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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
