On Thu, 12 Jul 2007, Hin-Tak Leung wrote: > Kasper Daniel Hansen wrote: >> On Jul 11, 2007, at 9:30 AM, Prof Brian Ripley wrote: > <snipped> >>>> The full Makevars file: >>>> >>>> MYCXXFLAGS=-O0 >>> You do realize that is highly non-portable? >> >> Yes, but I do not know of any other way to downgrade the optimization >> level. The SDK I am using breaks (due to memory alignment issues if a >> specific optimization flag for GCC is include - the flag is certainly >> implied by -O2 and as far as I recall also -O1). I guess the solution is >> to switch to an autoconfigure script. The main reason for not doing this >> is 1) time and actually more 2) the fact that the SDK does not come with >> an ac script. >> >> Thanks for the feedback, Kasper > <snipped> > > I think I probably know about the breakage - gcc 4.x mis-compiles > the Affymetrix toolkit at the default optimization (-02) shipped with the > toolkit. (Prof Ripley's comment was spot-on - why the reluctance > to just call it the Affymetrix toolkit bundled with the bioconductor > package affyparser?). I narrowed it down to the strict-aliasing > option... try '-O2 -fno-strict-aliasing' - it is not portable, but it > works around the funny way some part of the affy toolkit (actually one > particular file) is written. > > I did report it in the Affy forum and also directly to my Affymetrix > dev contacts about a year ago; gcc 4 is the default on the mac these > days, I think? > > On a related issue, I have some annoyance with cross-compiling leaving behind > *.o files (and *.d, etc) which get in the way of native > compile and vice versa, and I have been wondering if there is a > recommended solution? What I am currently doing is to have a
Hopefully the --clean options to INSTALL and SHLIB in R-devel will help. If they don't examples of what is needed will help improve. > "Makefile.utils" (I don't want or need a proper Makefile), and do > 'make -f Makefile.utils clean' when I need to clean up - it is better > than typing > rm -f *.o *.so *~ *.rc *.d *.dll Makedeps *.def > > (particularly with bash's file completion, all I am typing is > 'make -f M<tab>f<tab> clean' to clean up). I am sure somebody will laugh > at this... > > Hin-Tak > -- Brian D. Ripley, [EMAIL PROTECTED] 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
