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/download ed_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 [[alternative HTML version deleted]]