Hi,
I just tried installing the new package on a PPC apple laptop, and got
the following errors (I think they are the same as you listed before):
/usr/bin/ld: warning can't open dynamic library: libRblas.dylib
referenced from: /Users/mh/sage-2.8.4.1/local/lib/r/lib/libR.dylib
(checking 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
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
Error building RPY -- Python interface to R.
real 0m12.407s
user 0m2.730s
sys 0m1.237s
sage: An error occurred while installing rpy-1.0.1
On Dec 8, 5:10 am, "William Stein" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I've posted a new R 2.6.1 package. To try it do
>
> sage -i r-2.6.1
>
> It should build in about 5-6 minutes. WARNING: This still
> doesn't quite work on OSX10.4 yet -- it may fail building rpy at
> the very end, despite saying that it succeeds. Even on OSX10.4,
> R builds fine (just not the rpy interface).
>
> A simple test that everything built and works is
>
> 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}}
>
> You can also do
>
> sage: !R
>
> to run R itself.
>
> Notes:
> * R should now pick up X libraries if you have the devel headers, so you'll
> be able to do graphics.
> * this is a newer version of R than the last package
> * I changed the build to only build the core packages and not the
> recommended optional ones -- building those adds up to 15 minutes
> to the build time, and isn't really needed to get on our feet
> regarding R support.
> * It is not necessary to do "sage -f -m r-2.6.1" like before, since
> the correct directly is copied over.
>
> Problems:
> * too much is installed -- in particular local/lib/r/src should probably
> be deleted.
> * Probably the path is hardcoded -- this can be fixed by modifying
> local/bin/R slightly to use SAGE_LOCAL.
> * rpy isn't properly patched so that rpy.r.t_test([1..100]) works.
> * the pexpect interface isn't done (mike hansen is hard at work on it)
> * osx 10.4 support
> * gfortran support
>
> William
>
> On Dec 5, 2007 5:34 AM, mhampton <[EMAIL PROTECTED]> wrote:
>
>
>
>
>
> > I was too busy for the last couple of weeks to help seriously with
> > this, but I did try to install it on my PPC apple laptop and my Intel
> > OS X 10.4 desktop. It failed on both; the PPC problem is probably the
> > same as you mentioned. I will post the errors from the intel machine
> > when I get a chance.
>
> > I think its great that you guys started working on this; I think it
> > would help Sage a lot if we can say there is support for R before we
> > go to the joint meetings.
>
> > -Marshall Hampton
>
> > On Nov 26, 12:14 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
> > > 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
>
> --
> William Stein
> Associate Professor of Mathematics
> University of Washingtonhttp://wstein.org
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