R devel - Jul 2010 - R-2.11.1 build and 'so' libraries withouth the 'lib' prefix

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?


suggestions welcomed.

luxInteg

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

On Jul 12, 2010, at 5:29 AM, 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.
> 
Those are not shared libraries - they are shared objects loaded by R
dynamically.

Cheers,
Simon


> $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?
> 
> 
> suggestions welcomed.
> 
> luxInteg
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>