Running example(getSequence) returns an error. See below. Juerg, UMass Med School > library(biomaRt) > example(getSequence) gtSqnc> if(interactive()){ gtSqnc+ mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") gtSqnc+ gtSqnc+ seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) gtSqnc+ show(seq) gtSqnc+ gtSqnc+ seq = getSequence(id="1939_at", type="affy_hg_u95av2", seqType="gene_flank",upstream = 20, mart = mart) gtSqnc+ show(seq) gtSqnc+ gtSqnc+ } Checking attributes ... ok Checking filters ... ok Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : Query ERROR: caught BioMart::Exception: non-BioMart die(): DBD::mysql::st execute failed: File './sequence_mart_53/hsapiens_genomic_sequence__dna_chunks__main.MYD' not found (Errcode: 27) at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Dataset/GenomicSequence/DNAAdaptor.pm line 209. > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-pc-linux-gnu locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_2.3-0 [[alternative HTML version deleted]]

Hi Juerg, We appear to be having some server issues at the moment which is why you got this error. Hopefully we will be able to resume normal service soon. Many apologies for any inconvenience. Regards, Rhoda On 29 Apr 2009, at 15:23, Straubhaar, Juerg wrote: > > Running example(getSequence) returns an error. See below. > > Juerg, UMass Med School > > >> library(biomaRt) >> example(getSequence) > > gtSqnc> if(interactive()){ > gtSqnc+ mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") > gtSqnc+ > gtSqnc+ seq = getSequence(id="BRCA1", type="hgnc_symbol", > seqType="peptide", mart = mart) > gtSqnc+ show(seq) > gtSqnc+ > gtSqnc+ seq = getSequence(id="1939_at", type="affy_hg_u95av2", > seqType="gene_flank",upstream = 20, mart = mart) > gtSqnc+ show(seq) > gtSqnc+ > gtSqnc+ } > Checking attributes ... ok > Checking filters ... ok > Error in getBM(c(seqType, type), filters = type, values = id, mart = > mart, : > Query ERROR: caught BioMart::Exception: non-BioMart die(): > DBD::mysql::st execute failed: File './sequence_mart_53/ > hsapiens_genomic_sequence__dna_chunks__main.MYD' not found (Errcode: > 27) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ > Dataset/GenomicSequence/DNAAdaptor.pm line 209. > >> sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-pc-linux-gnu > > locale: > C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-1 XML_2.3-0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.