GGdata 0.99.3
VJ Carey
| Snapshot Date: 2009-04-10 00:03:00 -0700 (Fri, 10 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/GGdata | | Last Changed Rev: 745 / Revision: 760 | | Last Changed Date: 2008-12-14 21:34:35 -0800 (Sun, 14 Dec 2008) |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | [ ERROR ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | ERROR | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | ERROR | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/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 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 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 *source* package 'GGdata' ...
** R
** data
** inst
** preparing package 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
** help
>>> Building/Updating help pages for package 'GGdata'
Formats: text html latex example
fheadFits text html latex example
hmceuB36 text html latex example
** building package indices ...
Loading required package: methods
* DONE (GGdata)