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

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

[Thomas Kahle]

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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,
Thomas



-- 
Thomas Kahle
http://dev.gentoo.org/~tomka/

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

[Francois Bissey]

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.

Copying you directly in case it doesn't make it to the list.

Francois

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

[Thomas Kahle]

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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)

Hope this helps,
Cheers,
Thomas

-- 
Thomas Kahle
http://dev.gentoo.org/~tomka/

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

[Francois Bissey]

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

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

[Thomas Kahle]

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On 14:05 Sat 02 Jun 2012, Francois Bissey wrote:
[...]
> 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.


Yes, that worked.  Now I just get the two 'skipped update' warnings for
singular and pexpect.  Excellent.  Thanks so much!



-- 
Thomas Kahle
http://dev.gentoo.org/~tomka/

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