On 21 March 2009 at 13:13, Matthieu Stigler wrote: | 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.stig...@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=de8c7cb40809160055mbc5af8fu55cfd1c19f915...@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
I do not recommend that approach. As I just said in another reply, "it all works for me" without any effort whatsoever. On Ubuntu, I simply point to Ubuntu repos and the Ubuntu CRAN mirror. On Debian I use my packages. $ dpkg -S /usr/lib/R/modules/lapack.so r-base-core: /usr/lib/R/modules/lapack.so $ ldd /usr/lib/R/modules/lapack.so linux-vdso.so.1 => (0x00007fff01fff000) libR.so => /usr/lib/R/lib/libR.so (0x00007fc3f987c000) liblapack.so.3gf => /usr/lib/liblapack.so.3gf (0x00007fc3f8dba000) libblas.so.3gf => /usr/lib/libblas.so.3gf (0x00007fc3f8b2a000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007fc3f884e000) libm.so.6 => /lib/libm.so.6 (0x00007fc3f85c9000) libc.so.6 => /lib/libc.so.6 (0x00007fc3f8256000) libreadline.so.5 => /lib/libreadline.so.5 (0x00007fc3f8016000) libpcre.so.3 => /lib/libpcre.so.3 (0x00007fc3f7ded000) libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007fc3f7bdb000) libz.so.1 => /usr/lib/libz.so.1 (0x00007fc3f79c3000) libdl.so.2 => /lib/libdl.so.2 (0x00007fc3f77bf000) /lib64/ld-linux-x86-64.so.2 (0x00007fc3f9fd7000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fc3f75a6000) libncurses.so.5 => /lib/libncurses.so.5 (0x00007fc3f736b000) $ dpkg -S /usr/lib/libblas.so.3gf libblas3gf: /usr/lib/libblas.so.3gf $ Dirk | 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: | | e...@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-b...@r-project.org>. | e...@ron:~$ R CMD config --ldflags | -L/usr/lib/R/lib -lR | e...@ron:~$ R CMD config BLAS_LIBS | -lblas | e...@ron:~$ R CMD config LAPACK_LIBS | -llapack | e...@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@r-project.org | >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian | >> | > | > | > | | _______________________________________________ | R-SIG-Debian mailing list | R-SIG-Debian@r-project.org | https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Three out of two people have difficulties with fractions. _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian