[BioC] siggenes: sam2html + affymetrix zebrafish

[Sam Hunter]

Hi, I recently updated to R2.9 and after reinstalling Bioconductor
packages have run into the following error with annotations and the
sam2html function in siggenes:

"Error in FUN(X[[1L]], ...) : unknown repository 'GB' "

After running the following code:

> library(siggenes)

> sam.out.rma = sam(abatch.rma, cl=c(0,0,0,1,1,1), n.delta=20)

> library(zebrafish.db)
> sam2html(sam.out.rma, delta.rma, "sam_out_rma.html",
+   cdfname="zebrafish")
Error in FUN(X[[1L]], ...) : unknown repository 'GB'



This code worked in previous versions and as far as I can tell from
the documentation, I'm not doing anything wrong.  Any ideas?

thanks,

Sam


> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-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=C;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   stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] zebrafishcdf_2.4.0  annotate_1.22.0     zebrafish.db_2.2.11
 [4] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.0
 [7] limma_2.18.1        affy_1.22.0         siggenes_1.18.0
[10] multtest_2.0.0      Biobase_2.4.1

loaded via a namespace (and not attached):
[1] affyio_1.12.0        MASS_7.2-47          preprocessCore_1.6.0
[4] survival_2.35-4      tools_2.9.0          xtable_1.5-5