[BioC] UseMart not working
Amy Mikhail
a.mikhail at abdn.ac.uk
Fri Mar 31 18:30:51 CEST 2006
Hi Jim,
If I try that I get the same error:
> library(biomaRt)
Loading required package: XML
Loading required package: RCurl
> example(postForm)
pstFrm>
getURL("http://www.google.com/search?hl=en&lr=&ie=ISO-8859-1&q=RCurl&btnG=Search")
Error in curlPerform(curl = curl, .opts = opts) :
couldn't connect to host
So would that be a firewall? If so what should I do to get round it?
Cheers,
Amy
---------------------------------------------------------------------------
> 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)
>>
>> _______________________________________________
>> Bioconductor mailing list
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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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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-------------------------------------------
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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