Package: GGBase

Version: 3.11.5

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGBase_3.11.5.tar.gz

StartedAt: 2011-02-24 19:33:09 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:37:48 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 279.3 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/GGBase.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGBase/DESCRIPTION’ ... OK
* this is package ‘GGBase’ version ‘3.11.5’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GGBase’ can be installed ... 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
isCis: no visible global function definition for ‘lookUp’
snpsNear: no visible global function definition for ‘geneIdType’
snpsNear: no visible global function definition for ‘geneIds’
snpLocs.Hs,chrnum-missing: no visible binding for global variable
  ‘hsSnpLocs’
snpLocs.Hs,chrnum-rsid: no visible binding for global variable
  ‘hsSnpLocs’
snpLocs.Hs,missing-rsid: no visible binding for global variable
  ‘hsSnpLocs’
snpLocs.Hs,rsid-ANY: no visible binding for global variable ‘hsSnpLocs’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘GGBase’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loading required package: DBI
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GGBase)

name	user	system	elapsed
MAFfilter	3.085	0.142	3.259
SessionInfo-class	0.002	0.000	0.002
casting	0.009	0.000	0.009
featureFilter	1.081	0.056	1.166
gwSnpScreenResult-class	0.004	0.001	0.004
make_smlSet	0.320	0.005	0.325
multiCisTestResult-class	0.001	0.001	0.001
plot_EvG-methods	0.828	0.063	0.901
smlSet-class	0.214	0.013	0.244
smlSummary	0.246	0.033	0.284
snpLocs.Hs	21.474	0.614	22.265
snpLocs.Hsapiens	1.654	0.103	1.789
snpsNear	21.090	0.748	22.036