Package: GGBase

Version: 3.8.0

Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings GGBase_3.8.0.tar.gz

StartedAt: 2010-10-04 17:04:30 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:07:39 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 189.1 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/GGBase.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.8.0'
* 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 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
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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

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

Welcome to Bioconductor

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

Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: graph
Loading required package: survival
Loading required package: splines
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	1.13	0.02	1.16
SessionInfo-class	0.01	0.00	0.01
casting	0	0	0
featureFilter	0.85	0.01	0.96
gwSnpScreenResult-class	0	0	0
make_smlSet	0.3	0.0	0.3
multiCisTestResult-class	0	0	0
plot_EvG-methods	0.73	0.00	0.94
smlSet-class	0.38	0.00	0.37
smlSummary	0.43	0.00	0.44
snpLocs.Hs	13.61	0.14	13.75
snpsNear	12.61	0.27	12.87