[R-sig-Debian] LAPACK libraries improperly linked

[Ron Burns]

Thank you very much, Dirk. Installing libatlas-base-dev did the trick!

Best Regards,
  Ron

On 11/14/2010 03:20 PM, Dirk Eddelbuettel wrote:
>
> On 14 November 2010 at 14:52, Ron Burns wrote:
> | Dear All,
> |
> | As suggested in the reply from Dirk Eddelbuettel to my post to R-dev I
> | am reposting here as the problem still persists. Please see my post to
> | R-dev under same heading for additional description if needed.
> |
> | In summary I am starting from a new installation of Ubuntu 10.10 as the
> | single operating system on a reformatted disk with just the OS, ESS and
> | emacs installed before installing R version 2.12.0 (2010-10-15) in
> | accordance with the instructions on the CRAN site. All went well until I
> | started to install the additional packages I use and found multiple
> | cases of (e.g. for lme4) of the following compilation error:
> |
> |   gcc -shared -o lme4.so init.o lmer.o local_stubs.o -llapack -lf77blas
> |   -latlas -lgfortran -lm -L/usr/lib/R/lib -lR
> |   /usr/bin/ld: cannot find -lf77blas
> |   /usr/bin/ld: cannot find -latlas
> |
> |
> |   ---------BUT
> |   [ 48 ]<wow>  (ron) /usr/bin/R CMD config LAPACK_LIBS
> |   -llapack
> |
> |   ---------AND
> |<wow>  (ron) dpkg -l | grep lapack
> |   ii  liblapack-dev                        3.2.1-8
> |   library of linear algebra routines 3 - static version
> |   ii  liblapack3gf                         3.2.1-8
> |   library of linear algebra routines 3 - shared version
> |   [ 44 ]<wow>  (ron)
> |
> | Based on Dirk's suggestion:
> |
> | "I think you were pretty close by looking at lapack-dev and blas-dev,
> | but you
> | missed atlas-dev.  Simply do
> |
> |      $ sudo apt-get install r-base-dev "
> |
> | I had already done this but tried again with indication that the latest
> | version is already installed. Taking the clue that atlas-dev may be
> | missing I tried
> |
> |<wow>  (ron) dpkg -l | grep atlas
> |   ii  libatlas3gf-base                         3.2.1-8
> |   Automatically Tuned Linear Algebra Software, generic shared
> |
> | So don't see an atlas-dev and r-base-dev does not seem to be installing
> | it for me. The following does not help me either:
> |
> |<wow>  (ron) sudo apt-get install atlas-dev
> | [sudo] password for ron:
> | Reading package lists... Done
> | Building dependency tree
> | Reading state information... Done
> | Package atlas-dev is not available, but is referred to by another package.
> | This may mean that the package is missing, has been obsoleted, or
> | is only available from another source
> |
> | E: Package 'atlas-dev' has no installation candidate
> |
> | and does seem to verify the fact that another package need it.
> |
> | So I am still at a loss as to where to go from here. Sorry for the
> | multiple postings. I hope this is finally the right list!
>
> Sure is. Try 'libatlas-base-dev' -- I used the old package name atlas-dev earlier.
>
> This is definitely something that ought to work (and more easily to
> boot). We'll get there.
>
> Dirk
>


-- 
R. R. Burns
Physicist (Retired)
Oceanside, CA