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
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