[BioC] UseMart not working

[Amy Mikhail]

Dear list,

I have downloaded R 2.3 and bioconductor 1.8 devel but can't get the
useMart function to work... is this the connection error Wolfgang was
referring to earlier?  Here's my code:

library(biomaRt)
Loading required package: XML
Loading required package: RCurl
> mart <- useMart("ensembl_mart_37")
Error in curlPerform(curl = curl, .opts = opts) :
        couldn't connect to host


If I try it the old way, this is what I get:

 mart <- martConnect()

###############################################

This function will go out of use soon, please adapt by using the 'useMart'
function instead.

###############################################

Loading required package: RMySQL
Loading required package: DBI
connected to:  ensembl_mart_37
Warning message:
DLL attempted to change FPU control word from 8001f to 9001f

Nb. I have found posts in the archive with the same warning message as
above (relating to the control word) but did not find any suggestions as
to what to do about it.

Should I be worrying about this warning?

I can chose the species as follows:

> listDatasets(mart)
                      dataset    version
1       agambiae_gene_ensembl     AgamP3
2     amellifera_gene_ensembl    AMEL2.0
3        btaurus_gene_ensembl   Btau_2.0
4    cfamiliaris_gene_ensembl    BROADD1
5  cintestinalis_gene_ensembl       JGI2
6  dmelanogaster_gene_ensembl      BDGP4
7         drerio_gene_ensembl     ZFISH5
8      frubripes_gene_ensembl      FUGU4
9        ggallus_gene_ensembl    WASHUC1
10      hsapiens_gene_ensembl     NCBI35
11    mdomestica_gene_ensembl    BROADO2
12      mmulatta_gene_ensembl   MMUL_0_1
13     mmusculus_gene_ensembl    NCBIM34
14  ptroglodytes_gene_ensembl    CHIMP1A
15   rnorvegicus_gene_ensembl    RGSC3.4
16   scerevisiae_gene_ensembl       SGD1
17 tnigroviridis_gene_ensembl TETRAODON7
18   xtropicalis_gene_ensembl       JGI4
19      celegans_gene_ensembl     CEL150
> mart <- useDataset(dataset = "agambiae_gene_ensembl", mart = mart)
Reading database configuration of: agambiae_gene_ensembl
Checking main tables ... ok
Checking attributes and filters ... ok

On the other hand if I try specifying the species with useMart this is
what happens:

> mart <- useMart("ensembl", dataset = "agambiae_gene_ensembl")
Error in curlPerform(curl = curl, .opts = opts) :
        couldn't connect to host

So it seems like RCurl is not working and biomaRt is still using RMySQL? 
Why would useMart not work?

Looking forward to any suggestions,

Regards,
Amy

P.s. appologies if this should have been posted to the devel list - I just
suppose that if everyone is using the devel version of biomaRt it would be
appropriate here.

> sessionInfo()
Version 2.3.0 alpha (2006-03-27 r37590)
i386-pc-mingw32

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

other attached packages:
  RMySQL      DBI  biomaRt    RCurl      XML
 "0.5-6" "0.1-10" "1.5.12"  "0.6-0" "0.99-6"



-------------------------------------------
Amy Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Scotland
Email: a.mikhail at abdn.ac.uk
Phone: 00-44-1224-272880 (lab)