Jauhien Piatlicki | 15 Aug 13:36 2015

Remove wrong branch

Hi all,

I have pushed a branch named gentoo-master to the gentoo science git
repo on git.gentoo.org by a mistake. I can't remove it now. Please,
somebody, who has permissions, remove it.


François Bissey | 27 Jul 04:01 2015

[sage-on-gentoo] sage(math) 6.8 is out

And sage-on-gentoo has undergone a substantial change
during the development phase....

So what is different:
this is a monolithic ebuild, in the past we had split sage
in various components, the scripts, the sage-clib sage and
the documentation. Over the last year or two only the
separation of sage-clib was strictly necessary.

sage-clib being gone upstream we had an opportunity to house
everything under one roof. The separation was always
arbitrary as there is not much you can do with the scripts
without sage itself. Possibly you could have used sage from
python without needing the scripts (strictly speaking a couple
of files would probably need to be moved from one ebuild to
the other for it to work 100%).

The only things that are still separate are things that are
split in a different package upstream, sage-data packages.
Most of them cannot be used without sage and at least one is
needed for sage to start.

So when you move to sage-6.8 the following ebuilds will need
to go:
sage-doc or sage-doc-bin

Special notes:
* ntl 9.3.0: this version of sage moves to the latest version
(Continue reading)

Zeev Pekar | 21 Jul 20:10 2015

Packaging ASL

Dear Gentoo Developers,

We have just released the version 0.1.4 of ASL - Advanced Simulation
Library <http://asl.org.il>.

May I ask somebody to volunteer to package it for Gentoo?

Packaging efforts for other distros are underway and probably can be
helpful for Gentoo [1].

Thank you,
ps: opened an issue: https://github.com/gentoo-science/sci/issues/452

In short about the library:
It is an OpenCL-based multiphysics simulation software that can be
deployed (besides CPU) on different massively parallel architectures
like GPUs, FPGAs, DSPs etc. and covers a variety of physical and
phenomena. It can be utilized in a number of fields:

- CFD: http://asl.org.il/benchmarks/multicomponent_flow/
- image-guided surgery: http://avtechscientific.com/cryovision
- crystal growth:
- virtual sensing (i.a. medical): http://avtechscientific.com/brainshift
- R&D of biomed devices (i.a. microfluidics):
- etc., etc..
(Continue reading)

François Bissey | 21 Jul 04:44 2015

alternatives is broken on prefix

More precisely we have a double prefix problem.

Long long time ago I had inserted a band aid in the ebuild
and it is still there:
	if use prefix; then
		cd "${ED}"/usr/share/eselect/libs || die
		sed -i 
alternatives.bash || die

Unfortunately I am not sure if it still applies, but what is
certain is that there are double prefix somewhere else and I am
chasing them.

The first instance seems to be in
which may just be where the original double prefix I corrected
ended up but that has to be checked.
Correcting it there is however insufficient to restore functionality,
as in `eselect blas set xxx` doesn't seem to create the required link.


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?