Hi, I can no longer connect to the uniprot biomart as below; I imagine it has something to do with the Biomart 0.8 release, but could not find any information. Would you be able to offer any suggestions, or know of any planned outages? Many thanks in advance, Dana > uniProt <- useMart("unimart") Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "", : no lines available in input -- output of sessionInfo(): > sessionInfo() R version 2.14.2 (2012-02-29) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.10.0 BiocInstaller_1.2.1 rcom_2.2-3.1.1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] fortunes_1.5-0 RCurl_1.91-1.1 tools_2.14.2 XML_3.95-0.1 -- Sent via the guest posting facility at bioconductor.org.

Hi Dana, Thank you for reporting this issue. It is not related to a BioMart 0.8 release but the unimart has no BioMart version assigned to on the BioMart web service and the biomaRt function useMart currently requires that information. I let the BioMart developers know that unimart does not have a BioMart version. In addition, I also updated the biomaRt code so it can deal with this type of event as it is not a critical parameter for biomaRt to do queries. This updated biomaRt package should become available shortly from http://bioconductor.org/packages/2.12/bioc/html/biomaRt.html You'll need biomaRt version 2.15.1 to get this fix. Cheers, Steffen On Tue, Mar 5, 2013 at 8:17 PM, Dana Pascovici [guest] < guest@bioconductor.org> wrote: > > Hi, > > I can no longer connect to the uniprot biomart as below; I imagine it has > something to do with the Biomart 0.8 release, but could not find any > information. Would you be able to offer any suggestions, or know of any > planned outages? > > Many thanks in advance, > Dana > > > uniProt <- useMart("unimart") > Error in read.table(con, sep = "\t", header = FALSE, quote = "", > comment.char = "", : > no lines available in input > > > -- output of sessionInfo(): > > > sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 > LC_MONETARY=English_Australia.1252 > [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] biomaRt_2.10.0 BiocInstaller_1.2.1 rcom_2.2-3.1.1 > rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] fortunes_1.5-0 RCurl_1.91-1.1 tools_2.14.2 XML_3.95-0.1 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]