Dear bioconductors,

When trying to update the genome table for prokaryotes (lproks) I get an 
error message (see below), while for leuks (eukaryotes), everything 
seems to work just fine.

Has anyone encountered a similar problem?

Many thanks in advance,
Shinichi

 > source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://bioconductor.org
Change using chooseBioCmirror().
 > biocLite("genomes")
Using R version 2.13.0, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:
[1] "genomes"
Please wait...

Installing package(s) into 
'/Library/Frameworks/R.framework/Versions/2.13/Resources/library'
(as 'lib' is unspecified)
Warning in install.packages :
   cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
   cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
   unable to access index for repository 
http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.13
trying URL 
'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/contrib/2.13/genomes_1.8.0.tgz'
Content type 'application/x-gzip' length 627302 bytes (612 Kb)
opened URL
==================================================
downloaded 612 Kb

The downloaded packages are in
     
/var/folders/2D/2DSSSKLKH+ejMNgPcdYJzU++I5w/-Tmp-//RtmpvJR8k0/downloaded_packages
 > sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

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

other attached packages:
[1] genomes_1.8.0   lattice_0.19-26

loaded via a namespace (and not attached):
[1] XML_3.4-0    grid_2.13.0  tools_2.13.0

 > require(genomes)
 > data(lproks)
 > dim(lproks)
[1] 5439   32
 > update(lproks)
Error in update.genomes(lproks) :
   No update attribute found. 'lproks' is a subset of lproks.
 > traceback()
3: stop("No update attribute found. ", sQuote(substitute(object)),
        " is a subset of ", attr(object, "subsetof"), ".")
2: update.genomes(lproks)
1: update(lproks)
 > dim(lproks)
[1] 5439   32
 > data(leuks)
 > dim(leuks)
[1] 1090   20
 > update(leuks)
leuks has been successfully updated
130 new project IDs added
14 old project IDs removed
 > dim(leuks)
[1] 1206   20

-- 
SHINICHI SUNAGAWA
EMBL - Structural and Computational Biology
Meyerhofstraße 1, 69117 Heidelberg, Germany
http://sequoia.ucmerced.edu/Shini/index.php

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