On Nov 26, 7:14 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> On Nov 25, 2007 10:07 PM, William Stein <[EMAIL PROTECTED]> wrote:
>
> > Mike Hansen and I have put some work into making it possible to very
> > easily use R from Sage, and are
> > even maybe considering including R in Sage. This is very likely
> > definitely not ready yet, but we
> > have an experimental package that might work. It would be very
> > useful if some people could test
> > building it and report back whether or not it works, and how long it
> > takes to build.
>
> Responding to myself. R builds on ppc osx10.4 but rpy doesn't yet:
>
> gcc -bundle -undefined dynamic_lookup
> build/temp.macosx-10.3-ppc-2.5/src/rpymodule2061.o
> build/temp.macosx-10.3-ppc-2.5/src/R_eval2061.o build/temp.macos
> x-10.3-ppc-2.5/src/io2061.o
> -L/Users/was/sage-2.8.14.rc1/spkg/build/r-2.6.1rc.p1/src/bin
> -L/Users/was/sage-2.8.14.rc1/spkg/build/r-2.6.1rc.p1/src/lib -L/
> Users/was/sage-2.8.14.rc1/local/lib/gcc-lib/powerpc-apple-darwin6.8/4.0.3/
> -L/Users/was/sage-2.8.14.rc1/spkg/build/r-2.6.1rc.p1/src/bin
> -L/Users/was/sage
> -2.8.14.rc1/spkg/build/r-2.6.1rc.p1/src/lib
> -L/Users/was/sage-2.8.14.rc1/local/lib/gcc-lib/powerpc-apple-darwin6.8/4.0. 3/
> -lR -lf95 -o build/lib.macosx-1
> 0.3-ppc-2.5/_rpy2061.so
> /usr/bin/ld: warning can't open dynamic library: libRblas.dylib
> referenced from:
> /Users/was/sage-2.8.14.rc1/spkg/build/r-2.6.1rc.p1/src/lib/libR.dylib
> (c
> hecking for undefined symbols may be affected) (No such file or
> directory, errno = 2)
> /usr/bin/ld: Undefined symbols:
> _dgemm_ referenced from libR expected to be defined in libRblas.dylib
> _dsyrk_ referenced from libR expected to be defined in libRblas.dylib
> _zgemm_ referenced from libR expected to be defined in libRblas.dylib
> _dcopy_ referenced from libR expected to be defined in libRblas.dylib
> _dtrsm_ referenced from libR expected to be defined in libRblas.dylib
> _daxpy_ referenced from libR expected to be defined in libRblas.dylib
> _dswap_ referenced from libR expected to be defined in libRblas.dylib
> _ddot_ referenced from libR expected to be defined in libRblas.dylib
> __g95_sign_r8 referenced from libR expected to be defined in libRblas.dylib
> _dasum_ referenced from libR expected to be defined in libRblas.dylib
> _dscal_ referenced from libR expected to be defined in libRblas.dylib
> _dnrm2_ referenced from libR expected to be defined in libRblas.dylib
> _drot_ referenced from libR expected to be defined in libRblas.dylib
> _drotg_ referenced from libR expected to be defined in libRblas.dylib
Those are BLAS symbols, but how come R doesn't use the accelerate
FramWork for that?
Cheers,
Michael
> collect2: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1
>
> real 0m3.647s
> user 0m1.476s
> sys 0m0.957s
> sage: An error occurred while installing rpy-1.0-rc3-p1
> Please email sage-develhttp://groups.google.com/group/sage-devel
> explaining the problem and send the relevant part of
> of /Users/was/sage-2.8.14.rc1/install.log. Describe your computer,
> operating system, etc.
> If you want to try to fix the problem, yourself *don't* just cd to
> /Users/was/sage-2.8.14.rc1/spkg/build/rpy-1.0-rc3-p1 and type 'make'.
> Instead type "/Users/was/sage-2.8.14.rc1/sage -sh"
> in order to set all environment variables correctly, then cd to
> /Users/was/sage-2.8.14.rc1/spkg/build/rpy-1.0-rc3-p1
> (When you are done debugging, you can type "exit" to leave the
> subshell.)
>
>
>
>
>
> > All you have to do is:
>
> > (1) install R:
>
> > $ time ./sage -f -m r-2.6.1rc.p1
>
> > NOTE: If the package name changes, type
>
> > $ ./sage -experimental |grep r-
>
> > to see what the new name is. Note that we put "-f -m" above so that the R
> > build
> > directory gets left laying around in spkg/build/. This is because
> > there are still some
> > issues with "make install" and R. Also, R hardcodes install paths
> > in the R command,
> > which is something we'll have to deal with before releasing R as an
> > official optional
> > package.
>
> > (2)
> > Then to test it out see if this works:
>
> > sage: import rpy
> > sage: rpy.r.t_test(range(100))
> > {'alternative': 'two.sided',
> > 'conf.int': [43.743490583064158, 55.256509416935835],
> > 'data.name': '0:99',
> > 'estimate': {'mean of x': 49.5},
> > 'method': 'One Sample t-test',
> > 'null.value': {'mean': 0.0},
> > 'p.value': 3.0537578007169442e-31,
> > 'parameter': {'df': 99.0},
> > 'statistic': {'t': 17.062204191756354}}
>
> > sage: time rpy.r.t_test(range(1000000))
> > CPU times: user 1.97 s, sys: 0.12 s, total: 2.08 s
> > Wall time: 2.09
> > {'alternative': 'two.sided',
> > 'conf.int': [499433.7061652476, 500565.2938347524],
> > 'data.name': '0:999999',
> > 'estimate': {'mean of x': 499999.5},
> > 'method': 'One Sample t-test',
> > 'null.value': {'mean': 0.0},
> > 'p.value': 0.0,
> > 'parameter': {'df': 999999.0},
> > 'statistic': {'t': 1732.0482094941815}}
>
> > --
> > William Stein
> > Associate Professor of Mathematics
> > University of Washington
> >http://wstein.org
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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