[BioC] Loading problem with XML_1.9

[Herve Pages]

Hi Luo,

Try getting help on the appropriate channels i.e. on the R-SIG-Mac mailing
list (r-sig-mac at stat.math.ethz.ch) or with the XML maintainer directly.
All those warnings telling you that /usr/lib/libxml2.dylib does not
contain the requested architecture might indicate that something is wrong with
your xml _system_ lib. Not really a Bioconductor issue I'm afraid...
Also any reason why you are using R 2.3.1? The version of Bioconductor that
must be used with R 2.3.1 is BioC 1.8. This is an old released and is not
supported anymore (BTW, if you are using biocLite() with R 2.3.1, as you
claim, you should get XML_0.99-7.tgz, not XML_1.9).
Have you tried with a more recent version? R-2.5.1 was just released today
and works with our latest and greatest release: BioC 2.0 (which _is_ supported).

Cheers,
H.

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. 
> 
> 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
> 
> 
> 
>       ____________________________________________________________________________________
> Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor