[BioC] Problem using biomaRt with local database
Alessandro Bruselles
a.bruselles at gmail.com
Wed Jan 17 10:51:31 CET 2007
> Alessandro Bruselles <a.bruselles at ...> writes:
Hi,
I'm having some problems when trying to use biomaRt with a local install
database;
I've downloaded and installed locally the ensembl biomart database
version ensembl_mart_42,
(ftp://ftp.ensembl.org/pub/release-42/mart_42/data/mysql/ensembl_mart_42)
I created all the tables and populated them...
I get the following error when trying to connect to it with useMart:
> library(biomaRt)
Carico il pacchetto richiesto: XML
Carico il pacchetto richiesto: RCurl
> ensembl=useMart("ensembl_mart_42", dataset="hsapiens_gene_ensembl",
host="pendragon.bio.uniroma2.it", user="brusel", password="*******",
local = TRUE, mysql = TRUE)
Carico il pacchetto richiesto: RMySQL
Carico il pacchetto richiesto: DBI
Errore in `dimnames<-.data.frame`(`*tmp*`, value = list(character(0),
c("name", :
'dimnames' fornita per i ldata frame non valida
I'm using R 2.4.0 and biomaRt 1.8.1
Any help will be very very appreciated
Thanks.
For any of you having the same problem,
I solved the problem using the developmental version (1.9.14).
__________________________
Alessandro Bruselles
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