[BioC] build of bioconductor on R 2.6.1 on mac os 10.5

[Herve Pages]

Hi Jason,

Jason J. Evans wrote:
> I just built bioconductor with 'biocLite.R' and upgraded it on my  
> system running R 2.6.1 over Mac OS 10.5, Leopard, on 64-bit powerpc  
> based chips.

Given the problem you are reporting below, I don't think you "built"
Bioconductor. It looks like you installed the binary packages which
is very different.

> Upon trying to load Biobase it gives me an error  
> implying it was built for a different architecture or kernel as noted  
> below in its output.  Searching for this problem on the web,  
> bioconductor.org, or r-project.org turned up anything similar.  This  
> occurred with building a few python modules too, but they were  
> documented, though vaguely, on the web.  Has anyone else come up with  
> this problem or is it an isolated problem?
> 
>  > library(Biobase)
> Error: package 'Biobase' was built for universal-apple-darwin8.10.1

Have you tried with a CRAN package? Like the CRAN packages, the Bioconductor
universal binary packages are built for 2 archs only: i386 and ppc (maybe
this will change in the future with the addition of the x86_64 and ppc64
archs, but it's not here yet).
What do you get if you do:

  > install.packages("XML")
  > library(XML)

Personally I get the following on a Leopard system where I run R in x86_64
mode:

  Error: package 'XML' is not installed for 'arch=x86_64'

I would have expected you to get something similar but with 'arch=ppc64'
instead of 'arch=x86_64', so apparently something else is going on in
your case, maybe the R version (I'm using R-devel nightly build for
Leopard from http://r.research.att.com/ and I start it with R_ARCH=/x86_64 R).

But if I install from source:

  > install.packages("XML", type="source")

then everything is fine.

If you have troubles installing/loading XML, then your problem is not really
related to Bioconductor and the R-SIG-Mac mailing list would probably be a
better place to ask.

Cheers,
H.

>  >
> 
> 21-CC-/Users/bioaddix/Desktop/Biobase %  uname -a
> Darwin CC.bioaddica 9.1.0 Darwin Kernel Version 9.1.0: Wed Oct 31  
> 17:48:21 PDT 2007; root:xnu-1228.0.2~1/RELEASE_PPC Power Macintosh
> 22-CC-/Users/bioaddix/Desktop/Biobase %
> 
> 24-CC-/Users/bioaddix/Desktop/Biobase %  gcc -v
> Using built-in specs.
> Target: powerpc-apple-darwin9
> Configured with: /var/tmp/gcc/gcc-5465~16/src/configure --disable- 
> checking -enable-werror --prefix=/usr --mandir=/share/man --enable- 
> languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/ 
> $/-4.0/ --with-gxx-include-dir=/include/c++/4.0.0 --with-slibdir=/usr/ 
> lib --build=i686-apple-darwin9 --program-prefix= --host=powerpc-apple- 
> darwin9 --target=powerpc-apple-darwin9
> Thread model: posix
> gcc version 4.0.1 (Apple Inc. build 5465)
> 25-CC-/Users/bioaddix/Desktop/Biobase %
> 
> any ideas are good ideas,
> 
> 
> _jason
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> 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