BioC 2.12: CHECK report for gage on george2

Package: gage

Version: 2.10.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings gage_2.10.0.tar.gz

StartedAt: 2013-10-09 01:52:07 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 01:53:39 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 92.0 seconds

RetCode: 0

Status:  OK

CheckDir: gage.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/gage.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gage’ version ‘2.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘gage’ can be installed ... [4s/4s] 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
* 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
gagePipe: warning in objects(pat = "[.]p$"): partial argument match of
  'pat' to 'pattern'
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 ‘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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [28s/28s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/gage.Rcheck/00check.log’
for details.

* installing *source* package ‘gage’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gage)

name	user	system	elapsed
eg2sym	3.704	0.076	3.785
egSymb	2.836	0.008	2.868
essGene	0.812	0.004	0.817
esset.grp	3.416	0.028	3.448
gage	4.605	0.020	4.734
gageComp	1.852	0.016	1.945
gagePipe	2.140	0.024	2.164
geneData	0.636	0.008	0.643
gs.tTest	0.424	0.004	0.427
gse16873	0.844	0.008	0.867
heter.gage	1.464	0.012	1.473
kegg.gs	1.776	0.004	1.781
readExpData	0.024	0.000	0.023
readList	0.224	0.004	0.227
sigGeneSet	1.052	0.012	1.066