[BioC] UseMart not working

[James W. MacDonald]

Amy Mikhail wrote:
> 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

That is an odd error. AFAIK, you should just get an error saying you are 
  using the wrong name:

 > mart <- useMart("ensembl_mart_37")
Error in useMart("ensembl_mart_37") : Incorrect biomart name
 > mart <- useMart("ensembl")
 > mart
An object of class "Mart"
Slot "mysql":
[1] FALSE

Slot "connections":
list()

Slot "mysqldriver":
list()

Slot "mainTables":
list()

Slot "biomart":
[1] "ensembl"

Slot "host":
[1] "http://www.biomart.org/biomart/martservice"

Slot "dataset":
[1] ""

Slot "filters":
<environment: 01ABFEDC>

Slot "attributes":
<environment: 0219950C>

 > sessionInfo()
Version 2.3.0 Under development (unstable) (2006-02-17 r37375)
i386-pc-mingw32

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

other attached packages:
  biomaRt    RCurl      XML
"1.5.12"  "0.6-0" "0.99-6"
> 
> 
> 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

Odd. I get that to work.

 > mart <- useMart("ensembl", dataset = "agambiae_gene_ensembl")
Checking attributes and filters ... ok

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

biomaRt *can* still use RMySQL, but the default is to use RCurl because 
RMySQL can be a pain for win32 users to install.

> 
> Looking forward to any suggestions,

I'm wondering if you are behind a firewall and that is causing problems 
with RCurl. Can you get e.g., example(postForm) to work?

Best,

Jim


> 
> 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)
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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