Re: [gentoo-science] World updates with sage installed - portage bug?

[Francois Bissey <fbissey@slingshot.co.nz>]

On Fri, 01 Jun 2012 23:13:58 Thomas Kahle wrote:
> On 07:26 Sat 02 Jun 2012, Francois Bissey wrote:
> > On Fri, 01 Jun 2012 11:52:24 Thomas Kahle wrote:
> > > Hi,
> > > 
> > > now that I have sage-on-gentoo installed I can't do world updates with
> > > the -D option anymore.  Looks like a portage quirk to me.
> > > 
> > > There seem to be at least two problems:
> > > 
> > > I have sci-mathematics/singular in my world file and the -D option
> > > forces portage to think that I insist on the latest version.  Therefore
> > > it collides with sage-on-gentoo insisting on 3.1.3:
> > > 
> > > sci-mathematics/singular:0
> > > 
> > >   (sci-mathematics/singular-3.1.3.3::gentoo, installed) pulled in by
> > >   
> > >     ~sci-mathematics/singular-3.1.3.3 required by
> > > 
> > > (sci-mathematics/sage-5.0-r1::sage-on-gentoo, installed)
> > > 
> > >   (sci-mathematics/singular-3.1.4-r1::gentoo, ebuild scheduled for
> > >   merge)
> > > 
> > > pulled in by (no parents that aren't satisfied by other packages in this
> > > slot)
> > > 
> > > 
> > > There also is an eselect issue.  I don't know why, but eselect-blas and
> > > eselect-lapack are pulled in, although blocked by the new gsl:
> > > 
> > > [blocks B      ] app-admin/eselect-blas ("app-admin/eselect-blas" is
> > > blocking sci-libs/gsl-1.15-r2, sci-libs/cblas-reference-20110218)
> > > [blocks B
> > > 
> > >      ] app-admin/eselect-lapack ("app-admin/eselect-lapack" is blocking
> > > 
> > > sci-libs/gsl-1.15-r2, sci-libs/cblas-reference-20110218)
> > > 
> > > However, without the -D option I just get a warning:
> > > 
> > > WARNING: One or more updates have been skipped due to a dependency
> > > conflict:
> > > 
> > > sci-mathematics/singular:0
> > > 
> > >   (sci-mathematics/singular-3.1.4-r1::gentoo, ebuild scheduled for
> > >   merge)
> > > 
> > > conflicts with ~sci-mathematics/singular-3.1.3.3 required by
> > > (sci-mathematics/sage-5.0-r1::sage-on-gentoo, installed)
> > > 
> > > 
> > > Any ideas?  Shall I carry this to the portage mailing list?
> > > Cheers,
> > 
> > We need to know what pulls these eselect modules. What is the portage
> > output when you add the "t" option. It should show what wants what.
> 
> Goes back to dev-lang/R and sci-libs/superlu.  My setup has superlu
> stable, but R keyworded ~amd64 the entire slot.
> 
> [ebuild     U ~] sci-mathematics/singular-3.1.4-r1 [3.1.3.3] USE="boost doc
> emacs python%* readline -examples -test" 0 kB [nomerge       ]
> dev-lang/R-2.15.0  USE="X bash-completion cairo doc java jpeg lapack nls
> openmp perl png readline tiff tk -icu -minimal -profile -static-libs"
> [nomerge       ]  virtual/lapack-3.1
> [nomerge       ]   sci-libs/lapack-reference-3.1.1-r1  USE="-doc"
> [ebuild  N     ]    app-admin/eselect-lapack-0.1  0 kB
> [nomerge       ] sci-mathematics/sage-5.0-r1::sage-on-gentoo  USE="latex
> -testsuite" [nomerge       ]  sci-libs/scipy-0.9.0-r1  USE="-doc -umfpack"
> [nomerge       ]   sci-libs/superlu-4.1-r1  USE="-doc -examples -static-libs
> -test" [nomerge       ]    virtual/blas-1.0
> [nomerge       ]     sci-libs/blas-reference-20070226  USE="-doc"
> [ebuild  N     ]      app-admin/eselect-blas-0.1  0 kB
> [nomerge       ] sci-mathematics/sage-5.0-r1::sage-on-gentoo  USE="latex
> -testsuite" [nomerge       ]  dev-python/sympy-0.7.1  USE="gtk latex opengl
> pdf png -doc -examples -imaging -ipython -mathml -pyglet -test -texmacs"
> [ebuild     U  ]   dev-python/pexpect-2.4::gentoo [2.0-r1::sage-on-gentoo]
> USE="-doc% -examples%" 0 kB [blocks B      ] app-admin/eselect-lapack
> ("app-admin/eselect-lapack" is blocking sci-libs/gsl-1.15-r2,
> sci-libs/cblas-reference-20110218) [blocks B      ] app-admin/eselect-blas
> ("app-admin/eselect-blas" is blocking sci-libs/gsl-1.15-r2,
> sci-libs/cblas-reference-20110218)
> 
You have the virtual/{blas,lapack} from the main tree not from the science
overlay! Now I am not sure why eselect-blas blocks gsl which gives you cblas.
Anyway keyword virtual/{blas,cblas,lapack} and upgrade them. Then let's see
if you still have troubles.

Francois