[BioC] UseMart not working
HFL
lee at molgen.mpg.de
Sat Apr 1 18:24:46 CEST 2006
Dear Amy,
I had the same problem with the biomaRt package before.
But now it works fine with the option, *mysql = TRUE*, as Jim suggested.
=================================
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
# Error in curlPerform(curl = curl, .opts = opts) :
# Failed writing body
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl", mysql=T)
# connected to: ensembl
# Reading database configuration of: hsapiens_gene_ensembl
# Checking main tables ... ok
# Checking attributes and filters ... ok
mart <- useMart("ensembl_mart_37")
# Error in curlPerform(curl = curl, .opts = opts) :
# Failed writing body
mart <- useMart("ensembl_mart_37", mysql=T)
# connected to: ensembl_mart_37
================================
Regards,
Ho
>Amy Mikhail wrote:
>
>
>
>>> 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?
>>
>>
>
> I don't know if it is a firewall or not - I don't have a problem with
> ours, so I have no experience. However, try adding --internet2 to the
> target for your R shortcut, and see if you can run the postForm()
> example. If you really are having firewall problems, that may help (I
> know it is supposed to help with download.packages(), so it may well
> help here).
>
> If it doesn't help, then Duncan Temple Lang is probably the person to
> ask. He is the RCurl maintainer, so is the most likely person to have
> experience with this problem.
>
> Anyway, in my experience the RMySQL interface is faster, so if you have
> RMySQL installed, you can just add mysql = TRUE to your call to
> useMart() and all these problems will then be moot.
>
> Best,
>
> Jim
>
>>
>> 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
>>>>>>Bioconductor at stat.math.ethz.ch
>>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>Search the archives:
>>>>>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>>
>>>>
>>>>--
>>>>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
>>>>
>>>>
>>>>**********************************************************
>>>>Electronic Mail is not secure, may not be read every day, and should not
>>>>be used for urgent or sensitive issues.
>>>>
>>
>>
>>
>>
>>
>> -------------------------------------------
>> 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)
>>
>>
>
>
-- 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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