[R] trouble extracting R code from vignette using example from www.bioconductor.org

Mark W Kimpel mkimpel at iupui.edu
Mon Aug 20 19:17:29 CEST 2007

Not sure if this is an R or BioC question so will cross-post. I cannot 
extract R code from vignettes because system.file("doc", 
"my.bioc.package") returns "". I got this code directly off of 
http://www.bioconductor.org/docs/vignettes.html. A specific example 
using siggenes follows but I have tested this using multiple packages, 
including those for which I can clearly see the vignette *.Rnw in the 
doc directory.

One thing in my setup that I have customized, and which I wonder if is 
causing this problem, is that I am using a site-library as directed in 
the R install manual. I have this in my .Rprofile
.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is

In all other respects, however, my packages are working correctly.

Example and sessionInfo() follows.

thanks, Mark

 > require(siggenes)
Loading required package: siggenes
Loading required package: multtest

Latest major changes in siggenes:
Version 1.9.27: EBAM update completed. Added new vignette.
Version 1.11.7: Improved version of EBAM for categorical data.
Version 1.11.9: Added findDelta for determining the number of genes called
                 differentially expressed for a given FDR, and vice versa.

Attaching package: 'siggenes'

	The following object(s) are masked _by_ .GlobalEnv :


 > system.file("doc", "siggenes")
[1] ""
 > sessionInfo()
R version 2.6.0 Under development (unstable) (2007-08-08 r42441)


attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
  [1] siggenes_1.11.13       multtest_1.16.1        affycoretools_1.9.4
  [4] annaffy_1.9.1          KEGG_1.17.0            xtable_1.5-1
  [7] gcrma_2.9.1            matchprobes_1.9.10     biomaRt_1.11.4
[10] RCurl_0.8-3            XML_1.9-0              GOstats_2.3.9
[13] RBGL_1.13.4            GO_1.17.0              limma_2.11.10
[16] affy_1.15.7            preprocessCore_0.99.12 affyio_1.5.8
[19] Category_2.3.26        genefilter_1.15.10     survival_2.32
[22] annotate_1.15.6        AnnotationDbi_0.0.90   RSQLite_0.6-0
[25] DBI_0.2-3              Biobase_1.15.26        graph_1.15.10

loaded via a namespace (and not attached):
[1] cluster_1.11.7


Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

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