[BioC] makeTranscriptDbFromBiomart - chrominfo failure

[Stefanie Tauber]

Hi,

I get the following warning:

library(GenomicFeatures)

myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito"))

Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Warning message:
In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) :
  chromosome lengths and circularity flags are not available for this
TranscriptDb object


> sessionInfo()
R Under development (unstable) (2013-02-27 r62087)
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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomicFeatures_1.11.16 AnnotationDbi_1.21.14   Biobase_2.19.3
[4] GenomicRanges_1.11.37   IRanges_1.17.37         BiocGenerics_0.5.6

loaded via a namespace (and not attached):
 [1] biomaRt_2.15.1      Biostrings_2.27.11  bitops_1.0-5
 [4] BSgenome_1.27.1     DBI_0.2-5           RCurl_1.95-4.1
 [7] Rsamtools_1.11.22   RSQLite_0.11.2      rtracklayer_1.19.10
[10] stats4_3.0.0        tools_3.0.0         XML_3.95-0.2
[13] zlibbioc_1.5.0



Is this an issue of GenomicFeatures or Ensembl?
Best,
Stefanie