[R-sig-Debian] LAPACK libraries improperly linked

[Ron Burns]

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!

Thank you all for your consideration.
      Ron Burns


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