[Bioc-devel] biomaR + CosmicMart fails in devel

[Paul Shannon]

Hoping to use Sanger's COSMIC database ("Catalogue Of Somatic Mutations In Cancer") via biomaRt, I ran into some trouble: 'CosmicMart' connections usually fail.  A few lines to replicate the problem are included below.  SessionInfo output follows.  

 - Paul
  

library(biomaRt)
tbl <- listMarts()
dim(tbl)
colnames(tbl)

  # make sure the marts are recognized, spelled properly
tbl[grep('ensembl',    tbl$biomart),]   # 1
tbl[grep('CosmicMart', tbl$biomart),]   # 34

  # this works quickly, reliably
ensembl.mart<-useMart('ensembl')

  # this fails intermittently, and more often than not
cosmic.mart <- useMart('CosmicMart')
  # Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "",  :
  # no lines available in input

  # when it works, this becomes possible
tbl.datasets <- listDatasets(cosmic.mart)
grep('COSMIC', tbl.datasets$dataset, value=TRUE)

  # if we get this far, this next command has not yet worked for me
useMart("CosmicMart",dataset="COSMIC61")
  # Error in read.table(con, sep = "\t", header = FALSE, quote = "", comment.char = "",  :
  # no lines available in input

  # 'ensembl' works fine every time
ensembl.mart <-useMart('ensembl')
tbl.datasets <- listDatasets(ensembl.mart)
grep('hsapiens', tbl.datasets$dataset, value=TRUE)
human.mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")



sessionInfo()
  # R Under development (unstable) (2012-12-01 r61188)
  # Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
  #
  # locale:
  # [1] en_US.utf-8/en_US.utf-8/en_US.utf-8/C/en_US.utf-8/en_US.utf-8
  #
  # attached base packages:
  # [1] stats     graphics  grDevices utils     datasets  methods   base
  #
  # other attached packages:
  # [1] biomaRt_2.15.0      BiocInstaller_1.9.5
  #
  # loaded via a namespace (and not attached):
  # [1] compiler_2.16.0 RCurl_1.91-1    tools_2.16.0    XML_3.9-4