[BioC] Problems loading biomaRt and XML

[Jordi Altirriba Gutiérrez]

Dear Seth,
Thanks for your answer.

>What version of the XML package did you download?  Perhaps try one
>more time with biocLite:
>  source("http://bioconductor.org/biocLite.R")
>  biocLite("XML")
>  library("XML")
>
>I'm guessing that somehow you ended up with a bad/old version of the
>XML package, but am not sure.

The version of XML is 0.99-7.

-----------------

I've tried to obtain it from CRAN, from the Madrid and the London mirror, 
but I am obtaining the same results:
...
trying the  URL 
'http://cran.es.r-project.org/bin/windows/contrib/2.3/XML_0.99-7.zip'
...
trying the URL 
'http://www.sourcekeg.co.uk/cran/bin/windows/contrib/2.3/XML_0.99-7.zip'
...
package 'XML' successfully unpacked and MD5 sums checked (in both cases)

>library (biomaRt) (or library (XML))

The same error described below.

----------------------------------

I have used BioCLite, as you suggested, which obtains XML from Omegahat, 
obtaining:

>source("http://bioconductor.org/biocLite.R")
>biocLite("XML")
Running getBioC version 0.1.6 with R version 2.3.1
Running biocinstall version 1.8.4 with R version 2.3.1
Your version of R requires version 1.8 of Bioconductor.
trying the URL 
'http://bioconductor.org/packages/1.8/omegahat/bin/windows/contrib/2.3/XML_0.99-7.zip'
Content type 'application/zip' length 1323552 bytes
URL opened
downloaded 1292Kb

package 'XML' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Documents and Settings\BIO SANTANDER\Configuración 
local\Temp\RtmpIZV3pb\downloaded_packages
updating HTML package descriptions
>library(XML)

The same error described below.

-------------------------------

Any other suggestion?

Many thanks for your suggestions and time!

Yours sincerely,

Jordi Altirriba
PhD student
Hospital Clinic, Barcelona, Spain



>Jordi Altirriba Gutiérrez <altirriba at hotmail.com> writes:
>>After this I install XML (without any problems) and I re-load biomaRt, but 
>>an error message appears in a new window (I am translating it, as the 
>>messages are in Spainsh):
>>
>>The entrance point of _htmlDefaultSAXHandler procedure can.t be found in 
>>the library of dynamic links libxml2.dll
>>
>>Moreover in the R window appears:
>>
>>Loading required package: XML
>>Error in dyn.load(x, as.logical(local), as.logical(now)) :
>>         impossible to load the shared library  
>>'C:/ARCHIV~1/R/R-23~1.1/library/XML/libs/XML.dll':
>>   LoadLibrary failure:  The specified process was no found.
>>Error: .onLoad failed in 'loadNamespace' for 'XML'
>>Error: package 'XML' could not be loaded