[BioC] biomaRt not working?
john seers (IFR)
john.seers at bbsrc.ac.uk
Fri Jun 5 10:08:29 CEST 2009
Hi Steve
Thanks for that. Same problem using RCurl 0.94_1 though, so that
eliminates that idea.
> 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.
> 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_0.94-1 tools_2.9.0 XML_2.3-0
>
Regards
John
-----Original Message-----
From: Steve Pederson [mailto:stephen.pederson at adelaide.edu.au]
Sent: 05 June 2009 09:01
To: john seers (IFR)
Subject: Re: [BioC] biomaRt not working?
Hi John,
I can't remember where I found this, but I just had a quick poke around
online & couldn't find it again either. I'm sure emailing it is not the
done thing, but hopefully it helps.
I'm a Windows guy as well so this should work. I have an XP machine, a
Vista x64 machine and a Bill Gates dartboard.
Cheers,
Steve
john seers (IFR) wrote:
>
> 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_NAM
> E=
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICA
> TI
> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>
>
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