Discussion on science-related applications and integration in Gentoo.

Thomas Kahle | 1 Jun 2012 11:52

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World updates with sage installed - portage bug?

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:

(Continue reading)

Francois Bissey | 1 Jun 2012 21:26

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Re: World updates with sage installed - portage bug?

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)

(Continue reading)

Andrey G. Grozin | 1 Jun 2012 22:48

Picon

sci-mathematics/form

Hello *,

Could anybody with amd64 check if sci-mathematics/form-4.0_p20120529 compiles 
and runs? It would be nice to keyword it ~amd64.

Andrey

Thomas Kahle | 1 Jun 2012 23:13

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Re: World updates with sage installed - portage bug?

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

(Continue reading)

Thomas Kahle | 1 Jun 2012 23:17

Picon

Re: sci-mathematics/form

On 03:48 Sat 02 Jun 2012, Andrey G. Grozin wrote:
> Hello *,
> 
> Could anybody with amd64 check if sci-mathematics/form-4.0_p20120529 compiles 
> and runs? It would be nice to keyword it ~amd64.

Hi,  I tested it.  It runs fine so I keyworded it (I'm also in the arch-team).

Cheers,
Thomas

--

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

Francois Bissey | 2 Jun 2012 04:05

Picon

Re: World updates with sage installed - portage bug?

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

(Continue reading)

Thomas Kahle | 2 Jun 2012 13:05

Picon

Re: World updates with sage installed - portage bug?

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/

Thomas Kahle | 6 Jun 2012 16:37

Picon

When do I need to rebuild sage?

Hi,

My sage installation from a week ago is already broken.  What is wrong?
Is this a 'revdep-rebuild' type of problem?

sage: P[1].plot()
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

RuntimeError: module compiled against API version 6 but this version of numpy is 4
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (1008, 0))

ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (273, 0))

---------------------------------------------------------------------------

--

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

Francois Bissey | 6 Jun 2012 21:38

Picon

Re: When do I need to rebuild sage?

On Wed, 06 Jun 2012 16:37:01 Thomas Kahle wrote:
> Hi,
> 
> My sage installation from a week ago is already broken.  What is wrong?
> Is this a 'revdep-rebuild' type of problem?
> 
> sage: P[1].plot()
> ---------------------------------------------------------------------------
> RuntimeError                              Traceback (most recent call last)
> 
> 
> RuntimeError: module compiled against API version 6 but this version of
> numpy is 4 ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (1008, 0))
> 
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (273, 0))
> 
> ---------------------------------------------------------------------------

I am guessing matplotlib was originally compiled with numpy-1.6.x
and then you downgraded numpy without rebuilding matplotlib or scipy.

Francois

Francois Bissey | 6 Jun 2012 23:43

Picon

Re: When do I need to rebuild sage?

I should have added, just rebuild matplotlib.

Francois who will brave the snow shortly.

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