[BioC] XML and RCurl and biomaRt problem?

[john seers (IFR)]

Hi Patrick

Thank you for your sympathetic reply. Actually I am not particularly
frustrated with these; just getting a bit baffled as to whether there
were problems with these packages or whether I was using the wrong
versions. And if I was using the wrong versions how I find out which
versions I should be using and how to avoid installing versions I should
not be using... And on top of that trying to get my IT department to
tell me if anything had changed on the proxy server that might be
causing a problem. All to fix code that used to work.

Come to think of it perhaps I was a bit frustrated. :)

I have re-pasted my sessionInfo if you have anything to add. 


Regards

John Seers



Windows XP

> 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] RCurl_0.97-3   bitops_1.0-4.1 XML_2.3-0      biomaRt_2.0.0
RWinEdt_1.8-1 

loaded via a namespace (and not attached):
[1] tools_2.9.0
>



-----Original Message-----
From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org] 
Sent: 08 June 2009 18:55
To: john seers (IFR)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] XML and RCurl and biomaRt problem?

John,
I can understand your frustration over XML and RCurl. Both of these 
packages live primarily at omegahat.org and both CRAN and Bioconductor 
distribute some version of them to make them widely available. Given 
that these two packages receive special treatment makes it hard to 
create a turnkey process for managing updates. For all by Mac OS X 10.4 
Tiger, RCurl has been updated in the BioC extra repository to RCurl 
0.98-0. I just noticed that this is out of date since omegahat now hosts

RCurl 0.98-1. I will update BioC extra with the new RCurl sometime this 
week.

As far as your problem goes, I can't provide many specifics since I 
don't know what your configuration is. Based upon your e-mail trail it 
looks like you are using R 2.9.0 on a Windows machine. I installed R 
2.9.0 on a clean Windows box and was able to use the RCurl 0.98-0 
Windows binary package from BioC extra without issue.

 > library(RCurl)
Loading required package: bitops
 > curl <- getCurlHandle()
 > getURL("http://www.bioconductor.org/biocLite.R", curl = curl)
[1] "source(\"http://bioconductor.org/getBioC.R\")\n\nbiocLite <- 
function(pkgs, groupName=\"lite\", ...)\n{\n    if 
(missing(pkgs))\n        biocinstall(groupName=groupName, ...)\n    
else\n        biocinstall(pkgs=pkgs, groupName=groupName, ...)\n}\n\n"
 > 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 utils     datasets  methods   base    

other attached packages:
[1] RCurl_0.98-0   bitops_1.0-4.1



Patrick


john seers (IFR) wrote:
> Hi All
>
> Has RCurl been updated on Bioconductor?
>
> If I use that version then I get bioMart problems because RCurl cannot
> load. (Unfortunately I cannot see what version of RCurl it is.) If I
> return to the RCurl version from CRAN it works fine.
>
> I notice that in R-devel people are reporting problems with XML and
the
> solution is to load from "CRAN extras". 
>
> This is getting quite difficult to know which versions work and do not
> and if I should get them from bioconductor or CRAN or CRAN extras.
>
> Can anybody shine a bit of light on what goes with what and how to
> manage this?
>
> Regards
>
>
> John Seers
>
>
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of john
seers
> (IFR)
> Sent: 08 June 2009 11:10
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] XML and biomaRt problem?
>
>
>
> Hi All
>
> Just a warning to other people who might be about to update and I am
not
> sure how to guard against this sort of problem. How are bioconductor
and
> CRAN coordinated? I updated my version of XML (from CRAN) and had some
> problems using biomaRt. 
>
> On issuing library(bioMart) I got a message saying that iconv.dll
could
> not be downloaded and reinstalling the application might fix the
> problem. Also shown were messages about unable to load XML or the
> biomaRt namespace.
>
> I re-installed XML from bioconductor and it all worked again.
>
> My sessionInfo() below is the version that is working, not the problem
> configuration.
>
> 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 RWinEdt_1.8-1
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.97-3 tools_2.9.0  XML_2.3-0   
>   
>
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