[R-sig-Debian] LAPACK libraries improperly linked

[Dirk Eddelbuettel]

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

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