From lux-integ at btconnect.com  Mon Jul 12 20:50:55 2010
From: lux-integ at btconnect.com (lI)
Date: Mon, 12 Jul 2010 19:50:55 +0100
Subject: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib'
	prefix//update
In-Reply-To: <201007121107.23287.lux-integ@btconnect.com>
References: <201007121029.30870.lux-integ@btconnect.com>
	<201007121107.23287.lux-integ@btconnect.com>
Message-ID: <201007121950.55739.lux-integ@btconnect.com>

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



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