Package: GGdata

Version: 0.99.3

Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes GGdata_0.99.3.tar.gz

StartedAt: 2009-04-10 02:18:08 -0700 (Fri, 10 Apr 2009)

EndedAt: 2009-04-10 02:24:30 -0700 (Fri, 10 Apr 2009)

EllapsedTime: 382.2 seconds

RetCode: 1

Status: ERROR

CheckDir: GGdata.Rcheck

Warnings: NA

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-data-experiment/meat/GGdata.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'GGdata/DESCRIPTION' ... OK
* this is package 'GGdata' version '0.99.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GGdata' 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 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 ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... NOTE
  
  Welcome to Bioconductor
  
    Vignettes contain introductory material. To view, type
    'openVignette()'. To cite Bioconductor, see
    'citation("Biobase")' and for packages 'citation(pkgname)'.
  
Portable packages use only ASCII characters in their datasets.
* creating GGdata-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'GGdata-Ex.R' failed.
The error most likely occurred in:

> ### * fheadFits
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: fheadFits
> ### Title: forkhead box F2 gene set eQTL search result using CEU
> ### Aliases: fheadFits
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(fheadFits)
> fheadFits
filtered multi genome-wide snp screen result:
gene set used as response:
setName: (((V$FREAC2_01 | V$FREAC2_01) | V$FREAC2_01) | V$FREAC2_01) 
geneIds: OFCC1, LMO4, ..., FOSL2 (total: 192)
geneIdType: Symbol (illuminaHumanv1.db)
collectionType: Broad
  bcCategory: c3 (Motif)
  bcSubCategory:  NA
details: use 'details(object)'
there are 192 results.
the call was:
combine(x = fheadFits, y = fhm_141_192)
> fheadFits[["CPNE1"]]
filtered gwSnpScreenResult for gene  CPNE1  [probe  GI_23397697-A ]
> library(GGtools)
Loading required package: geneplotter
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

Attaching package: 'geneplotter'


	The following object(s) are masked from package:lattice :

	 panel.smoothScatter 

Loading required package: RColorBrewer
Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:Biobase :

	 annotation 


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

	 cbind,
	 rbind,
	 sapply 


Attaching package: 'Biostrings'


	The following object(s) are masked from package:graph :

	 complement 


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

	 chartr,
	 order,
	 substr,
	 substring 

Loading required package: rtracklayer
Loading required package: RCurl
Loading required package: rpart
> topSnps(fheadFits[["CPNE1"]])[[20]]
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "p.value", for signature "snp.tests.glm", "numeric"
Calls: topSnps ... topSnps -> .local -> lapply -> FUN -> p.value -> <Anonymous>
Execution halted

installing R.css in E:/biocbld/bbs-2.3-data-experiment/meat/GGdata.Rcheck


---------- Making package GGdata ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  preparing package GGdata for lazy loading
Loading required package: Biobase
Loading required package: tools

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: GGBase
Loading required package: GSEABase
Loading required package: AnnotationDbi
Loading required package: annotate
Loading required package: xtable
Loading required package: graph
Loading required package: snpMatrix
Loading required package: survival
Loading required package: splines
Loading required package: RSQLite
Loading required package: DBI
Loading required package: illuminaHumanv1.db
  installing man source files
  installing indices
Loading required package: methods
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'GGdata'
     Formats: text html latex example chm 
  fheadFits                         text    html    latex   example chm
  hmceuB36                          text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-data-experiment\meat\GGdata.Rcheck\00_pkg_src\GGdata\chm\GGdata.chm


Compile time: 0 minutes, 0 seconds
3	Topics
4	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-data-experiment\meat\GGdata.Rcheck\00_pkg_src\GGdata\chm\GGdata.chm, 17,755 bytes
Compression increased file by 8,267 bytes.
  adding MD5 sums

* DONE (GGdata)