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

On Jul 12, 2010, at 5:59 PM, lI wrote:

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.

Of course as you should expect. Why would you edit? It has nothing to do
 with BLAS ...

Also did you read the manual? It explicitly covers your case ...

Cheers,
Simon

 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?