Package: gage

Version: 2.1.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gage_2.1.0.tar.gz

StartedAt: 2011-03-17 16:18:43 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:19:56 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 72.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: gage.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/gage.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gage' version '2.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'gage' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
deComp: no visible global function definition for 'annot.db'
eg2sym: no visible binding for global variable 'egSymb'
esset.grp: no visible global function definition for 'biocLite'
esset.grp: no visible global function definition for 'make.graph'
sym2eg: no visible binding for global variable 'egSymb'
* 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 ... WARNING
Files not of a type allowed in a 'data' directory:
  c2.demo.gmt gse16873.demo
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  '/Users/biocbuild/bbs-2.8-bioc/meat/gage.Rcheck/00check.log'
for details

* installing *source* package 'gage' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (gage)

name	user	system	elapsed
eg2sym	1.465	0.095	1.561
egSymb	1.404	0.103	1.506
essGene	0.561	0.031	0.592
esset.grp	3.032	0.059	3.092
gage	2.947	0.142	3.089
gageComp	1.539	0.107	1.654
gagePipe	1.549	0.110	1.660
geneData	0.475	0.032	0.506
gs.tTest	0.399	0.026	0.426
gse16873	0.534	0.029	0.563
heter.gage	1.166	0.070	1.235
kegg.gs	1.512	0.130	1.642
readExpData	0.015	0.001	0.016
readList	0.112	0.009	0.121
sigGeneSet	0.765	0.047	0.811