Hi Robert, The release 63 archive registry has now been fixed. Regards Rhoda On 20 Oct 2011, at 15:30, Rhoda Kinsella wrote: > Hi Robert > It looks like the registry information for that archive is not > correct. I will forward this bug to our web team and let you know > when it has been fixed. Apologies for any inconvenience. > Regards > Rhoda > > On 20 Oct 2011, at 15:17, Robert Castelo wrote: > >> Dear Rhoda, >> >> i was unsuccessfully trying to connect to the human ensembl genes >> dataset of the archived Ensembl release 63 and i just wondered >> whether >> this problem has anything to do with your annoucement below or >> whether >> i'm doing anything wrong. here is the code: >> >> ## following the example of page 15 of the biomaRt vignette >> ## adapted to the release 63 >> library(biomaRt) >> listMarts(host="jun2011.archive.ensembl.org") >> biomart version >> 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 63 >> 2 ENSEMBL_MART_SNP Ensembl Variation 63 >> 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 63 >> 4 ENSEMBL_MART_VEGA Vega 43 >> 5 REACTOME Reactome >> 6 pride PRIDE (EBI UK) >> ensembl63 <- useMart(host="jun2011.archive.ensembl.org", >> biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") >> Error in useDataset(mart = mart, dataset = dataset, verbose = >> verbose) : >> The given dataset: hsapiens_gene_ensembl , is not valid. Correct >> dataset names can be obtained with the listDatasets function. >> sessionInfo() >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets >> methods >> [8] base >> >> other attached packages: >> [1] Biobase_2.12.1 biomaRt_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.5-0 XML_3.4-0 >> >> >> thanks! >> robert. >> >> >> On Thu, 2011-10-20 at 13:11 +0100, Rhoda Kinsella wrote: >>> Dear all >>> >>> All Sanger-based Ensembl websites and related services will go >>> offline >>> around midday tomorrow, Friday 21st October until the evening of >>> Sunday 23rd October. This will affect the main Ensembl website, >>> archives, Pre! and beta. Mirror sites (US and Asia) will remain >>> available, but Sanger-dependent services, including BLAST and user >>> accounts, will be disabled. >>> >>> For Ensembl BioMart users this will mean that you will not be able >>> to >>> query the Ensembl marts from www.biomart.org or www.ensembl.org. You >>> will be able to access release 64 Ensembl marts via the mirrors at: >>> >>> http://uswest.ensembl.org/index.html >>> http://useast.ensembl.org/index.html >>> http://asia.ensembl.org/index.html >>> >>> >>> We hope that the datacentre restart will go smoothly and the sites >>> will be back online by Monday morning at the latest - if you find a >>> site is not working as expected by noon UK time, please let us >>> know so >>> that we can investigate. >>> >>> Please accept our apologies for any inconvenience caused. >>> >>> >>> Regards >>> Rhoda >>> >>> >>> Rhoda Kinsella Ph.D. >>> Ensembl Production Project Leader, >>> European Bioinformatics Institute (EMBL-EBI), >>> Wellcome Trust Genome Campus, >>> Hinxton >>> Cambridge CB10 1SD, >>> UK. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > Rhoda Kinsella Ph.D. > Ensembl Production Project Leader, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. > Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]