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This may be an issue between a target specific (PPC 64) R binary installed on your machine and the universal binary packages hosted on CRAN/BioC. Installing BioC using the 'type="source"' option (i.e. biocLite(type="source")) may help clear up the issue. If this does work, also use the type="source" option for install.packages(). -kyle On 11/28/07 1:59 AM, "Jason J. Evans" <jason.evans at="" marquette.edu=""> 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. 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 > 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 This email message, including any attachments, is for th...{{dropped:6}}

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