[BioC] Is there a place to download GenomicFeatures'

[Wenzhang Wang]

Dear all, 

When I am trying to run the follwing codes , the R is dead with no response:
either

> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene")
or 
> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="knownGene")

And

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936  LC_CTYPE=Chinese_People's Republic of China.936    LC_MONETARY=Chinese_People's Republic of China.936
[4] LC_NUMERIC=C                                       LC_TIME=Chinese_People's Republic of China.936    

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

other attached packages:
[1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2   IRanges_1.8.7        

loaded via a namespace (and not attached):
[1] Biobase_2.10.0     biomaRt_2.6.0      Biostrings_2.18.2  BSgenome_1.18.2    DBI_0.2-5          RCurl_1.5-0.1      RSQLite_0.9-4      rtracklayer_1.10.6
[9] XML_3.2-0.2    

Wenzhang Wang

************************************
State Key Lab of Genetic Engineering
School of Lifescince
Fudan University
************************************
Shanghai,China
************************************
> Message: 1
> Date: Wed, 15 Dec 2010 05:31:33 -0800
> From: Michael Lawrence <lawrence.michael at gene.com>
> To: Fabrice Tourre <fabrice.ciup at gmail.com>
> Cc: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] Is there a place to download GenomicFeatures'
> sqlite from ensembl.
> Message-ID:
> <AANLkTinyB-cEbCh8WHRAg+mT6GXj-THo2QVpjGS_drmt at mail.gmail.com>
> Content-Type: text/plain
> 
> On Wed, Dec 15, 2010 at 2:03 AM, Fabrice Tourre <fabrice.ciup at gmail.com>wrote:
> 
>> Dear all,
>> I am trying to make TranscriptDb Object. First I used
>> makeTranscriptDbFromUCSC, it is no problem. The command is this:
>> library("GenomicFeatures")
>> hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
>> "knownGene")
>>
>> But I also want to look the anotation from ensembl, some isoform
>> defined different in ucsc and ensembl. I run this comand, it took two
>> days and not finished.
>> library("GenomicFeatures")
>> hgensembl<-
>> makeTranscriptDbFromBiomart(biomart="ensembl",dataset="hsapiens_gene_ensembl")
>>
>> So I think is there a place to download the sqlite file directtly by
>> http or ftp?
>>
>>
> No, but that sounds like a bug. I would mention though that UCSC has the
> Ensembl gene predictions, under the "ensGene" table.
> 
> Thanks.
>>
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>