marco restelli | 20 May 15:34 2016
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Failed emerge for sci-visualization/mayavi-4.4.2

Hi,
   I have a problem emerging sci-visualization/mayavi-4.4.2: here is
the error message:

>>> Compiling source in /var/tmp/portage/sci-visualization/mayavi-4.4.2/work/mayavi-4.4.2 ...
 * python2_7: running distutils-r1_run_phase distutils-r1_python_compile
/usr/bin/python2.7 setup.py build
running build
----------------------------------------------------------------------
Building TVTK classes.../var/tmp/portage/sci-visualization/mayavi-4.4.2/temp/environment:
line 1434: 13669 Segmentation fault      "${ <at> }"
 * ERROR: sci-visualization/mayavi-4.4.2::science failed (compile phase):
 *   (no error message)
 *
 * Call stack:
 *     ebuild.sh, line  133:  Called src_compile
 *   environment, line 3657:  Called distutils-r1_src_compile
 *   environment, line  949:  Called _distutils-r1_run_foreach_impl
'distutils-r1_python_compile'
 *   environment, line  370:  Called python_foreach_impl
'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line 3189:  Called multibuild_foreach_variant
'_python_multibuild_wrapper' 'distutils-r1_run_phase'
'distutils-r1_python_compile'
 *   environment, line 2291:  Called _multibuild_run
'_python_multibuild_wrapper' 'distutils-r1_run_phase'
'distutils-r1_python_compile'
 *   environment, line 2289:  Called _python_multibuild_wrapper
'distutils-r1_run_phase' 'distutils-r1_python_compile'
 *   environment, line  632:  Called distutils-r1_run_phase
(Continue reading)

marco restelli | 7 Apr 16:28 2016
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Re: Failed emerge for sci-libs/trilinos-12.2.1

2016-04-07 12:25 GMT+0200, marco restelli <mrestelli <at> gmail.com>:
> Dear all,
>    I am having problems emerging sci-libs/trilinos-12.2.1.
>
> The build fails during configuration with
>
> Processing enabled TPL: BinUtils (enabled explicitly, disable with
> -DTPL_ENABLE_BinUtils=OFF)
> -- Must find at least one lib in each of the lib sets "bfd;iberty"
> -- Searching for libs in BinUtils_LIBRARY_DIRS=''
> -- Searching for a lib in the set "bfd":
> --   Searching for lib 'bfd' ...
> -- ERROR: Did not find a lib in the lib set "bfd" for the TPL 'BinUtils'!
> -- Searching for a lib in the set "iberty":
> --   Searching for lib 'iberty' ...
> -- ERROR: Did not find a lib in the lib set "iberty" for the TPL
> 'BinUtils'!
> -- ERROR: Could not find the libraries for the TPL 'BinUtils'!
> -- TIP: If the TPL 'BinUtils' is on your system then you can set:
>      -DBinUtils_LIBRARY_DIRS='<dir0>;<dir1>;...'
>    to point to the directories where these libraries may be found.
>    Or, just set:
>      -DTPL_BinUtils_LIBRARIES='<path-to-libs0>;<path-to-libs1>;...'
>    to point to the full paths for the libraries which will
>    bypass any search for libraries and these libraries will be used without
>    question in the build.  (But this will result in a build-time error
>    if not all of the necessary symbols are found.)
> -- ERROR: Failed finding all of the parts of TPL 'BinUtils' (see
> above), Aborting!

(Continue reading)

marco restelli | 7 Apr 12:25 2016
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Failed emerge for sci-libs/trilinos-12.2.1

Dear all,
   I am having problems emerging sci-libs/trilinos-12.2.1.

The build fails during configuration with

Processing enabled TPL: BinUtils (enabled explicitly, disable with
-DTPL_ENABLE_BinUtils=OFF)
-- Must find at least one lib in each of the lib sets "bfd;iberty"
-- Searching for libs in BinUtils_LIBRARY_DIRS=''
-- Searching for a lib in the set "bfd":
--   Searching for lib 'bfd' ...
-- ERROR: Did not find a lib in the lib set "bfd" for the TPL 'BinUtils'!
-- Searching for a lib in the set "iberty":
--   Searching for lib 'iberty' ...
-- ERROR: Did not find a lib in the lib set "iberty" for the TPL 'BinUtils'!
-- ERROR: Could not find the libraries for the TPL 'BinUtils'!
-- TIP: If the TPL 'BinUtils' is on your system then you can set:
     -DBinUtils_LIBRARY_DIRS='<dir0>;<dir1>;...'
   to point to the directories where these libraries may be found.
   Or, just set:
     -DTPL_BinUtils_LIBRARIES='<path-to-libs0>;<path-to-libs1>;...'
   to point to the full paths for the libraries which will
   bypass any search for libraries and these libraries will be used without
   question in the build.  (But this will result in a build-time error
   if not all of the necessary symbols are found.)
-- ERROR: Failed finding all of the parts of TPL 'BinUtils' (see
above), Aborting!

Thank you,
   Marco
(Continue reading)

François Bissey | 2 Apr 23:45 2016
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sage-on-gento/gap-on-gentoo

Hi all,

It occurred to me a few months ago, that the sage-on-gentoo overlay
was also the place to get a recent `gap`. The version in the main tree
is 4.4.12 and in the sage-on-gentoo overlay we have some 4.7.x and 
4.8.x. However while functional and sufficient to work with sage,
gap from the overlay stinks. And then there is the issue of gap packages.

Unlike R, gap doesn’t have a nice package installer and you cannot
just drop them in a user space (that I know off).
Also package’s documentation is messy and expected inside the 
package. The format seems to be html, new style doc, or tex, old
style doc. So often we have both in separate folder.

I also discovered there is something called `gac` to precompile
packages that hasn’t been exposed by the current ebuild. And a 
good thing too since it is fairly broken. But looking at it explains a
lot about the requirement of keeping gap’s object files around I was
told about.

So later today I will merge a new gap branch which will include a clean
up of files that we don’t want. Expose gac, offer an archive instead of
object files for gac to use, and a first batch of gap packages in a new
dev-gap category. Anyone wanting to know why I want a new category,
there are a lots of packages at 
http://www.gap-system.org/Packages/packages.html 
and a new category will eft any possible ambiguity. 
I am concentrating on packages standardly used in sage but I’ll take 
request and certainly PR for new packages.

(Continue reading)

Justin Lecher (jlec | 17 Feb 15:20 2016
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Gravatar

BOINC needs maintainer

Hi,

currently BOINC supposed to be maintained by the science team, but we
are not really carrying about it. Is there anyone around whole likes to
take this over?

Thanks for your help,

Justin

Thomas Kahle | 27 Jan 12:36 2016
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Gravatar

Singular in sage-on-gentoo

Hi,

Can somebody from sage-on-gentoo please check
https://bugs.gentoo.org/show_bug.cgi?id=572626
This is a build failure with the sage-on-gentoo version of singular that
was assigned to me.  Maybe the metadata in sage-on-gentoo should be
fixed too.  I don't really feel responsible for this branch.

Cheers,
Thomas

--

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

Jauhien Piatlicki | 12 Jan 22:25 2016
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Gravatar

Re: [Herwig] Herwig 7.0.0 release

Hi David,

thank you very much for answer. I will proceed this way.

Regards,
Jauhien

On 01/11/2016 10:35 AM, David Grellscheid wrote:
> Hi Jauhien,
> 
> The package should certainly be called just Herwig from now on. I don't
> know the Gentoo system well, but is it possible to do a transitional
> meta-package Herwig++-3.0.0 that only has a hard requirement on
> Herwig-7.0.0? This would help users with the transition.
> 
> Thanks,
> 
>   David
> 
> 
> On 03/01/2016 11:33, Jauhien Piatlicki wrote:
>> Hi,
>>
>> Herwig 7.0.0 has been released recently: https://herwig.hepforge.org/
>> http://arxiv.org/abs/1512.01178. Its code base is a direct development
>> of the Herwig++ code, but the name was changed to Herwig, as Herwig++
>> completely replaces old HERWIG now.
>>
>> The question is under what name should we package it now and how to
>> proceed, so users get the expected updates?
(Continue reading)

Justin Lecher (jlec | 7 Jan 14:50 2016
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Gravatar

packages to grab


Dear everyone,

due to changes in real life I need to cut back vastly my day to day
maintainer work starting in February. So far I have no clue how much
time I can devote to Gentoo in nearer future.

I will move all packages I maintain [1] to the associated projects if
possible. All devs are free to take what ever you are interested in. I
am also happy to proxy contributors if they like to maintain a package.

My plan is to focus more on task which I can handle more flexible.

Regarding the projects I am involved in I have the following ideas:

_Recruiters_

We are again actively looking for someone who is doing the review
session. The candidate should have solid knowledge about the various
aspects for Gentoo reaching from packaging to institutional aspects.
Further, you should be able to work with inexperienced contributors
and have fun teaching the necessary bits.

Secondly, I would like to work strategically on our recruitment
process. This includes reworking of the quizzes and a general
assessment of the process as well as new options. We won't change
anything over night, but I really think we can do simpler and better.

In case you are interested in either topic, feel free to drop a mail
to recruiters <at> gentoo.org.
(Continue reading)

Jauhien Piatlicki | 3 Jan 12:33 2016
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Gravatar

Herwig 7.0.0 release

Hi,

Herwig 7.0.0 has been released recently: https://herwig.hepforge.org/
http://arxiv.org/abs/1512.01178. Its code base is a direct development
of the Herwig++ code, but the name was changed to Herwig, as Herwig++
completely replaces old HERWIG now.

The question is under what name should we package it now and how to
proceed, so users get the expected updates?

--
Jauhien

marco restelli | 3 Dec 14:47 2015
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File collision with mpich under empi

Hi,
   I have installed mpich (sys-cluster/mpich-3.1.4-r1, with uses cxx,
fortran, mpi-threads, romio, -doc, -threads) and I would also like
having the same MPI implementation under "eselect mpi", using empi as
described here:

https://wiki.gentoo.org/wiki/Empi

The problem is that if I do

/usr/bin/empi --create --class mpi-mpich sys-cluster/mpich

I see the following file collisions:

 * Detected file collision(s):
 *
 * 	/usr/share/doc/mpich-3.1.4-r1/README.bz2
 * 	/usr/share/doc/mpich-3.1.4-r1/README.envvar.bz2
 * 	/usr/share/doc/mpich-3.1.4-r1/CHANGES.bz2

Removing those 3 files fixes the problem, until the next emerge.

Marco

François Bissey | 1 Dec 01:56 2015
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lapack 3.6.0 harmful for scipy

So lapack 3.6.0 landed while I wasn't looking.
scipy (0.16.1) doesn't like it:
ldd -r /usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so
         linux-vdso.so.1 (0x00007fff84da2000)
         libopenblas_threads.so.0 => /usr/lib64/libopenblas_threads.so.0 
(0x00007f5ac2513000)
         libreflapack.so.3 => /usr/lib64/libreflapack.so.3 
(0x00007f5ac1d4d000)
         libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 
(0x00007f5ac198e000)
         libc.so.6 => /lib64/libc.so.6 (0x00007f5ac15f3000)
         libm.so.6 => /lib64/libm.so.6 (0x00007f5ac12ee000)
         libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f5ac10d2000)
         libgfortran.so.3 => 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libgfortran.so.3 (0x00007f5ac0daa000)
         libgcc_s.so.1 => 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libgcc_s.so.1 (0x00007f5ac0b92000)
         libdl.so.2 => /lib64/libdl.so.2 (0x00007f5ac098e000)
         libutil.so.1 => /lib64/libutil.so.1 (0x00007f5ac078b000)
         /lib64/ld-linux-x86-64.so.2 (0x00007f5ac2da9000)
         libquadmath.so.0 => 
/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3/libquadmath.so.0 (0x00007f5ac054c000)
undefined symbol: sgegv_ 
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: dgegv_ 
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: cgegv_ 
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
undefined symbol: zgegv_ 
(/usr/lib64/python2.7/site-packages/scipy/linalg/_flapack.so)
(Continue reading)


Gmane