Vadim | 3 Sep 22:27 2006
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scipy build failure

Dear maintainers,

I get build failure when doing
 USE="umfpack fftw" emerge -v scipy

I will appreciate any advice on the matter.

i686-pc-linux-gnu-gcc: Lib/io/numpyiomodule.c
Lib/io/numpyiomodule.c: In function 'PyTypeFromChar':
Lib/io/numpyiomodule.c:698: error: 'PyArray_SBYTE' undeclared (first use
in this function)
Lib/io/numpyiomodule.c:698: error: (Each undeclared identifier is
reported only once
Lib/io/numpyiomodule.c:698: error: for each function it appears in.)
Lib/io/numpyiomodule.c: In function 'PyTypeFromChar':
Lib/io/numpyiomodule.c:698: error: 'PyArray_SBYTE' undeclared (first use
in this function)
Lib/io/numpyiomodule.c:698: error: (Each undeclared identifier is
reported only once
Lib/io/numpyiomodule.c:698: error: for each function it appears in.)
error: Command "i686-pc-linux-gnu-gcc -pthread -fno-strict-aliasing
-DNDEBUG -O3 -march=i686 -pipe -fomit-frame-pointer
-mpreferred-stack-boundary=2 -falign-functions=0 -falign-jumps=0
-falign-loops=0 -fPIC
-I/usr/lib/python2.4/site-packages/numpy/core/include
-I/usr/include/python2.4 -c Lib/io/numpyiomodule.c -o
build/temp.linux-i686-2.4/Lib/io/numpyiomodule.o" failed with exit status 1

!!! ERROR: sci-libs/scipy-0.4.9 failed.
Call stack:
(Continue reading)

Nuno Sucena Almeida | 13 Sep 15:35 2006

website python error

Hello,
	while visiting the gentoo science overlay website I get python errors, which 
disapear when I reload the page, but keeps popping up randomly...

						Nuno
--

-- 
Davide Cittaro | 13 Sep 15:40 2006
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ncbi c++ toolkit

Hi there, I see (and I have installed) that there is an ebuild for ncbi C toolkit, that includes many well known biology applications. I wonder why there is no ebuild for the ncbi C++ toolkit, also available on NCBI ftp server (and this is true also for many other package/port managers, i.e. in freebsd).

Cheers

d
/*
Davide Cittaro
HPC and Bioinformatics Systems <at> Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303355
*/




Andrey G. Grozin | 13 Sep 16:07 2006
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Re: website python error

On Wed, 13 Sep 2006, Nuno Sucena Almeida wrote:
> 	while visiting the gentoo science overlay website I get python errors, which 
> disapear when I reload the page, but keeps popping up randomly...
Yes, this is exactly what I have reported some time ago. No progress yet 
:-(

By the way, why there is no link to gentooscience.org from 
overlays.gentoo.org? It seems that there is still no regular way to find 
gentooscience.org; only those fortunate few who already know about its 
existence can use it :-(

Andrey
--

-- 
gentoo-science <at> gentoo.org mailing list

Olivier Fisette | 13 Sep 16:21 2006
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Re: ncbi c++ toolkit

On Wednesday, 13 September 2006 09:40, Davide Cittaro wrote:
> Hi there, I see (and I have installed) that there is an ebuild for
> ncbi C toolkit, that includes many well known biology applications. I
> wonder why there is no ebuild for the ncbi C++ toolkit, also
> available on NCBI ftp server (and this is true also for many other
> package/port managers, i.e. in freebsd).

Hi Davide,

The reason is lack of human resources. I think no one in the Gentoo 
development team is familiar with the NCBI C++ toolkit, so nobody has had any 
particular interest in adding it to Portage. We already have lots of new 
package requests that we try to work on from time to time, but most of our 
time is spent updating existing packages or fixing bugs.

You can help by filing an enhancement request on the Gentoo Bugzilla 
(bugzilla.gentoo.org). It will be assigned to the sci-biology project and 
maybe, eventually, we will have the time to work on it. If you can write an 
ebuild for the package yourself, that would speed up the process 
tremendously.

Cheers,

--

-- 
Olivier Fisette (ribosome)
Gentoo Linux Developer
Scientific applications, Developer relations
Davide Cittaro | 13 Sep 16:37 2006
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Re: ncbi c++ toolkit

Hi Olivier, 
On Sep 13, 2006, at 4:21 PM, Olivier Fisette wrote:

The reason is lack of human resources. I think no one in the Gentoo 
development team is familiar with the NCBI C++ toolkit, so nobody has had any 
particular interest in adding it to Portage. We already have lots of new 
package requests that we try to work on from time to time, but most of our 
time is spent updating existing packages or fixing bugs.


Just to know... how many people are involved as *active* developers in gentoo-science? I wrote some ebuilds and I submitted them on bugzilla. I wonder if it would be the case to join gentoo-science...

You can help by filing an enhancement request on the Gentoo Bugzilla 
(bugzilla.gentoo.org). It will be assigned to the sci-biology project and 
maybe, eventually, we will have the time to work on it. If you can write an 
ebuild for the package yourself, that would speed up the process 
tremendously.

At time of writing I'm testing a ncbi-c++ compilation on my system, if everything goes fine I'll write down an ebuild to submit.


Cheers,


d

-- 
Olivier Fisette (ribosome)
Gentoo Linux Developer
Scientific applications, Developer relations

/*
Davide Cittaro
HPC and Bioinformatics Systems <at> Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303355
*/




Olivier Fisette | 13 Sep 18:53 2006
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Re: ncbi c++ toolkit

On Wednesday, 13 September 2006 10:37, Davide Cittaro wrote:
> Just to know... how many people are involved as *active* developers
> in gentoo-science? I wrote some ebuilds and I submitted them on
> bugzilla. I wonder if it would be the case to join gentoo-science...

There are 10 developers (with various degrees of activity) in the gentoo 
science project, but only 3 of them are also members of the gentoo 
sci-biology subproject. Not much considering the number and diversity of 
packages we maintain.

We are always looking for more help. If you are interested, I suggest you 
begin by helping us on Bugzilla. Regular contributors are often invited to 
join the development team.

> At time of writing I'm testing a ncbi-c++ compilation on my system,
> if everything goes fine I'll write down an ebuild to submit.

Then I will definitely have a look at it.

--

-- 
Olivier Fisette (ribosome)
Gentoo Linux Developer
Scientific applications, Developer relations
Donnie Berkholz | 13 Sep 20:01 2006
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Re: ncbi c++ toolkit

Olivier Fisette wrote:
> On Wednesday, 13 September 2006 10:37, Davide Cittaro wrote:
>> Just to know... how many people are involved as *active* developers
>> in gentoo-science? I wrote some ebuilds and I submitted them on
>> bugzilla. I wonder if it would be the case to join gentoo-science...
> 
> There are 10 developers (with various degrees of activity) in the gentoo 
> science project, but only 3 of them are also members of the gentoo 
> sci-biology subproject. Not much considering the number and diversity of 
> packages we maintain.

Indeed, and one of them (me) hardly counts as biology. I'm just in there
for structural biology stuff.

Thanks,
Donnie

Marcus D. Hanwell | 14 Sep 12:24 2006
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Re: website python error

On Wednesday 13 September 2006 15:07, Andrey G. Grozin wrote:
> On Wed, 13 Sep 2006, Nuno Sucena Almeida wrote:
> > 	while visiting the gentoo science overlay website I get python errors,
> > which disapear when I reload the page, but keeps popping up randomly...
>
> Yes, this is exactly what I have reported some time ago. No progress yet
>
> :-(
>
> By the way, why there is no link to gentooscience.org from
> overlays.gentoo.org? It seems that there is still no regular way to find
> gentooscience.org; only those fortunate few who already know about its
> existence can use it :-(

I never received an email about the issue, but when I saw the post you made to 
this list I investigated and fixed the issue. I cannot reproduce this issue 
now at all. It is an amd64 Gentoo hardened web server - I will see about 
rebuilding apache, mod_python, trac etc.

Not sure about the links from the overlays.g.o, gentooscience.org was created 
before the overlays think had even been discussed as a solution to a problem. 
It is advertised here, and on the IRC channel but it would be good to get it 
more widely advertised. 

If trac has issues this does not actually effect subversion or overlay 
checkout/updates/use. I am not sure how effective trac really is on an 
ongoing basis.

I do read these lists when I get the time, but I hate to have to tell you guys 
I am swamped in real life writing up my thesis, writing papers and looking 
for a job to pay the bills... My time is severely limited right now and that 
will probably remain so until Xmas, may be November...
Andrey G. Grozin | 14 Sep 12:49 2006
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Re: website python error

On Thu, 14 Sep 2006, Marcus D. Hanwell wrote:
> Not sure about the links from the overlays.g.o, gentooscience.org was created 
> before the overlays think had even been discussed as a solution to a problem. 
> It is advertised here, and on the IRC channel but it would be good to get it 
> more widely advertised. 
Yes. Now there is a link path from www.gentoo.org to overlays.gentoo.org, 
and there is no link path from www.gentoo.org to gentooscience.org. And 
this means that the whole world knows about the overlays at 
overlays.gentoo.org, and nobody (except a few developers subscribed to 
this list) knows about gentooscience.org.

By the way, overlays.gentooscience.org uses trac and works stable.

Andrey
--

-- 
gentoo-science <at> gentoo.org mailing list


Gmane