Multiple platform build/check report for BioC 3.6 - CHECK report for RTopper on tokay1

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### Running command:
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###   rm -rf RTopper.buildbin-libdir RTopper.Rcheck && mkdir RTopper.buildbin-libdir RTopper.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RTopper.buildbin-libdir RTopper_1.24.0.tar.gz >RTopper.Rcheck\00install.out 2>&1 && cp RTopper.Rcheck\00install.out RTopper-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RTopper.buildbin-libdir --install="check:RTopper-install.out" --force-multiarch --no-vignettes --timings RTopper_1.24.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTopper.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 'RTopper/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTopper' 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 'RTopper' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsHTrxI/R.INSTALL392c5c1d6e12/RTopper/man/fgsList.Rd:37: missing file link 'org.Hs.eg'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsHTrxI/R.INSTALL392c5c1d6e12/RTopper/man/fgsList.Rd:41: missing file link 'GO'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsHTrxI/R.INSTALL392c5c1d6e12/RTopper/man/fgsList.Rd:42: missing file link 'KEGG'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTopper.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'limma'
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
computeScore: no visible global function definition for 'glm'
computeScore: no visible global function definition for 'binomial'
computeScore: no visible global function definition for 'AIC'
convertToDr: no visible binding for global variable 'data'
myMean : medianM: no visible binding for global variable 'median'
Undefined global functions or variables:
  AIC binomial data glm median
Consider adding
  importFrom("stats", "AIC", "binomial", "glm", "median")
  importFrom("utils", "data")
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
computeDrStat 10.89   0.03   10.92
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
computeDrStat 14.22   0.05   14.28
* 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/RTopper.Rcheck/00check.log'
for details.


install for i386

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

    combineGSE                              html  
    computeDrStat                           html  
    convertToDr                             html  
    dat                                     html  
    fgsList                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsHTrxI/R.INSTALL392c5c1d6e12/RTopper/man/fgsList.Rd:37: missing file link 'org.Hs.eg'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsHTrxI/R.INSTALL392c5c1d6e12/RTopper/man/fgsList.Rd:41: missing file link 'GO'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpsHTrxI/R.INSTALL392c5c1d6e12/RTopper/man/fgsList.Rd:42: missing file link 'KEGG'
    gseResultsSep                           html  
    intScores                               html  
    pheno                                   html  
    runBatchGSE                             html  
    sepScores                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RTopper' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTopper' as RTopper_1.24.0.zip
* DONE (RTopper)
In R CMD INSTALL
In R CMD INSTALL

CHECK report for RTopper on tokay1

Summary

Command output

Installation output

Tests output

Example timings