[BioC] biomaRt not working?
john seers (IFR)
john.seers at bbsrc.ac.uk
Fri Jun 5 09:53:07 CEST 2009
Hi Paul
The same combination as me - the major difference is I am on Windows and
you are on Linux. But James below was running from Windows with the same
versions.
Thanks for the information.
Does anybody know how I can get an earlier version of RCurl? I have had
a look around but cannot find any. (Not even source code.)
Regards
John
-----Original Message-----
From: Paul Leo [mailto:p.leo at uq.edu.au]
Sent: 05 June 2009 08:35
To: john seers (IFR)
Cc: Steve Pederson; James W. MacDonald; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] biomaRt not working?
In case this helps : These 2 combinations of biomart and Rcurl work
fine for me :
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.U
TF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATI
ON=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] biomaRt_2.0.0
loaded via a namespace (and not attached):
[1] RCurl_0.97-3 XML_1.95-3
>
################## developement version
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-06-02 r48703)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] BSgenome.Mmusculus.UCSC.mm9_1.3.11
BSgenome_1.13.6
[3] Biostrings_2.13.11
IRanges_1.3.21
[5] biomaRt_2.1.0
loaded via a namespace (and not attached):
[1] Biobase_2.5.2 RCurl_0.97-3 XML_2.5-0
-
Dr Paul Leo
Bioinformatician
Diamantina Institute for Cancer, Immunology and Metabolic Medicine
University of Queensland
------------------------------------------------------------------------
--------------
Research Wing, Bldg 1
Princess Alexandria Hospital
Woolloongabba, QLD, 4102
Tel: +61 7 3240 7740 Mob: 041 303 8691 Fax: +61 7 3240 5946
Email: p.leo at uq.edu.au Web: http://www.di.uq.edu.au
-----Original Message-----
From: john seers (IFR) <john.seers at bbsrc.ac.uk>
To: Steve Pederson <stephen.pederson at adelaide.edu.au>
Cc: James W. MacDonald <jmacdon at med.umich.edu>,
bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] biomaRt not working?
Date: Fri, 5 Jun 2009 08:23:56 +0100
Hi Steve
All useful information. I notice there were some messages in the forum
about problems with biomaRT/RCurl in the development version but I
assumed that was not much to do with my problem.
I have gone in the other direction with RCurl_0.97-3 in the hope it
would fix it. Obviously the wrong direction!
I am not sure how to get hold of an older version of a package -
RCurl_0.94-1. I'll go and have an explore. Do you build it from source?
Regards
John
-----Original Message-----
From: Steve Pederson [mailto:stephen.pederson at adelaide.edu.au]
Sent: 05 June 2009 02:45
To: john seers (IFR)
Cc: James W. MacDonald; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] biomaRt not working?
Hi John,
I had some similar trouble with RCurl_0.95-1, but everything worked fine
again when I rolled back to RCurl_0.94-1.
The command listMarts() would work, but getBM() gave me a similar error.
Hope that's vaguely useful,
Steve
john seers (IFR) wrote:
>
> Hi James
>
> Thanks for the reply. That is useful to know it is probably not the
> biomart end. I have run a traceback() and results are below. I have
also
> updated my sessionInfo() as that has changed.
>
> (I think I will also contact our IT department to see if something has
> changed).
>
> Regards
>
> John
>
>>
>> listMarts()
> Error in value[[3L]](cond) :
> Request to BioMart web service failed. Verify if you are still
> connected to the internet. Alternatively the BioMart web service is
> temporarily down.
>> traceback()
> 7: stop("Request to BioMart web service failed. Verify if you are
still
> connected to the internet. Alternatively the BioMart web service is
> temporarily down.")
> 6: value[[3L]](cond)
> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 4: tryCatchList(expr, classes, parentenv, handlers)
> 3: tryCatch(getURL(request), error = function(e) {
> stop("Request to BioMart web service failed. Verify if you are
> still connected to the internet. Alternatively the BioMart web
service
> is temporarily down.")
> })
> 2: bmRequest(paste("http://", host, ":", port, path,
> "?type=registry&requestid=biomaRt",
> sep = ""))
> 1: listMarts()
>
>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
>
> other attached packages:
> [1] biomaRt_2.0.0 RWinEdt_1.8-1
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.97-3 XML_2.3-0
>
>
>
>
>
>
> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: 04 June 2009 13:50
> To: john seers (IFR)
> Cc: bioconductor at stat.math.ethz.ch; maria traka (IFR)
> Subject: Re: [BioC] biomaRt not working?
>
> Hi John,
>
>
>
> john seers (IFR) wrote:
>> Hello All
>>
>> Can anyone tell me why I get this error using Biomart? I am connected
> to
>> the internet (as in I can install R packages). So is the Biomart
> website
>> really down? I have been having this problem for at least 2 or 3
days.
>>
>> If I access http://www.biomart.org/ using a web browser it appears to
> be
>> available.
>>
>>
>>> listMarts()
>> Error in value[[3L]](cond) :
>> Request to BioMart web service failed. Verify if you are still
>> connected to the internet. Alternatively the BioMart web service is
>> temporarily down.
>
> Works for me:
>
> > listMarts()
> biomart
> 1 ensembl
> 2 snp
> 3 vega
> 4 msd
> [snip]
>
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] affy_1.22.0 Biobase_2.4.1 limma_2.18.1 biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.97-3
> [4] XML_2.3-0
>
>
> If you are still having problems, run traceback() after the error and
> post the output.
>
> Best,
>
> Jim
>
>
>> If I access http://www.biomart.org/ using a web browser it appears to
> be
>> available.
>>
>>
>> Any suggestions as to what is going on or things to try are very
>> welcome.
>>
>> Regards
>>
>> John Seers
>>
>>
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
>> Kingdom.1252;LC_MONETARY=English_United
>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices datasets utils methods base
>>
>>
>> other attached packages:
>> [1] biomaRt_2.0.0 limma_2.18.0 affy_1.22.0 Biobase_2.4.1
>> RWinEdt_1.8-1
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.12.0 preprocessCore_1.6.0 RCurl_0.95-1
>> tools_2.9.0 XML_2.3-0
>>
>> _______________________________________________
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>
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