Package: categoryCompare

Version: 1.28.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings categoryCompare_1.28.0.tar.gz

StartedAt: 2019-10-16 02:26:15 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:30:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 255.8 seconds

RetCode: 0

Status:  OK

CheckDir: categoryCompare.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:categoryCompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings categoryCompare_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/categoryCompare.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.28.0'
* 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
* 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 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
.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'
.ccCompareKEGG: no visible binding for global variable
  'KEGGPATHID2NAME'
.cytOutNodes: ... may be used in an incorrect context:
  exportImage(filename = fileName, type = "png", network = cwObj, ...)
.getDesc : : no visible global function definition for
  'Term'
show,HyperGResultCC: no visible global function definition for
  'description'
Undefined global functions or variables:
  GOBPPARENTS GOCCPARENTS GOMFPARENTS GOTERM KEGGPATHID2NAME Term
  description
* 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 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-3.9-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/categoryCompare_1.28.0.tar.gz && rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=categoryCompare.buildbin-libdir categoryCompare_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL categoryCompare_1.28.0.zip && rm categoryCompare_1.28.0.tar.gz categoryCompare_1.28.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 1767k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1767k  100 1767k    0     0  5577k      0 --:--:-- --:--:-- --:--:-- 5684k

install for i386

* installing *source* package 'categoryCompare' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: ... may be used in an incorrect context 
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'categoryCompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.28.0.zip
* DONE (categoryCompare)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'categoryCompare' successfully unpacked and MD5 sums checked