Package: GOFunction

Version: 1.26.0

Command: rm -rf GOFunction.buildbin-libdir GOFunction.Rcheck && mkdir GOFunction.buildbin-libdir GOFunction.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOFunction.buildbin-libdir GOFunction_1.26.0.tar.gz >GOFunction.Rcheck\00install.out 2>&1 && cp GOFunction.Rcheck\00install.out GOFunction-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOFunction.buildbin-libdir --install="check:GOFunction-install.out" --force-multiarch --no-vignettes --timings GOFunction_1.26.0.tar.gz

StartedAt: 2018-04-12 00:27:39 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:48:04 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 1224.4 seconds

RetCode: 0

Status:  OK

CheckDir: GOFunction.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GOFunction.buildbin-libdir GOFunction.Rcheck && mkdir GOFunction.buildbin-libdir GOFunction.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOFunction.buildbin-libdir GOFunction_1.26.0.tar.gz >GOFunction.Rcheck\00install.out 2>&1 && cp GOFunction.Rcheck\00install.out GOFunction-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOFunction.buildbin-libdir --install="check:GOFunction-install.out" --force-multiarch --no-vignettes --timings GOFunction_1.26.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOFunction.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 'GOFunction/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GOFunction' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase' 'graph' 'Rgraphviz' 'GO.db' 'AnnotationDbi' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GOFunction' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'Biobase' 'graph' 'Rgraphviz' 'GO.db' 'AnnotationDbi' 'SparseM'
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'GO.db' 'Rgraphviz' 'SparseM' 'graph' 'methods'
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  'GO.db' 'Rgraphviz' 'graph'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'GO.db' 'Rgraphviz' 'graph'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'GOFunction/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

GOFunction: no visible global function definition for 'nodes'
GOFunction: no visible global function definition for 'write.csv'
createGODAG: no visible global function definition for 'sparseM2Graph'
createGODAG: no visible global function definition for 'graph2SparseM'
enrichmentFunction: no visible global function definition for 'phyper'
enrichmentFunction: no visible global function definition for
  'p.adjust'
globalRedundancy : calculateEachTerm : calculateExtraTerm: no visible
  global function definition for 'phyper'
localRedundancy: no visible global function definition for 'phyper'
showSigNodes: no visible global function definition for
  'getDefaultAttrs'
showSigNodes: no visible global function definition for 'heat.colors'
showSigNodes: no visible global function definition for 'edgeWeights'
showSigNodes: no visible global function definition for 'nodes'
showSigNodes: no visible global function definition for 'bmp'
showSigNodes: no visible global function definition for 'plot'
showSigNodes: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  bmp dev.off edgeWeights getDefaultAttrs graph2SparseM heat.colors
  nodes p.adjust phyper plot sparseM2Graph write.csv
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "heat.colors")
  importFrom("graphics", "plot")
  importFrom("stats", "p.adjust", "phyper")
  importFrom("utils", "write.csv")
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
Examples with CPU or elapsed time > 5s
             user system elapsed
GOFunction 463.74  77.73  541.51
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
GOFunction 479.73  79.67   559.5
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOFunction.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GOFunction' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GOFunction'
    finding HTML links ... done
    GOFunction-package                      html  
    GOFunction                              html  
    createGODAG                             html  
    enrichmentFunction                      html  
    globalRedundancy                        html  
    interestGenes                           html  
    localRedundancy                         html  
    refGenes                                html  
    showSigNodes                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GOFunction' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOFunction' as GOFunction_1.26.0.zip
* DONE (GOFunction)
In R CMD INSTALL
In R CMD INSTALL