From lux-integ at btconnect.com  Mon Jul 12 12:07:23 2010
From: lux-integ at btconnect.com (lI)
Date: Mon, 12 Jul 2010 11:07:23 +0100
Subject: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib'
	prefix//update
In-Reply-To: <201007121029.30870.lux-integ@btconnect.com>
References: <201007121029.30870.lux-integ@btconnect.com>
Message-ID: <201007121107.23287.lux-integ@btconnect.com>

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?


sincerely
luxInteg



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