[BioC] biomaRt installation: unable to download XML library

[Martin Morgan]

raffaele.calogero at unito.it writes:

> Hi,
> I am trying to install, on a linux machine, biomaRt
> I used:
> biocLite("biomaRt")
> the installation however fails due to the foolwing error:
>> biocLite("biomaRt")
> Running biocinstall version 2.2.9 with R version 2.7.0
> Your version of R requires version 2.2 of BioConductor.
> also installing the dependency XML
>
> trying URL
> 'http://cran.fhcrc.org/src/contrib/XML_1.95-3.tar.gz'
> Error in download.file(url, destfile, method, mode = "wb",
> ...) :
>   cannot open URL
> 'http://cran.fhcrc.org/src/contrib/XML_1.95-3.tar.gz'
>
> I tryed to download XML package directly from R CRAN but I
> get:
> IWSS Security Event (itdmzas055)
> InterScan Web Security detected the following in HTTP
> traffic:
> Item: http://cran.r-project.org/src/contrib/XML_1.95-3.tar.gz
> Action: deleted
> Reason: Violation of a compressed file restriction
> -- File: XML_1.95-3.tar.gz, security warning:
> Corrupted_Zip_file
> The uncleanable file is deleted

This sounds like your organization has some security software that is
getting in the way. You'll need to speak with your local IT people;
perhaps the source (cran.r-project.org) is different from most of the
other Bioconductor packages?

Martin


> This happen also for older versions of the library.
>
> Any idea where an uncorrupted version of the XML library
> can be found?
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> x86_64-unknown-linux-gnu
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets 
> methods   base
> loaded via a namespace (and not attached):
> [1] tools_2.7.0
>
>
> Cheers
> Raffaele
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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