[BioC] XML and RCurl and biomaRt problem?

john seers (IFR) john.seers at bbsrc.ac.uk
Mon Jun 8 17:46:11 CEST 2009


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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