Ok, so I have done a *tiny* amount of benchmarking ... I first thought that the problem was that I didn't compile it with --system- zlib (which probably was a problem), but It is clear that the "data" call is taking much longer in 2.6. I have seen this with "load" as well and on a variety of objects, note neither of these I compiled myself. All objects which I have tried to load were constructed with 2.5.1, so I'll probably try to construct a couple of objects with 2.5 and 2.6 and see if that is an issue, unless someone chimes and says: "thats definitely [not] an issue"
thanks for all of the help... jim == R-2.6.0 (http://r.research.att.com/R-devel-42657.dmg) == > system.time(data(davidTiling)) user system elapsed 135.607 2.355 138.219 > system.time({ davidRaw <- log2(exprs(davidTiling)[,4:6]) ; + davidDNA <- log2(exprs(davidTiling[,1:3])) }) user system elapsed 11.981 2.203 24.346 > system.time({ rm(davidTiling); gc() }) user system elapsed 1.520 0.093 1.643 == R-2.5.1 (Obtained from a CRAN mirror today) == > system.time(data(davidTiling)) user system elapsed 61.909 2.388 84.032 > system.time({ davidRaw <- log2(exprs(davidTiling)[,4:6]) ; + davidDNA <- log2(exprs(davidTiling[,1:3])) }) user system elapsed 8.667 2.130 27.041 > system.time({ rm(davidTiling); gc() }) user system elapsed 0.667 0.047 0.715 On Aug 27, 2007, at 2:46 PM, Simon Urbanek wrote: > James, > > On Aug 27, 2007, at 5:35 PM, James Bullard wrote: > >> I have checked out R-devel from subversion and configured it with >> the following command >> >> ./configure --with-blas='-framework vecLib' CFLAGS="-g -O2 - >> march=nocona" CXXFLAGS="-g -O2 -march=nocona" FFLAGS="-g -O2 - >> march=nocona" FCFLAGS="-g -O2 -march=nocona" >> >> followed by make && make install. This works in the sense that R >> starts up fine. However, my session seems to be very slow compared >> to R-2.5.1 (which I had installed from the binaries at CRAN). Slow >> means for example that loading a large RData file takes much >> longer. Is there any configure flag I am missing? What are the >> exact configure command used to build the CRAN binary? >> > > I don't think it should be any slower - actually is should be > faster, because the CRAN binary has memory profiling enabled. There > were some changes in R-devel that can make it slower, but not > noticeably I suppose. Can you test the CRAN binary of R-devel (from > http://r.research.att.com) to see if it exhibits the same slow-down? > > FWIW the full flags used for the CRAN i386 build are the following: > > CC="gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk" > CXX="g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk" > F77="gfortran-4.0 -arch i386 -isysroot /Developer/SDKs/ > MacOSX10.4u.sdk" FC="gfortran-4.0 -arch i386 -isysroot /Developer/ > SDKs/MacOSX10.4u.sdk" CPPFLAGS=-msse3 CFLAGS="-g -O2 -std=gnu99 - > march=nocona" CXXFLAGS="-g -O2 -march=nocona" FFLAGS="-g -O2 - > march=nocona" FCFLAGS="-g -O2 -march=nocona" --enable-BLAS-shlib -- > with-system-zlib --enable-memory-profiling > > Using the universal SDK supposedly results in faster executables, > but I didn't test it ... > > Cheers, > Simon > > >> (I am using the latest version of OS X on an Intel MacBook with the >> newest Xcode and the gfortran from CRAN). >> >> Jim >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
