R devel - Jul 2014 - Error when compiling R with openblas

Hi,

I tried to compile R with openblas on a ubuntu 12.04 machine. I have to 
say that I normally use the package system and that I have no experience 
with compiling R.

I did the following:

./configure --enable-BLAS-shlib --enable-R-shlib LIBnn=lib 
--with-blas="-L/usr/lib/openblas-base/ -lopenblas" 
--enable-memory-profiling --with-x=yes


go the output:

R is now configured for x86_64-unknown-linux-gnu

   Source directory:          .
   Installation directory:    /usr/local

   C compiler:                gcc -std=gnu99  -g -O2
   Fortran 77 compiler:       gfortran  -g -O2

   C++ compiler:              g++  -g -O2
   C++ 11 compiler:           g++  -std=c++0x -g -O2
   Fortran 90/95 compiler:    gfortran -g -O2
   Obj-C compiler:

   Interfaces supported:      X11
   External libraries:        readline, BLAS(generic), lzma
   Additional capabilities:   PNG, JPEG, NLS
   Options enabled:           shared R library, shared BLAS, R 
profiling, memory profiling

   Recommended packages:      yes

configure: WARNING: you cannot build info or HTML versions of the R manuals



Then: make - and then comes the error:

make[4]: Entering directory `/home/ab/Downloads/R-3.1.0/src/main'
make[4]: Leaving directory `/home/ab/Downloads/R-3.1.0/src/main'
make[3]: Leaving directory `/home/ab/Downloads/R-3.1.0/src/main'
make[3]: Entering directory `/home/ab/Downloads/R-3.1.0/src/main'
gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L/usr/local/lib -o R.bin 
Rmain.o  -L../../lib -lR -lRblas
../../lib/libR.so: undefined reference to `drot_'
../../lib/libR.so: undefined reference to `dtrsm_'
../../lib/libR.so: undefined reference to `dswap_'
../../lib/libR.so: undefined reference to `dcopy_'
../../lib/libR.so: undefined reference to `ddot_'
../../lib/libR.so: undefined reference to `dgemm_'
../../lib/libR.so: undefined reference to `dscal_'
../../lib/libR.so: undefined reference to `dnrm2_'
../../lib/libR.so: undefined reference to `dsyrk_'
../../lib/libR.so: undefined reference to `dasum_'
../../lib/libR.so: undefined reference to `daxpy_'
../../lib/libR.so: undefined reference to `drotg_'
../../lib/libR.so: undefined reference to `zgemm_'
collect2: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/home/ab/Downloads/R-3.1.0/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/home/ab/Downloads/R-3.1.0/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/home/ab/Downloads/R-3.1.0/src'
make: *** [R] Error 1


I am wondering why libR.so wants to find these functions and not 
libRblas.so. The lib libRblas.so can be found in

 > locate libRblas.so

/home/ab/Downloads/R-3.1.0/lib/libRblas.so
/home/ab/Downloads/R-3.1.0/src/extra/blas/libRblas.so

they have both the same size.


can anyone help me with this?

cheers,

alex

On 1 July 2014 at 12:00, Alexander Braumann wrote:
| I tried to compile R with openblas on a ubuntu 12.04 machine. I have to 
| say that I normally use the package system and that I have no experience 
| with compiling R.

You do not need to do that.  Just install the existing OpenBLAS package via

    libopenblas-base

(which you may already have) and R will use as the BLAS interface is
generic. That is what the package tries to tell you via [edited]

  edd at max:~$ dpkg -s r-base-core
  Package: r-base-core
  [...]
  Version: 3.1.0-1trusty0
  Depends: [...], libblas3 | libblas.so.3, [...], liblapack3 | liblapack.so.3,
[...]
                  ^^^^^^^^^^^^^^^^^^^^^^^         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Any suitable LAPACK and BLAS package providing libblas3 / liblapack3 can be
used -- plug and play. And OpenBLAS plays along.

Also:
 
| I did the following:
| 
| ./configure --enable-BLAS-shlib --enable-R-shlib LIBnn=lib 
| --with-blas="-L/usr/lib/openblas-base/ -lopenblas" 
| --enable-memory-profiling --with-x=yes
| 
| 
| go the output:
| 
| R is now configured for x86_64-unknown-linux-gnu
| 
|    Source directory:          .
|    Installation directory:    /usr/local
| 
|    C compiler:                gcc -std=gnu99  -g -O2
|    Fortran 77 compiler:       gfortran  -g -O2
| 
|    C++ compiler:              g++  -g -O2
|    C++ 11 compiler:           g++  -std=c++0x -g -O2
|    Fortran 90/95 compiler:    gfortran -g -O2
|    Obj-C compiler:
| 
|    Interfaces supported:      X11
|    External libraries:        readline, BLAS(generic), lzma
                                          ^^^^^^^^^^^^^^

tells you that you failed to tell the build about your OpenBLAS. It fell back
to generic.

This is all in the 'Installation + Administration' manual. But you
really
don't need to do this by hand.

I suggest you send follow-up to the r-sig-debian list. Its archives also have
past discussions of this and related questions.

Regards,  Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org