank.buildbin-libdir --install="check:staRank-install.out" --force-multiarch --no-vignettes --timings staRank_1.20.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/staRank.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'staRank/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'staRank' version '1.20.0'
* 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 'staRank' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
OPIScore : <anonymous>: no visible global function definition for
  'phyper'
aggregRank : <anonymous>: no visible global function definition for
  'median'
mwTest2samp: no visible global function definition for 'pwilcox'
mwTest2samp: no visible global function definition for 'pnorm'
show,RankSummary: no visible global function definition for 'head'
stabilityRanking,cellHTS: no visible global function definition for
  'channelNames'
stabilityRanking,cellHTS: no visible global function definition for
  'sampleNames'
stabilityRanking,cellHTS: no visible global function definition for
  'featureNames'
stabilityRanking,numeric: no visible global function definition for
  'avrgRank<-'
stabilityRanking,numeric: no visible global function definition for
  'cor'
summaryStats,list : <anonymous>: no visible global function definition
  for 'median'
summaryStats,list : <anonymous>: no visible global function definition
  for 't.test'
summaryStats,matrix : <anonymous>: no visible global function
  definition for 'median'
summaryStats,matrix : <anonymous>: no visible global function
  definition for 't.test'
Undefined global functions or variables:
  avrgRank<- channelNames cor featureNames head median phyper pnorm
  pwilcox sampleNames t.test
Consider adding
  importFrom("stats", "cor", "median", "phyper", "pnorm", "pwilcox",
             "t.test")
  importFrom("utils", "head")
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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/staRank.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'staRank' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'staRank'
    finding HTML links ... done
    Pi-methods                              html  
    RankSummary-class                       html  
    aggregRank                              html  
    avrgRank-methods                        html  
    baseRank-methods                        html  
    dataFormatRSA                           html  
    getRankmatrix                           html  
    getSampleScores-methods                 html  
    getStability                            html  
    method-methods                          html  
    mwTest2samp                             html  
    rankCor-methods                         html  
    runRSA                                  html  
    salmonellaInfection                     html  
    salmonellaStability                     html  
    show-methods                            html  
    staRank-package                         html  
    stabRank-methods                        html  
    stabilityRanking-methods                html  
    stableSetSize-methods                   html  
    summary-methods                         html  
    summaryStats-methods                    html  
    uniqueRSARanking                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'staRank' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'staRank' as staRank_1.20.0.zip
* DONE (staRank)
In R CMD INSTALL
In R CMD INSTALL