R SIG Debian - Mar 2009 - How to change Rlapack by lapack (for rpy2 installation)?

(I asked an earlier question on the rpy2 installation
to the rpy2 list, the solution there was to
edit the setup.py script, but this looks beyond what I can do unless
someone tells me exactly what to modify).

I have R 2.8.1 on 2 machines running ubuntu 8.04
(packages R-base and R-base-dev, among others, installed using Synaptic) 
and while the installation
of rpy2 went fine on machine1, failed on machine2 with:

python setup.py install
/usr/bin/ld: cannot find -lRlapack
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

I think that the reason is that while on machine1 I get:
R CMD config LAPACK_LIBS
-llapack

on machine2 I get
R CMD config LAPACK_LIBS
-L/usr/lib/R/lib -lRlapack

Could someone tell me (or point me to a relevant link) what should I do 
in order to reconfigure R on machine2
so that it has the same liblapack settings than machine1 ?
(I really don't remember having done anything different on
machine2 for installing R, but probably I did)

Thanks

Agus

Sorry, my e-mail went too early, give some more complements about the
problem I had which may be similar to yours

2009/3/21, Matthieu Stigler <Matthieu.Stigler at
gmail.com>:
> I had I similar problem and could not really resolve it... I can give you
> nevertheless some hints:
>
>
> It looks like there is a bug, missing library, or change in the set-up of
> libRlapack with Ubuntu 8.04,
> see:
>
-http://sourceforge.net/mailarchive/forum.php?thread_name=de8c7cb40809160055mbc5af8fu55cfd1c19f915f08
at mail.gmail.com&forum_name=rkward-users
The solution I found was to
cd /usr/lib/R/modules
sudo ln -s ./lapack.so ./libRlapack.so

But this is pretty dirty... Dirk Eddelbuettel kindly directed me to:

R actually tells you what to use, so this is easy to fix with a modicum of
configure scripting knowledge:

edd at ron:~$ R CMD config --help
Usage: R CMD config [options] [VAR]

Get the value of a basic R configure variable VAR which must be among
those listed in the 'Variables' section below, or the header and
library flags necessary for linking against R.

Options:
  -h, --help            print short help message and exit
  -v, --version         print version info and exit
      --cppflags        print pre-processor flags required to compile
			a program using R as a library
      --ldflags         print linker flags needed for linking against
			the R library

Variables:
  BLAS_LIBS     flags needed for linking against external BLAS libraries
  CC            C compiler command
  CFLAGS        C compiler flags
  CPICFLAGS     special flags for compiling C code to be turned into a
		shared library
  CPP           C preprocessor
  CPPFLAGS      C/C++ preprocessor flags, e.g. -I<dir> if you have
		headers in a nonstandard directory <dir>
  CXX           C++ compiler command
  CXXCPP        C++ preprocessor
  CXXFLAGS      C++ compiler flags
  CXXPICFLAGS   special flags for compiling C++ code to be turned into a
		shared library
  DYLIB_EXT	file extension (including '.') for dynamic libraries
  DYLIB_LD      command for linking dynamic libraries which contain
		object files from a C or Fortran compiler only
  DYLIB_LDFLAGS
		special flags used by DYLIB_LD
  F77           Fortran 77 compiler command
  FFLAGS        Fortran 77 compiler flags
  FLIBS         linker flags needed to link Fortran code
  FPICFLAGS     special flags for compiling Fortran code to be turned
		into a shared library
  FC            Fortran 9x compiler command
  FCFLAGS       Fortran 9x compiler flags
  FCPICFLAGS    special flags for compiling Fortran 9x code to be turned
		into a shared library
  JAR           Java archive tool command
  JAVA          Java interpreter command
  JAVAC         Java compiler command
  JAVAH         Java header and stub generator command
  JAVA_HOME     path to the home of Java distribution
  JAVA_LIBS     flags needed for linking against Java libraries
  JAVA_CPPFLAGS C preprocessor flags needed for compiling JNI programs
  LAPACK_LIBS   flags needed for linking against external LAPACK libraries
  LIBnn         location for libraries, e.g. 'lib' or 'lib64' on
this platform
  LDFLAGS       linker flags, e.g. -L<dir> if you have libraries in a
		nonstandard directory <dir>
  OBJC          Objective C compiler command
  OBJCFLAGS     Objective C compiler flags
  MAKE          Make command
  SAFE_FFLAGS   Safe (as conformant as possible) Fortran 77 compiler flags
  SHLIB_CFLAGS  additional CFLAGS used when building shared objects
  SHLIB_CXXLD   command for linking shared objects which contain
		object files from a C++ compiler
  SHLIB_CXXLDFLAGS
		special flags used by SHLIB_CXXLD
  SHLIB_EXT	file extension (including '.') for shared objects
  SHLIB_FFLAGS  additional FFLAGS used when building shared objects
  SHLIB_LD      command for linking shared objects which contain
		object files from a C or Fortran compiler only
  SHLIB_LDFLAGS
		special flags used by SHLIB_LD
  SHLIB_FCLD, SHLIB_FCLDFLAGS
		ditto when using Fortran 9x
  TCLTK_CPPFLAGS
		flags needed for finding the tcl.h and tk.h headers
  TCLTK_LIBS    flags needed for linking against the Tcl and Tk libraries

Report bugs to <r-bugs at r-project.org>.
edd at ron:~$ R CMD config --ldflags
-L/usr/lib/R/lib -lR
edd at ron:~$ R CMD config BLAS_LIBS
-lblas
edd at ron:~$ R CMD config LAPACK_LIBS
-llapack
edd at ron:~$

Hope that helps
> -the bug I commited:
> https://bugs.launchpad.net/ubuntu/+source/rmatrix/+bug/299141
> Agustin Lobo a ?crit :
>>
>> (I asked an earlier question on the rpy2 installation
>> to the rpy2 list, the solution there was to
>> edit the setup.py script, but this looks beyond what I can do unless
>> someone tells me exactly what to modify).
>>
>> I have R 2.8.1 on 2 machines running ubuntu 8.04
>> (packages R-base and R-base-dev, among others, installed using
Synaptic)
>> and while the installation
>> of rpy2 went fine on machine1, failed on machine2 with:
>>
>> python setup.py install
>> /usr/bin/ld: cannot find -lRlapack
>> collect2: ld returned 1 exit status
>> error: command 'gcc' failed with exit status 1
>>
>> I think that the reason is that while on machine1 I get:
>> R CMD config LAPACK_LIBS
>> -llapack
>>
>> on machine2 I get
>> R CMD config LAPACK_LIBS
>> -L/usr/lib/R/lib -lRlapack
>>
>> Could someone tell me (or point me to a relevant link) what should I do
in
>> order to reconfigure R on machine2
>> so that it has the same liblapack settings than machine1 ?
>> (I really don't remember having done anything different on
>> machine2 for installing R, but probably I did)
>>
>> Thanks
>>
>> Agus
>>
>>
>>
>> ________________________________
>> _______________________________________________
>> R-SIG-Debian mailing list
>> R-SIG-Debian at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>>
>
>
>

On 21 March 2009 at 08:04, Agustin Lobo wrote:
| (I asked an earlier question on the rpy2 installation
| to the rpy2 list, the solution there was to
| edit the setup.py script, but this looks beyond what I can do unless
| someone tells me exactly what to modify).
| 
| I have R 2.8.1 on 2 machines running ubuntu 8.04
| (packages R-base and R-base-dev, among others, installed using Synaptic) 
| and while the installation
| of rpy2 went fine on machine1, failed on machine2 with:
| 
| python setup.py install
| /usr/bin/ld: cannot find -lRlapack
| collect2: ld returned 1 exit status
| error: command 'gcc' failed with exit status 1
| 
| I think that the reason is that while on machine1 I get:
| R CMD config LAPACK_LIBS
| -llapack
| 
| on machine2 I get
| R CMD config LAPACK_LIBS
| -L/usr/lib/R/lib -lRlapack
| 
| Could someone tell me (or point me to a relevant link) what should I do 
| in order to reconfigure R on machine2
| so that it has the same liblapack settings than machine1 ?
| (I really don't remember having done anything different on
| machine2 for installing R, but probably I did)

I think you need to figure how you installed R and try to do the same thing
on both machines, preferably getting the R packages from CRAN.

If you have inconsistent behaviour on both machines you probably installed
different versions, or from different places, or ...   Bytes don't flip like
that by themselves.

Dirk

-- 
Three out of two people have difficulties with fractions.