Package: GGBase

Version: 3.10.0

Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings GGBase_3.10.0.tar.gz

StartedAt: 2011-04-07 07:14:50 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 07:18:13 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 202.1 seconds

RetCode: 0

Status:  OK

CheckDir: GGBase.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/GGBase.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.10.0'
* 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
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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

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	1.94	0.05	2.01
SessionInfo-class	0	0	0
casting	0.01	0.00	0.02
featureFilter	0.70	0.05	0.94
gwSnpScreenResult-class	0.02	0.00	0.01
make_smlSet	0.39	0.01	0.41
multiCisTestResult-class	0	0	0
plot_EvG-methods	0.58	0.03	0.73
smlSet-class	0.19	0.00	0.19
smlSummary	0.5	0.0	0.5
snpLocs.Hs	15.00	0.16	15.17
snpLocs.Hsapiens	1.38	0.05	1.50
snpsNear	16.08	0.14	16.42