Package: cnvGSA

Version: 1.2.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings cnvGSA_1.2.0.tar.gz

StartedAt: 2013-03-25 00:22:30 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:24:03 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 92.6 seconds

RetCode: 0

Status:  OK

CheckDir: cnvGSA.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/cnvGSA.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cnvGSA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cnvGSA’ version ‘1.2.0’
* 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 ‘cnvGSA’ 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 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
f.add_binned_bhfdr: no visible binding for global variable ‘GsSize’
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
cnvGSAFisher 52.631  0.488  53.523
* 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/cnvGSA.Rcheck/00check.log’
for details.

* installing *source* package ‘cnvGSA’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘cnvGSA’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘cnvGSA-vignette.Rnw’ 
** testing if installed package can be loaded

* DONE (cnvGSA)

name	user	system	elapsed
CnvGSAInput-class	0	0	0
CnvGSAOutput-class	1.756	0.088	1.964
cnvGSAFisher	52.631	0.488	53.523
cnvGSAexportBurdenStats	1.316	0.056	1.618
getCnvGenes	3.776	0.132	4.268
readGMT	1.356	0.016	1.395
readGVF	1.556	0.000	1.605
readParamsRFile	0.004	0.000	0.013
summary-methods	1.112	0.056	1.183