[BioC] FW: biomaRt not working?

john seers (IFR) john.seers at bbsrc.ac.uk
Fri Jun 5 14:33:46 CEST 2009


Hi All 

I think we have found the problem and a workaround. Thanks to all who
offered help and advice.

Using the "--internet2" option to specify the proxy appears to not be
good enough any more. Using the "http_proxy" option to specify the proxy
server directly worked.

I think "--internet2" says use the Explorer/browser options. 

Why this does not work any more I do not know. It could be a fix/change
to Windows at my end that does not pass back the information as it used
to? Or perhaps biomart/RCurl does not handle it well any more? 

Anyway, we are up and running again.

Regards

John








-----Original Message-----
From: john seers (IFR) 
Sent: 05 June 2009 09:23
To: 'Paul Leo'
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] biomaRt not working?


Hi Paul

That does not sound very hopeful. :(  I am not sure I know how to go
figure that.

Perhaps the time has nearly come to approach the package owner for a
suggestion. Perhaps I will try a bit more digging first. Perhaps see if
I can trace the problem a bit deeper.

Regards


John  




-----Original Message-----
From: Paul Leo [mailto:p.leo at uq.edu.au] 
Sent: 05 June 2009 09:08
To: john seers (IFR)
Subject: RE: [BioC] biomaRt not working?

I had something vaguely similar happen to me this week, using
update.packages() I had the correct versions of BioMart and RCurl but it
kept failing. I reinstalled R and BioC and all of a sudden it was
fine ... go figure.... But that was on R.10 for linux....
-  
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: Paul Leo <p.leo at uq.edu.au>
Cc: Steve Pederson <stephen.pederson at adelaide.edu.au>, 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 08:53:07 +0100


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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