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

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?