BioC 2.12: CHECK report for dyebias on moscato2

Package: dyebias

Version: 1.17.0

Command: rm -rf dyebias.buildbin-libdir && mkdir dyebias.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=dyebias.buildbin-libdir dyebias_1.17.0.tar.gz >dyebias-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=dyebias.buildbin-libdir --install="check:dyebias-install.out" --force-multiarch --no-vignettes --timings dyebias_1.17.0.tar.gz && mv dyebias.buildbin-libdir/* dyebias.Rcheck/ && rmdir dyebias.buildbin-libdir

StartedAt: 2013-03-25 02:07:58 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:10:16 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 138.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: dyebias.Rcheck

Warnings: 1

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/dyebias.Rcheck'
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'dyebias/DESCRIPTION' ... OK
* this is package 'dyebias' version '1.17.0'
* 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 'dyebias' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 for unstated 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
dyebias.apply.correction: no visible global function definition for
  'maR<-'
dyebias.apply.correction: no visible global function definition for
  'maG<-'
* checking Rd files ... WARNING
checkRd: (3) dyebias.application.subset.Rd:16-20: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.apply.correction.Rd:10-19: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.boxplot.Rd:17-23: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.estimate.iGSDBs.Rd:12-14: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.rgplot.Rd:17-32: \synopsis will be removed in R 3.1.0
checkRd: (3) dyebias.trendplot.Rd:22-38: \synopsis will be removed in R 3.1.0
* 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [41s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
dyebias.rgplot             8.31   0.06    8.37
dyebias.apply.correction   7.84   0.11    7.96
dyebias.application.subset 7.24   0.05    7.66
dyebias.boxplot            6.84   0.06    6.89
dyebias.trendplot          5.85   0.05    5.90
** running examples for arch 'x64' ... [42s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
dyebias.rgplot             7.86   0.05    7.91
dyebias.application.subset 7.44   0.09    7.57
dyebias.boxplot            7.41   0.03    7.44
dyebias.trendplot          7.20   0.06    7.25
dyebias.apply.correction   7.03   0.00    7.04
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/dyebias.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'dyebias' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'dyebias-vignette.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'dyebias' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dyebias' as dyebias_1.17.0.zip
* DONE (dyebias)

Summary

Command output