Package: GGBase

Version: 3.11.5

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings GGBase_3.11.5.tar.gz

StartedAt: 2011-02-24 19:57:24 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 20:00:55 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 210.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GGBase.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/GGBase.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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' ... WARNING
Package vignettes without corresponding PDF:


D:/biocbld/bbs-2.8-bioc/meat/GGBase.Rcheck/00_pkg_src/GGBase/inst/doc/newSNPloc.Rnw
 SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/GGBase.Rcheck/00check.log'
for details

* 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	3.04	0.06	3.14
SessionInfo-class	0	0	0
casting	0.02	0.00	0.01
featureFilter	0.84	0.06	0.94
gwSnpScreenResult-class	0	0	0
make_smlSet	0.22	0.00	0.21
multiCisTestResult-class	0	0	0
plot_EvG-methods	0.60	0.02	0.63
smlSet-class	0.17	0.01	0.27
smlSummary	0.45	0.00	0.45
snpLocs.Hs	15.50	0.19	15.69
snpLocs.Hsapiens	1.45	0.08	1.69
snpsNear	13.98	0.12	14.12