Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix//update

From: lI <lux-integ_at_btconnect.com>
Date: Mon, 12 Jul 2010 19:50:55 +0100

On Monday 12 July 2010 11:07:23 lI wrote:
> On Monday 12 July 2010 10:29:30 lI wrote:
> > Greetings,
> >
> > I have a computer with the following setup:
> > 1)cblfs (pure 64-bit (amd64) linux), kernel2.6.34 gcc4.4.2
> > 2)R-2.11.1
> >
> > I compiled R with BLAS and lapack using the switched ( --with-blas="-
> > lpthread -latlas -lfptf77blas"
> > --with-lapack="-llapack -lcblas" ).
> > ((
http://cran.r-project.org/doc/manuals/R-admin.html#Linear-algebra) )
> >
> > Prior to compiling R-2.11.1
> > sh conigure --help gave options including the following
> > SHLIB_LD command for linking shared libraries
> > which contain object files from a C or Fortran compiler
> > only SHLIB_LDFLAGS special flags used by SHLIB_LD
> > SHLIB_CXXLDFLAGS special flags used by SHLIB_CXXLD
> > SHLIB_FCD command for linking shared libraries which contain object
> > files from the Fortran 95 compiler
> > SHLIB_FCLDFLAGS special flags used by SHLIB_FCLD
> >
> >
> > I did not know what to set for these and accepted whatever the defaults
> > were. I ended up with shared-libraries which are as follows:-
> >
> > $R_HOME/lib/{libRblas.so,libRlapack.so } i.e. with the prefix 'lib'
> > and the following shared-libraries without the 'lib' prefix.
> >
> > $R_HOME/modules/{R_X11.so,internet.so,lapack.so,vfonts.so }
> > $R_HOME/library/cluster/libs/cluster.so
> > $R_HOME/library/foreign/libs/foreign.so
> > $R_HOME/library/grDevices/libs/grDevices.so
> > $R_HOME/library/grid/libs/grid.so
> > $R_HOME/library/KernSmooth/libs/KernSmooth.so
> > $R_HOME/library/lattice/libs/lattice.so
> > $R_HOME/library/MASS/libs/MASS.so
> > $R_HOME/library/Matrix/libs/Matrix.so
> > $R_HOME/library/methods/libs/methods.so
> > $R_HOME/library/mgcv/libs/mgcv.so
> > $R_HOME/library/nlme/libs/nlme.so
> > $R_HOME/library/nnet/libs/nnet.so
> > $R_HOME/library/rpart/libs/rpart.so
> > $R_HOME/library/spatial/libs/spatial.so
> > $R_HOME/library/splines/libs/splines.so
> > $R_HOME/library/stats/libs/stats.so
> > $R_HOME/library/survival/libs/survival.so
> > $R_HOME/library/tools/libs/tools.so
> >
> >
> > In linux builds the linker usually looks for libs with the 'lib'
> > prefix. In this installation all the libraries
> > ---in $R_HOME/modules
> > ---in $R_HOME/library/patha/to/whatevr
> >
> > do not have the 'lib' prefix.
> >
> > QUESTION:
> > A) does any on list know SHLIB_LD SHLIB_LDFLAGS SHLIB_CXXLDFLAGS
> > SHLIB_FCD SHLIB_FCLDFLAGS settings for compiling R and do these
> > result in so libs with the 'lib' prefix?
> > B) If all of A) is negative what is there to be done to to enable
> > generation libraries in $R_HOME/modules $R_HOME/library/~ with the
> > 'lib' prefix?
>
> I forgot to add my configure/make options. These were:-
> ########################
> export BUILD64="-m64"
> sh configure \
> CC="gcc $BUILD64" \
> CXX="g++ $BUILD64" \
> F77="gfortran $BUILD64" \
> FC="gfortran $BUILD64" \
> JAVA_HOME=$JAVA_HOME \
> LIBnn=lib64 \
> CPPFLAGS="-I$ATLAS_HOME/include -I/opt/acml4.4.0/gfortran64_mp/include -
> I/opt/acml4.4.0/gfortran64/include -I/usr/local/numerics/include" \
> LDFLAGS="-L$ATLAS_HOME/lib -L/opt/acml4.4.0/gfortran64_mp/lib -
> L/usr/local/numerics/lib -L/usr/lib" \
> --prefix=/opt/TEST/R-2.11.1 \
> --x-includes=$XORG_PREFIX/include \
> --x-libraries=$XORG_PREFIX/lib \
> --with-tcl-config=/usr/lib \
> --with-tk-config=/usr/lib \
> --with-system-zlib=/usr \
> --with-system-bzlib=/usr \
> --with-system-pcre=/usr \
> --with-x \
> --with-libpth-prefix=/usr \
> --with-libintl-prefix=/usr \
> --with-blas="-lpthread -latlas -lfptf77blas" \
> --with-lapack="-llapack -lcblas" \
> --enable-R-shlib \
> --enable-BLAS-shlib
> ################
>
> The sources compiled trouble-free. with 'make' as normal user.
> I then ran 'make install' as super-user and int installed in the prefix
> as set..
>
> A reply to the following questions would be much appreciateed:-
> QUESTION:
> A) does any on list know SHLIB_LD SHLIB_LDFLAGS SHLIB_CXXLDFLAGS
> SHLIB_FCD SHLIB_FCLDFLAGS settings for compiling R and do these
> result in so libs with the 'lib' prefix?
> B) If all of A) is negative what is there to be done to enable
> generation of shared-libraries in $R_HOME/modules/ and
> $R_HOME/library/~ directories/sub-directories with the 'lib' prefix?
>
>
thanks everyone for the help in clarifying what were share-libraries and otherwise.

As stated above I used two switches
 --enable-R-shlib \
 --enable-BLAS-shlib
in the configure options of the downloaded R-2.11.1 source prior to compilation.

I am compiling R-2.11.1 as an optional dependency of kdeedu-4.4.5. This asks for R-shlib )which I noticed it is disable by the default in the configure script.)

After compile and install of R-2.11.1, I am only able to start R from the command line when I move the generated libRblas.so to libRblas.soDUFF and symlink libacml.so to libRblas.so and update $R_HOME/etc/ldpaths accordingly. I am unable to start R with the compiled-in $R_HOME/libR.so and $R_HOME/libRblas.so.

QUESTIONS:
A) How does one start R with the the generated libR.so and libRblas.so? B) is the generated libR.so interchangable with libRblas.so (i.e. R library without blas enhanced algebra capabilities?)

advice welcomed



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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Mon 12 Jul 2010 - 18:51:42 GMT

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