[BioC] Loading problem with XML_1.9

[Kasper Daniel Hansen]

On Jun 27, 2007, at 8:09 PM, Luo Weijun wrote:

> 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 in a
> previous message that Sys.getenv("PATH") needs to be
> revised in the file XML/R/zzz.R, but I can’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.

XML is a CRAN package, not a Bioconductor package. Try R-help

People will likely point out that you are using a 1-year old version  
of R and that you should upgrade if you want help.

Kasper

> 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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