problems loading blas with R 2.11.0~20100402-1
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 ? 06:17 -0500, Dirk Eddelbuettel a ?crit :
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