Package: Roleswitch

Version: 1.16.0

Command: rm -rf Roleswitch.buildbin-libdir Roleswitch.Rcheck && mkdir Roleswitch.buildbin-libdir Roleswitch.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Roleswitch.buildbin-libdir Roleswitch_1.16.0.tar.gz >Roleswitch.Rcheck\00install.out 2>&1 && cp Roleswitch.Rcheck\00install.out Roleswitch-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Roleswitch.buildbin-libdir --install="check:Roleswitch-install.out" --force-multiarch --no-vignettes --timings Roleswitch_1.16.0.tar.gz

StartedAt: 2018-04-12 02:48:53 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:53:34 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 280.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Roleswitch.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf Roleswitch.buildbin-libdir Roleswitch.Rcheck && mkdir Roleswitch.buildbin-libdir Roleswitch.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Roleswitch.buildbin-libdir Roleswitch_1.16.0.tar.gz >Roleswitch.Rcheck\00install.out 2>&1 && cp Roleswitch.Rcheck\00install.out Roleswitch-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Roleswitch.buildbin-libdir --install="check:Roleswitch-install.out" --force-multiarch --no-vignettes --timings Roleswitch_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Roleswitch.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 'Roleswitch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Roleswitch' version '1.16.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'pracma' 'reshape' 'plotrix' 'microRNA' 'biomaRt' 'Biostrings'
  'Biobase' 'DBI'
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 'Roleswitch' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiWUZfC/R.INSTALL39583e7c4d4d/Roleswitch/man/roleswitch.Rd:42: missing file link 'eSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiWUZfC/R.INSTALL39583e7c4d4d/Roleswitch/man/roleswitch.Rd:42: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiWUZfC/R.INSTALL39583e7c4d4d/Roleswitch/man/roleswitch.Rd:45: missing file link 'eSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Roleswitch.Rcheck/00install.out' for details.
* 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
diagnosticPlot: no visible global function definition for 'par'
diagnosticPlot: no visible global function definition for 'axis'
diagnosticPlot: no visible global function definition for 'plot'
getSeedMatrix: no visible global function definition for 'data'
getTranscriptIDwithLongest3UTR: no visible global function definition
  for 'aggregate'
roleswitch: no visible global function definition for 'aggregate'
Undefined global functions or variables:
  aggregate axis data par plot
Consider adding
  importFrom("graphics", "axis", "par", "plot")
  importFrom("stats", "aggregate")
  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
getSeedMatrix 4.34   0.29   70.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
getSeedMatrix 5.23   0.36   70.59
* 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, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/Roleswitch.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Roleswitch' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'Roleswitch'
    finding HTML links ... done
    Roleswitch-package                      html  
    diagnosticPlot                          html  
    getSeedMatrix                           html  
    roleswitch                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiWUZfC/R.INSTALL39583e7c4d4d/Roleswitch/man/roleswitch.Rd:42: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiWUZfC/R.INSTALL39583e7c4d4d/Roleswitch/man/roleswitch.Rd:42: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpiWUZfC/R.INSTALL39583e7c4d4d/Roleswitch/man/roleswitch.Rd:45: missing file link 'eSet'
    tcga_gbm_testdata                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Roleswitch' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Roleswitch' as Roleswitch_1.16.0.zip
* DONE (Roleswitch)
In R CMD INSTALL
In R CMD INSTALL