BioC 2.12: CHECK report for geNetClassifier on moscato2

Package: geNetClassifier

Version: 1.0.2

Command: rm -rf geNetClassifier.buildbin-libdir && mkdir geNetClassifier.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geNetClassifier.buildbin-libdir geNetClassifier_1.0.2.tar.gz >geNetClassifier-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=geNetClassifier.buildbin-libdir --install="check:geNetClassifier-install.out" --force-multiarch --no-vignettes --timings geNetClassifier_1.0.2.tar.gz && mv geNetClassifier.buildbin-libdir/* geNetClassifier.Rcheck/ && rmdir geNetClassifier.buildbin-libdir

StartedAt: 2013-10-09 02:15:55 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 02:19:19 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 203.9 seconds

RetCode: 0

Status:  OK

CheckDir: geNetClassifier.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/geNetClassifier.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' version '1.0.2'
* 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 'geNetClassifier' can be installed ... OK
* checking installed package size ... OK
* checking package 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 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
calculateGenesRanking: no visible global function definition for
  'brewer.pal'
plotErrorNumGenes: no visible global function definition for
  'brewer.pal'
plotNetwork: no visible global function definition for
  'graph.data.frame'
plotNetwork: no visible global function definition for 'vcount'
plotNetwork: no visible global function definition for
  'layout.fruchterman.reingold'
plotNetwork: no visible global function definition for
  'get.vertex.attribute'
plotNetwork: no visible global function definition for
  'get.edge.attribute'
plotNetwork: no visible global function definition for 'ecount'
plotNetwork: no visible global function definition for 'tkplot'
* 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 examples ...
** running examples for arch 'i386' ... [44s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
plot.GeNetClassifierReturn 8.75   0.19    8.95
plotNetwork                6.29   0.11    6.41
** running examples for arch 'x64' ... [46s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
plot.GeNetClassifierReturn 8.05   0.25    8.88
plotNetwork                5.80   0.13    5.94
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [3s]
 [3s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [3s]
 [3s] OK
* 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

NOTE: There was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/geNetClassifier.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'geNetClassifier' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'geNetClassifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geNetClassifier' as geNetClassifier_1.0.2.zip
* DONE (geNetClassifier)