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

[lI]

On Monday 12 July 2010 20:52:15 Simon Urbanek wrote:
> On Jul 12, 2010, at 2:50 PM, lI wrote:
> > 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
> 
> How are you starting it? The R start script does setup everything so that
>  you should never touch anything inside.
> 
> > 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?
> 
> bin/R
> 
> > B) is the generated  libR.so  interchangable with libRblas.so  (i.e. R
> > library without blas   enhanced algebra  capabilities?)
> 
> No - those are two entirely different libraries. The libRblas can be
>  interchanged with a suitably complete BLAS implementation, but please do
>  read the manuals for details.
> 
> Cheers,
> Simon
> 

Thanks to you for your help.  Following your guidance,  kdeedu-4.4.5  now 
builds successfully against R-2.11.1.   However when I    edit ~/etc/ldpaths 
with  the line

export LD_LIBRARY_PATH=path/to/acml/lib:$LD_LIBRARY_PATH

R fails to start.  it only starts when   the above point to $R_HOME/lib. (nb I 
have  a symbolic link of libacml.so  to libRblas.so
any ideas?