Package: categoryCompare

Version: 1.22.0

Command: rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.22.0.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.22.0.tar.gz

StartedAt: 2018-04-11 22:43:25 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:48:06 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 281.0 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf categoryCompare.buildbin-libdir categoryCompare.Rcheck && mkdir categoryCompare.buildbin-libdir categoryCompare.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.22.0.tar.gz >categoryCompare.Rcheck\00install.out 2>&1 && cp categoryCompare.Rcheck\00install.out categoryCompare-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/categoryCompare.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 'categoryCompare/DESCRIPTION' ... OK
* this is package 'categoryCompare' version '1.22.0'
* 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 'categoryCompare' 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
.annotateOutData: no visible global function definition for
  'write.table'
.ccCompare: no visible global function definition for 'new'
.ccCompareGO: no visible binding for global variable 'GOBPPARENTS'
.ccCompareGO: no visible binding for global variable 'GOMFPARENTS'
.ccCompareGO: no visible binding for global variable 'GOCCPARENTS'
.ccCompareGO: no visible binding for global variable 'GOTERM'
.ccCompareGO: no visible binding for global variable 'Term'
.ccCompareGO: no visible global function definition for 'new'
.ccCompareGeneric: no visible global function definition for 'new'
.ccCompareKEGG: no visible global function definition for 'getGeneric'
.ccCompareKEGG: no visible binding for global variable
  'KEGGPATHID2NAME'
.ccCompareKEGG: no visible global function definition for 'new'
.colorData: no visible global function definition for 'colors'
.compData: no visible global function definition for 'combn'
.cwReload: possible error in existing.CytoscapeWindow(windowName,
  rpcPort = rpcPort, host = host, copy.graph.from.cytoscape.to.R =
  FALSE): unused argument (rpcPort = rpcPort)
.extractRes: no visible global function definition for 'getGeneric'
.getDesc : <anonymous>: no visible global function definition for
  'Term'
.goEnrich: no visible global function definition for 'new'
.headerOutData: no visible global function definition for 'write.table'
.initGraphAtts: no visible global function definition for 'as'
.keggEnrich: no visible global function definition for 'new'
.mergeLists: no visible global function definition for 'new'
createGraph: no visible global function definition for 'new'
createGraph2: no visible global function definition for 'new'
hyperGTestCC: no visible global function definition for
  '.valueClassTest'
hyperGTestCat: no visible global function definition for 'new'
[,GENccEnrichResult-ANY-ANY-ANY: no visible global function definition
  for 'new'
[,ccEnrichResult-ANY-ANY-ANY: no visible global function definition for
  'new'
ccEnrich,ccGeneList: no visible global function definition for 'new'
initialize,ccGeneList: no visible global function definition for
  'callNextMethod'
initialize,ccOptions: no visible global function definition for
  'callNextMethod'
show,HyperGResultCC: no visible global function definition for
  'description'
show,ccCompareCollection: no visible global function definition for
  'show'
show,ccCompareResult: no visible global function definition for 'show'
show,ccEnrichCollection: no visible global function definition for
  'show'
show,ccEnrichResult: no visible global function definition for 'show'
Undefined global functions or variables:
  .valueClassTest GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM
  KEGGPATHID2NAME Term as callNextMethod colors combn description
  getGeneric new show write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("methods", ".valueClassTest", "as", "callNextMethod",
             "getGeneric", "new", "show")
  importFrom("utils", "combn", "write.table")
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 ... 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
Examples with CPU or elapsed time > 5s
                user system elapsed
ccOptions-class 0.04      0   13.25
** 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/categoryCompare.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'categoryCompare' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'categoryCompare'
    finding HTML links ... done
    GENccEnrichResult-class                 html  
    finding level-2 HTML links ... done

    HyperGParamsCC-class                    html  
    HyperGResultCC-class                    html  
    breakEdges-methods                      html  
    categoryCompare-package                 html  
    ccCompare                               html  
    ccCompareCollection-class               html  
    ccCompareGeneric-methods                html  
    ccCompareResult-class                   html  
    ccData                                  html  
    ccEnrich                                html  
    ccEnrichCollection-class                html  
    ccEnrichResult-class                    html  
    ccGeneList-class                        html  
    ccOptions-class                         html  
    ccOutCyt-methods                        html  
    ccSigList-class                         html  
    cwReload-methods                        html  
    cytOutData-methods                      html  
    cytOutNodes-methods                     html  
    fdr                                     html  
    getGeneSymbol                           html  
    graphType-methods                       html  
    hyperGTestCC                            html  
    listNames                               html  
    mergeLists-methods                      html  
    mergedData-class                        html  
    minCount                                html  
    minNodes                                html  
    pvalueType                              html  
    resetColors-methods                     html  
    show-methods                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'categoryCompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.22.0.zip
* DONE (categoryCompare)
In R CMD INSTALL
In R CMD INSTALL