Juergen Rose | 17 Jun 20:36 2015

sage-6.7 and downgrade of python packages


I removed sage-6.7 from my gentoo system, because it requires old
python packages. These old python generates further bugs. I posted a
gentoo bug https://bugs.gentoo.org/show_bug.cgi?id=547064 , but I did
not get any answer.

If I now try to reinstall sage, three python packages should be
downgraded generating a slot conflict:

root <at> lynx:/root(43)# emerge -pvD sage

These are the packages that would be merged, in order:

Calculating dependencies... done!
[ebuild     UD ] dev-python/numpy-1.8.2::gentoo [1.9.2::gentoo]
USE="doc lapack {-test}" PYTHON_TARGETS="python2_7 python3_3 
-python3_4" 0 KiB
[ebuild     UD ] dev-python/sphinx-1.2.2::sage-on-gentoo
[1.3.1::gentoo] USE="doc latex {-test}" PYTHON_TARGETS="python2_7
python3_3 -pypy -python3_4" 0 KiB
[ebuild     UD ] dev-python/matplotlib-1.3.1::sage-on-gentoo
[1.4.3::gentoo] USE="cairo examples excel fltk gtk gtk3 latex tk
wxwidgets -doc -pyside -qt4* {-test} (-qt5%*)"
PYTHON_TARGETS="python2_7 python3_3 -python3_4" 0 KiB
[ebuild     UD ] sci-mathematics/maxima-5.35.1-r2::sage-on-gentoo
[5.36.1::gentoo] USE="X ecls emacs latex nls sbcl tk unicode -clisp 
-clozurecl (-cmucl) -gcl -xemacs" LINGUAS="-es -pt -pt_BR" 0 KiB
[ebuild  N     ] sci-mathematics/sage-6.7::sage-on-gentoo  USE="latex
testsuite -arb -bliss -debug -modular_decomposition"
(Continue reading)

Zeev Pekar | 8 Jun 12:30 2015

Open-sourced: OpenCL-based multiphysics simulation software package

Dear Gentoo community,

we would like to announce the recent open-source release of our
GPU-enabled multiphysics software - Advanced Simulation Library.

Here are some remarkable benchmarks:

I hope that it will be included in Gentoo as a package in some near
future (any volunteers?) but till then you might find it useful in its
current form.

Happy hacking,

ps: Please, "like" us on Facebook, if you find ASL cool:

Justin Lecher (jlec | 6 Jun 14:44 2015

eselect alternatives module

Hi everyone,

I worked on the alternatives module and released it to the wild.

If there are no serious bugs coming up in the next month, I will make
it ready for merge into the main eselect.

meanwhile the code is here https://github.com/gentoo-science/eselect
and please comment or report any bug.

We finally need this thing to be finished.

grozin | 21 Apr 04:09 2015

problem syncing the science overlay

Hello *,

Today I get

dns ~ # layman -s science

  * Fetching remote list...
  * Fetch Ok

  * Syncing selected overlay(s)...
  * Running Git... # ( cd /var/lib/layman/science  && /usr/bin/git pull )
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
  * Failure result returned from Git
  * Errors:
  * ------
  * Failed to sync overlay "science".
  * Error was: Syncing overlay "science" returned status 1!
  * db.sync()

  * CLI: Errors occurred processing action sync
  * Errors:
  * ------
  * Failed to sync overlay "science".
(Continue reading)

François Bissey | 15 Apr 12:25 2015

[sage-on-gentoo] sage-6.6 is out

Hi all,

after a protracted release cycle (especially towards the end)
sage 6.6 is finally out.

I have committed ebuild in the overlay and we are ready to 
deal with issue that escaped during the development phase.

For most release from now on there will be an initial
release of sage-doc-bin with documentation I personally 
built. This will be replaced once upstream issue their
own tarballs.

There is a big milestone in term of sage-doc. We now
have some LINGUAS support for sage-doc and 
sage-doc-bin. The only restriction is that if you want html
doc (as required by the sage notebook) LINGUAS=en
is mandatory. This was also committed for 6.5 earlier this

“en” is the only complete set of documentation amongst
all the languages provided by sage. It is also the default
when loading help from the notebook. Making that bit
LINGUAS aware is not trivial at all.

We are continuing on improving the sage-doc ebuild
and trying to reduce its size. I have a very significant
slimming feature in the live ebuild that is undergoing tests.
I hope it will prove effective and we’ll be able to deploy
it soon.
(Continue reading)

Thomas Kahle | 25 Mar 17:08 2015

ntl bump


dev-libs/ntl is at 8.1.2 already (we have 6.* in the tree).  I'd work on
the bump if nobody else is.

For the 6.* versions there is a patch which implements an error callback
mechanism which is used in sage.  In the 8.* versions ntl has its own
error callback, but it has a different interface than the one in our patch.

Will sage (when?) be able to deal with ntl's native mechanism or do we
need the patch?  I can translate it to the new version, but it may make
no sense.



Thomas Kahle

Thomas Kahle | 9 Mar 14:50 2015


Hi everybody,

I bumped sci-mathematics/singular to 4.0.2 in the main tree, thereby
importing the first version of the 4.0 branch there.

The 4.0.0 version does not compile anymore for me.  I think it could be
dropped from the science-overlay, but I'm not sure what its relation to
sage-on-gentoo is?

I also had to drop ppc keyword unfortunately since we don't have the new
deps sci-math/flint and sci-math/4ti2 on ppc.  Do we need Singular on ppc?


François Bissey | 3 Mar 22:13 2015

[sage-on-gentoo] sage is not blocking gmpy anymore in sage 6.5 and 9999


Almost 2 years ago almost to the day I included a line blocking the
installation of gmpy alongside sage in the sage ebuild.
This was done because I had regular reports of people breaking
sympy when both were installed at the same time - ultimately
sage was broken too but the big symptom was an un-ability to
build/reinstall sympy.

The fundamental issue seems to have fixed in mpmath upstream
so I lift the restriction today.

But it will be back if new issue are discovered.

A quick note for people wanting to use gmpy as the backend
for mpmath/sympy. By default if both gmpy and sage are installed
mpmath will use sage as its backend for arbitrary precision
computation. This is a runtime behavior that cannot be altered
by useflags. If you want to use gmpy over sage as the backend
you need to define the variable MPMATH_NOSAGE (its value is not
checked, just its existence). Similarly there is a MPMATH_NOGMPY
People interested in the mechanics of the backend should look at


Guilherme Amadio | 20 Feb 16:43 2015

Formal request to join the team

Hello everyone,

I think my announcement is still a bit fresh, so you probably know that
I recently became a Gentoo dev.

One of the areas of interest for me is gentoo-science, more
specifically, sci-physics packages, as I actually work on development of
a geant sucessor, called geantv. So I would like to formally request to
join the science team and possibly I would like to maintain geant and
related packages on Gentoo if there isn't already someone maintaining
these packages. Here are some packages I am interested in maintaining:

sci-phyiscs/geant and related geant-docs, geant-data, etc.
sci-physics/root and related packages
dev-libs/vc (currently maintained by kde herd for some reason, used in geantv)
sci-physics/clhep, dependency of geant

If there is any of you around, I'm currently working at Fermilab (as a
visitor, as I'm a postdoc at a Brazilian university).

Well, nice to "meet" you all!

Best regards,

christoph irrenfried | 5 Feb 16:03 2015

Re: Mathematica issue

On 02/05/2015 03:52 PM, Markus Oehme wrote:
> (a) Does the license server still operate (maybe your university changed the
>     setup)?
All the others on in my department have no problem with the connection
to the server. The only difference is that they are using Debian.
> (b) Are you able to reach the license server on the network (issue a ping or
>     similar)?
yes if i ping the server i get a positive response!
> (c) If both have positive answers I would contact the operator of the
>     license server for further trouble shooting.
I contacted than with the answer: That you get from using gentoo (not
the same words but it was what they meant ;( ).

The wired thing is that when I installed it after I had a fresh
installation of gentoo it worked but than I installed other stuff and it
stopped working. I installed gentoo a couple of times but it looks like
it always stops after different installations. It definitely is caused
by gentoo.

Therefore I wanted to know if someone else works with mathematica on
gentoo and if that person can give me his configuration to check it
against mine.


christoph irrenfried | 5 Feb 14:40 2015

Mathematica issue

my name is Chris and I have a huge Mathemaica problem. I need it for
work on a daily bases but after I did my regular update a couple mounths
ago it just wont start again. I filed this issue on the gentoo forum but
I cant find a way to get rid of this problem. The error message is as a
pic included.
Than a couple weeks ago I bought a laptop and installed gentoo with
gnome on it but there aswell and I got the same error. I have
no idea what's the problem. I wanted to ask you if someone has a
gentoo/gnome system with mathematica running and if so if it is possible
to get the USE flags from your make.conf or I don't know if there is a
way to compare my settings with your system and see if maybe (or
definitely) I messed something up e.g. fonts or something ....

Thanks in advance,