R SIG Debian - Oct 2012 - [R-sig-hpc] Debian/Ubuntu + threaded BLAS/ATLAS (solved)

On 15 March 2012 14:09, Simon Urbanek <simon.urbanek@r-project.org> wrote:
> I thought I'll post this here since I could not find an answer anywhere
I
> searched: how to setup R with threaded BLAS on Debian/Ubuntu.
>
> First, neither Debian nor Ubuntu come with optimized ATLAS binaries,
> simply because by definition they need to be optimized for a particular
> machine. The good news: it is easy to build:
>
> apt-get source atlas
> cd atlas-3.*
> # less debian/README.Debian # read the docs - it's short
> # sudo apt-get build-dep atlas # <- you may need this if you don't
have
> all tools installed
> fakeroot debian/rules custom
>
> That will give you (after a long while) a bunch of libatlas*.deb files
> that you can easily install with sudo dpkg -i
>
>
I tried following these instructions with ATLAS 3.8.4-8 on Ubuntu 12.04,
got the .deb files, but I get conflicts with libblas3gf (see below), any
ideas?

Thanks,
Gad

$ sudo dpkg -i *.deb
dpkg: regarding libatlas3-base_3.8.4-8ubuntu1+custom2_amd64.deb containing
libatlas3-base:
 libatlas3-base breaks libblas3gf (<< 1.2.20110419-3)
  libblas3gf (version 1.2.20110419-2ubuntu1) is present and installed.
dpkg: error processing libatlas3-base_3.8.4-8ubuntu1+custom2_amd64.deb
(--install):
 installing libatlas3-base would break libblas3gf, and
 deconfiguration is not permitted (--auto-deconfigure might help)
Selecting previously unselected package libatlas3gf-base.
(Reading database ... 142932 files and directories currently installed.)
Unpacking libatlas3gf-base (from
libatlas3gf-base_3.8.4-8ubuntu1+custom2_all.deb) ...
dpkg: regarding libatlas-base-dev_3.8.4-8ubuntu1+custom2_amd64.deb
containing libatlas-base-dev:
 liblapack-dev conflicts with liblapack-3.so
  libatlas-base-dev provides liblapack-3.so and is to be installed.
dpkg: error processing libatlas-base-dev_3.8.4-8ubuntu1+custom2_amd64.deb
(--install):
 conflicting packages - not installing libatlas-base-dev
Selecting previously unselected package libatlas-dev.
Unpacking libatlas-dev (from libatlas-dev_3.8.4-8ubuntu1+custom2_all.deb)
...
Selecting previously unselected package libatlas-doc.
Unpacking libatlas-doc (from libatlas-doc_3.8.4-8ubuntu1+custom2_all.deb)
...
Selecting previously unselected package libatlas-test.
Unpacking libatlas-test (from
libatlas-test_3.8.4-8ubuntu1+custom2_amd64.deb) ...
dpkg: dependency problems prevent configuration of libatlas3gf-base:
 libatlas3gf-base depends on libatlas3-base; however:
  Package libatlas3-base is not installed.
dpkg: error processing libatlas3gf-base (--install):
 dependency problems - leaving unconfigured
Setting up libatlas-dev (3.8.4-8ubuntu1+custom2) ...
Setting up libatlas-doc (3.8.4-8ubuntu1+custom2) ...
Setting up libatlas-test (3.8.4-8ubuntu1+custom2) ...
Errors were encountered while processing:
 libatlas3-base_3.8.4-8ubuntu1+custom2_amd64.deb
 libatlas-base-dev_3.8.4-8ubuntu1+custom2_amd64.deb
 libatlas3gf-base

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