Hi there! I've run into a problem with biomaRt and the biomart on ensembl.org. When I try to load the Ensembl Genes 67 I run into trouble. Until a month a go it did load like it should. The strange thing is when I use the same code but change the host from "may2012.archive.ensembl.org" to "www.ensembl.org" it loads without any trouble. Other archived hosts also do not load, only the most recent version seems to work. I cannot use the most recent version, because it is based on mm10. In the script below I first show that the most recent Ensembl Genes 69 does load and last that the Ensembl Genes 67 does not. Does anyone have any idea what is going on and can anyone suggest a possible solution? Thank you in Advance, Johan Brandsma Erasmus MC, Rotterdam, The Netherlands. > library(biomaRt) > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.10.0 rkward_0.5.6 loaded via a namespace (and not attached): [1] RCurl_1.95-3 tools_2.14.1 XML_3.95-0.1 > listMarts("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 69 2 ENSEMBL_MART_SNP Ensembl Variation 69 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 69 4 ENSEMBL_MART_VEGA Vega 49 5 REACTOME REACTOME (CSHL US) 6 pride PRIDE (EBI UK) > mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="www.ensembl.org") > listMarts("ENSEMBL_MART_ENSEMBL", host="may2012.archive.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 67 2 ENSEMBL_MART_SNP Ensembl Variation 67 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 67 4 ENSEMBL_MART_VEGA Vega 47 5 REACTOME REACTOME (CSHL US) 6 pride PRIDE (EBI UK) > mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="may2012.archive.ensembl.org") Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "", : no lines available in input Calls: useMart -> bmVersion -> read.table

Hi Johan, Thanks for reporting this. It looks like this is caused by an error in a configuration of the Ensembl side which they need to fix, I will contact them about this issue. Here's a quick workaround to make your queries work again until Ensembl fixes the configuration file: mart <- useMart("ENSEMBL_MART_ENSEMBL", host="may2012.archive.ensembl.org") mart@host="http://may2012.archive.ensembl.org:80/biomart/martservice" mart = useDataset("mmusculus_gene_ensembl",mart=mart) This should enable you to do your queries on the may2012 archive. Here's a more detailed report on what is exactly wrong in the current Ensembl configuration file and how to find this: listMarts(host="may2012.archive.ensembl.org",verbose=TRUE,includeHosts =TRUE) gives Attempting web service request: http://may2012.archive.ensembl.org:80/biomart/martservice?type=registr y&requestid=biomaRt $biomart [1] "ENSEMBL_MART_ENSEMBL" "ENSEMBL_MART_SNP" "ENSEMBL_MART_FUNCGEN" [4] "ENSEMBL_MART_VEGA" "REACTOME" "pride" $version [1] "Ensembl Genes 67" "Ensembl Variation 67" "Ensembl Regulation 67" [4] "Vega 47" "REACTOME (CSHL US)" "PRIDE (EBI UK)" $host [1] "archive.ensembl.org" "archive.ensembl.org" "archive.ensembl.org" [4] "archive.ensembl.org" "reactome.oicr.on.ca" "www.ebi.ac.uk" Notice that the host is changed from may2012.archive.ensembl.org to just archive.ensembl.org so this is pointing to the wrong URL making the useMart trying to connect to archive.ensembl.org instead of may2012.archive.ensembl.org. Cheers, Steffen On Wed, Jan 9, 2013 at 6:31 AM, J.H. Brandsma <j.h.brandsma@erasmusmc.nl>wrote: > mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host=" > may2012.archive.ensembl.org") > [[alternative HTML version deleted]]