Package: GeneExpressionSignature

Version: 1.24.0

Command: rm -rf GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && mkdir GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.24.0.tar.gz >GeneExpressionSignature.Rcheck\00install.out 2>&1 && cp GeneExpressionSignature.Rcheck\00install.out GeneExpressionSignature-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneExpressionSignature.buildbin-libdir --install="check:GeneExpressionSignature-install.out" --force-multiarch --no-vignettes --timings GeneExpressionSignature_1.24.0.tar.gz

StartedAt: 2018-04-12 00:12:10 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:14:33 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 143.1 seconds

RetCode: 0

Status:  OK

CheckDir: GeneExpressionSignature.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && mkdir GeneExpressionSignature.buildbin-libdir GeneExpressionSignature.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneExpressionSignature.buildbin-libdir GeneExpressionSignature_1.24.0.tar.gz >GeneExpressionSignature.Rcheck\00install.out 2>&1 && cp GeneExpressionSignature.Rcheck\00install.out GeneExpressionSignature-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GeneExpressionSignature.buildbin-libdir --install="check:GeneExpressionSignature-install.out" --force-multiarch --no-vignettes --timings GeneExpressionSignature_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneExpressionSignature.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 'GeneExpressionSignature/DESCRIPTION' ... OK
* this is package 'GeneExpressionSignature' version '1.24.0'
* 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 'GeneExpressionSignature' 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 ... NOTE
Packages in Depends field not imported from:
  'Biobase' 'PGSEA'
  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
RankMerging: no visible global function definition for 'exprs'
RankMerging: no visible global function definition for 'as'
RankMerging: no visible global function definition for 'phenoData'
RankMerging: no visible global function definition for 'new'
ScoreGSEA : PRL.Distance: no visible global function definition for
  'exprs'
ScoreGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'exprs'
ScorePGSEA: no visible global function definition for 'new'
ScorePGSEA: no visible global function definition for 'PGSEA'
ScorePGSEA: no visible global function definition for 'pnorm'
getRLs : Check.Log: no visible global function definition for 'median'
integratePRL: no visible global function definition for 'phenoData'
integratePRL: no visible global function definition for 'exprs'
integratePRL: no visible global function definition for 'new'
integratePRL: no visible global function definition for 'as'
Undefined global functions or variables:
  PGSEA as exprs median new phenoData pnorm
Consider adding
  importFrom("methods", "as", "new")
  importFrom("stats", "median", "pnorm")
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
ScoreGSEA         7.71   0.09    7.80
SignatureDistance 7.22   0.05    7.27
ScorePGSEA        6.16   0.03    6.19
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
ScoreGSEA         7.17   0.10    7.27
SignatureDistance 6.55   0.04    6.57
ScorePGSEA        5.23   0.10    5.35
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GeneExpressionSignature.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'GeneExpressionSignature' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GeneExpressionSignature'
    finding HTML links ... done
    GeneExpressionSignature                 html  
    RankMerging                             html  
    ScoreGSEA                               html  
    ScorePGSEA                              html  
    SignatureDistance                       html  
    exampleSet                              html  
    getRLs                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GeneExpressionSignature' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneExpressionSignature' as GeneExpressionSignature_1.24.0.zip
* DONE (GeneExpressionSignature)
In R CMD INSTALL
In R CMD INSTALL