[R-sig-Debian] problems loading blas with R 2.11.0~20100402-1

[Sebastian P. Luque]

On Fri, 09 Apr 2010 10:09:04 -0500,
"Sebastian P. Luque" <spluque at gmail.com> wrote:

> On Fri, 09 Apr 2010 14:27:30 +0200,
> Sylvestre Ledru <sylvestre at debian.org> wrote:

> Le vendredi 09 avril 2010 à 06:17 -0500, Dirk Eddelbuettel a écrit :
>>> On 8 April 2010 at 23:15, Sebastian P. Luque wrote:
>>> | Hi,
>>> | 
>>> | Since upgrading to version 2.11.0~20100402-1, starting R fails
>>> with:
>>> | 
>>> | /usr/lib64/R/bin/exec/R: error while loading shared libraries:
>>> libblas.so.3gf: cannot open shared object file: No such file or
>>> directory
>>> | 
>>> | Is this occurring to others on sid?

>>> I use Debian testing, and that same version works fine there.

>>> This could be related to the recent Atlas / Blas change in
>>> unstable. CCing Sylvestre just in case. Maybe we take this off-line
>>> and compare blas + atlas package versions?
>> Can you tell me which versions of blas and lapack (and atlas if
>> relevant) you are using ?  Both libraries and developments packages,

> Sure, this is with:

> $ dpkg-query -l 'libblas*'
> Desired=Unknown/Install/Remove/Purge/Hold
> | Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name              Version           Description
> +++-=================-=================-==================================================
> un  libblas-3.so      <none>            (no description available)
> un  libblas-3gf.so    <none>            (no description available)
> ii  libblas-dev       1.2-7             Basic Linear Algebra Subroutines 3, static library
> un  libblas.so.3gf    <none>            (no description available)
> ii  libblas3gf        1.2-7             Basic Linear Algebra Reference implementations, sh
> $ dpkg-query -l 'liblapack*'
> Desired=Unknown/Install/Remove/Purge/Hold
> | Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name              Version           Description
> +++-=================-=================-==================================================
> un  liblapack-3.so    <none>            (no description available)
> un  liblapack-3gf.so  <none>            (no description available)
> ii  liblapack-dev     3.2.1-7           library of linear algebra routines 3 - static vers
> un  liblapack.so.3gf  <none>            (no description available)
> ii  liblapack3gf      3.2.1-7           library of linear algebra routines 3 - shared vers
> $ dpkg-query -l 'libatlas*'
> Desired=Unknown/Install/Remove/Purge/Hold
> | Status=Not/Inst/Cfg-files/Unpacked/Failed-cfg/Half-inst/trig-aWait/Trig-pend
> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
> ||/ Name              Version           Description
> +++-=================-=================-==================================================
> un  libatlas-base-dev <none>            (no description available)
> un  libatlas.so.3gf   <none>            (no description available)
> un  libatlas3gf-3dnow <none>            (no description available)
> ii  libatlas3gf-base  3.8.3-19          Automatically Tuned Linear Algebra Software, gener
> un  libatlas3gf-sse   <none>            (no description available)
> un  libatlas3gf-sse2  <none>            (no description available)

Following-up here, rather than forwarding in a separate message (as I
just did!), to keep the thread.

One of the Debian maintainers of the Blas and Lapack packages (Silvestre
Ledru) suggested to try this:

---<--------------------cut here---------------start------------------->---
$ sudo update-alternatives --verbose  --auto libblas.so.3gf
update-alternatives: warning: forcing reinstallation of alternative /usr/lib/atlas-base/atlas/libblas.so.3gf because link group libblas.so.3gf is broken.
$ sudo update-alternatives --verbose  --auto liblapack.so.3gf
update-alternatives: warning: forcing reinstallation of alternative /usr/lib/atlas-base/atlas/liblapack.so.3gf because link group liblapack.so.3gf is broken.
---<--------------------cut here---------------end--------------------->---

which indeed fixed the problem in my case.  Thanks Silvestre and Dirk
for all the work!


-- 
Seb