Re: [R] Loading problem with XML_1.9

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Thu, 28 Jun 2007 12:35:00 -0700

Weijun --

If memory is a problem, you might try using the 'handler' argument of xmlTreeParse. This provides access to each node as it is processed, so that you can, for instance, choose to ignore nodes, or save only numeric values, or ... I'm not sure whether the entire document is read into a C 'external pointer', or whether the savings is just in the R representation of the document.

Also, depending on how you use the resulting document, you might want to watch out for the memory leak mentioned in http://www.omegahat.org/RSXML/Changes

Martin

Luo Weijun <luo_weijun_at_yahoo.com> writes:

> Hello all,
> I have loading problem with XML_1.9 under 64 bit
> R2.3.1, which I got from http://R.research.att.com/.
> XML_1.9 works fine under 32 bit R2.5.0. I thought that
> could be installation problem, and I tried
> install.packages or biocLite, every time the package
> installed fine, except some warning messages below:
> ld64 warning: in /usr/lib/libxml2.dylib, file does not
> contain requested architecture
> ld64 warning: in /usr/lib/libz.dylib, file does not
> contain requested architecture
> ld64 warning: in /usr/lib/libiconv.dylib, file does
> not contain requested architecture
> ld64 warning: in /usr/lib/libz.dylib, file does not
> contain requested architecture
> ld64 warning: in /usr/lib/libxml2.dylib, file does not
> contain requested architecture
>
> Here is the error messages I got, when XML is loaded:
>> library(XML)
> Error in dyn.load(x, as.logical(local),
> as.logical(now)) :
> unable to load shared library
> '/usr/local/lib64/R/library/XML/libs/XML.so':
> dlopen(/usr/local/lib64/R/library/XML/libs/XML.so,
> 6): Symbol not found: _xmlMemDisplay
> Referenced from:
> /usr/local/lib64/R/library/XML/libs/XML.so
> Expected in: flat namespace
> Error: .onLoad failed in 'loadNamespace' for 'XML'
> Error: package/namespace load failed for 'XML'
>
> I understand that it has been pointed out that
> Sys.getenv("PATH") needs to be revised in the file
> XML/R/zzz.R, but I canâ�t even find that file under
> XML/R/ directory. Does anybody have any idea what
> might be the problem, and how to solve it? Thanks a
> lot!
> BTW, the reason I need to use R64 is that I have
> memory limitation issue with R 32 bit version when I
> load some very large XML trees.
>
> Session information
>> sessionInfo()
> Version 2.3.1 Patched (2006-06-27 r38447)
> powerpc64-apple-darwin8.7.0
>
> attached base packages:
> [1] "methods" "stats" "graphics" "grDevices"
> "utils" "datasets"
> [7] "base"
>
> Weijun
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org

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Received on Thu 28 Jun 2007 - 20:05:12 GMT

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