[BioC] UseMart not working

[Amy Mikhail]

Hi Wolfgang,

Just tried both of these and I get the same error:

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

Also anytime I have put "useMart" in the argument at all it just comes up
with that error.

Any ideas?

Cheers,
Amy

---------------------------------------------------------------------------
> Hi Amy,
>
> the following works for me:
>
> mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
>
> or
>
>   mart=useMart("ensembl")
>   listDatasets(mart)
>
> (see the man page of 'useMart'). Did the syntax you used ever work?
>
> Cheers
>   Wolfgang

---------------------------------------------------------------------------
> 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
>>
>>
>> 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)
>


-------------------------------------------
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)