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 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
Please don't post to multiple lists: I have removed the BioC-devel list. This is about MacOS X, and the appropriate list is R-sig-mac. There is no intrinsic 64-bit problem: package XML 1.9-0 (sic) works fine on 64-bit versions of Solaris and Linux. Most likely there was an installation problem, and you do not have a 64-bit version of libxml2 installed or in the run-time library path. On Wed, 27 Jun 2007, 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/.For MacOS X, unstated.> 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 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-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
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 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 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org