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 : list.siggenes > system.file("doc", "siggenes") [1] "" > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-08 r42441) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C 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 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)