Package: gene2pathway

Version: 2.2.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch gene2pathway_2.2.0.tar.gz

StartedAt: 2011-10-20 14:23:54 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:26:35 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 160.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gene2pathway.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/gene2pathway.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gene2pathway/DESCRIPTION' ... OK
* this is package 'gene2pathway' version '2.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: doMC
* checking if this is a source package ... OK
* checking whether package 'gene2pathway' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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
gene2pathway: no visible global function definition for 'registerDoMC'
gene2pathway: no visible global function definition for '%dopar%'
gene2pathway: no visible global function definition for 'foreach'
gene2pathway: no visible binding for global variable 'g'
gene2pathway: no visible binding for global variable 'p'
gene2pathway.signaltrans: no visible global function definition for
  'registerDoMC'
gene2pathway.signaltrans: no visible global function definition for
  '%dopar%'
gene2pathway.signaltrans: no visible global function definition for
  'foreach'
gene2pathway.signaltrans: no visible binding for global variable 'p'
getKEGGHierarchy: no visible binding for global variable 'keggOrthDF'
predict.gene2pathway : testallBag: no visible global function
  definition for '%dopar%'
predict.gene2pathway : testallBag: no visible global function
  definition for 'foreach'
predict.gene2pathway : testallBag: no visible binding for global
  variable 'm'
predict.gene2pathway: no visible global function definition for
  'registerDoMC'
test.overrepresentation: no visible global function definition for
  'registerDoMC'
test.overrepresentation: no visible global function definition for
  '%dopar%'
test.overrepresentation: no visible global function definition for
  'foreach'
test.overrepresentation: no visible binding for global variable 'p'
trainallBag: no visible global function definition for 'registerDoMC'
trainallBag: no visible global function definition for '%dopar%'
trainallBag: no visible global function definition for 'foreach'
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   gene2pathway.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/gene2pathway.Rcheck/00check.log'
for details

* installing *source* package 'gene2pathway' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (gene2pathway)

name	user	system	elapsed
gene2pathway	0	0	0
gene2pathway.signaltrans	0	0	0
getComponents	0	0	0
retrain	0	0	0
retrain.signaltrans	0	0	0
run.crossvalidation	0	0	0