Package: gage

Version: 2.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gage_2.4.0.tar.gz

StartedAt: 2012-03-24 01:09:37 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:11:25 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 108.6 seconds

RetCode: 0

Status:  OK

CheckDir: gage.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/gage.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '2.4.0'
* 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 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 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
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 ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
              old_size new_size compress
  egSymb.rda     260Kb    143Kb       xz
  go.gs.rda       93Kb     55Kb       xz
  kegg.gs.rda     28Kb     20Kb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... 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

* installing *source* package 'gage' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'gage.Rnw' 
** testing if installed package can be loaded

* DONE (gage)

name	user	system	elapsed
eg2sym	2.522	0.461	3.028
egSymb	2.219	0.449	2.698
essGene	0.740	0.120	0.869
esset.grp	3.622	0.269	4.040
gage	4.702	0.686	5.734
gageComp	2.192	0.368	2.846
gagePipe	2.243	0.380	3.022
geneData	0.638	0.115	0.792
gs.tTest	0.517	0.087	0.633
gse16873	0.745	0.151	0.974
heter.gage	1.558	0.233	1.824
kegg.gs	2.143	0.412	2.828
readExpData	0.015	0.002	0.019
readList	0.174	0.021	0.214
sigGeneSet	1.147	0.181	1.456