BioC 2.13: CHECK report for gage on zin1

Package: gage

Version: 2.12.3

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings gage_2.12.3.tar.gz

StartedAt: 2014-04-05 01:15:09 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:17:01 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 112.5 seconds

RetCode: 0

Status:  OK

CheckDir: gage.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/gage.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.12.3’
* 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 ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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 ‘make.graph’
kegg.gsets: no visible binding for global variable ‘khier’
kegg.species.code: no visible binding for global variable ‘korg’
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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RNA-seqWorkflow.Rnw’, ‘dataPrep.Rnw’, ‘gage.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [17s/22s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	1.300	0.016	1.316
egSymb	1.020	0.000	1.022
essGene	0.324	0.004	0.326
esset.grp	1.936	0.028	1.963
gage	2.408	0.012	2.427
gageComp	1.024	0.008	1.218
gagePipe	1.024	0.008	1.078
geneData	0.268	0.008	0.288
gs.tTest	0.244	0.000	0.243
gse16873	0.456	0.004	0.464
heter.gage	0.716	0.004	0.720
kegg.gs	1.104	0.000	1.106
kegg.gsets	0.717	0.004	4.709
readExpData	0.012	0.000	0.011
readList	0.128	0.004	0.133
sigGeneSet	0.512	0.004	0.553