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Steven Trogdon | 7 Jun 2010 18:34
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[sage-on-gentoo] sage-clib-4.4.3[mpir]

Hello,

I've been keeping one system with a mpir enabled Sage. I noticed that

	USE="mpir" ebuild sage-clib-4.4.3.ebuild prepare

fails because sage-clib-4.3.4-replace-gmp-with-mpir.patch doesn't take.  
It appears the SConstruct file that's shipped in the c_lib directory  
for Sage-4.4.3 is slightly different from what's shipped with  
Sage-4.4.2.

Steve
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Christopher Schwan | 7 Jun 2010 18:59
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Re: [sage-on-gentoo] sage-clib-4.4.3[mpir]

Hi,

On Monday 07 June 2010 18:34:42 Steven Trogdon wrote:
> Hello,
> 
> I've been keeping one system with a mpir enabled Sage. I noticed that
> 
> 	USE="mpir" ebuild sage-clib-4.4.3.ebuild prepare
> 
> fails because sage-clib-4.3.4-replace-gmp-with-mpir.patch doesn't take.
> It appears the SConstruct file that's shipped in the c_lib directory
> for Sage-4.4.3 is slightly different from what's shipped with
> Sage-4.4.2.

Thanks for reporting! Fixed in overlay.

> 
> Steve

Christopher
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Steven Trogdon | 14 Jun 2010 21:13
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sage-notebook & jmol

Hello,

I believe Jmol is the default Sage 3D viewer. However, it seems to be  
broken from the notebook. A

	sphere()

from the sage prompt works as expected but not so from the notebook.  
Here I get that the problem is in locating the JmolApplet class. It  
appears that sagenb is coded to look in the data directory under sagenb  
for package data, i.e. relative to the python tree in  
site-packages/sagenb/data. After opening the notebook the contents of  
the directory can be viewed by pointing one's browser to

	http://localhost:8000/java/

In particular the notebook seems to look in  
site-packages/sagenb/data/jmol for the JmolApplet class data which was  
removed with the advent of the sage-on-gentoo package,  
sci-chemistry/jmol. Now here I'm able to get Jmol to work from the  
notebook if I create either of the symlinks,

	site-packages/sagenb/data/jmol ->  
/usr/share/webapps/jmol/11.6.16/htdocs
or
	site-packages/sagenb/data/jmol -> /var/www/localhost/htdocs/jmol

There should be a better way to do this but I'm unable to find a way to  
get the sagenb package to access external data other than through a  
symlink. If the first of the above is done then a version bump of jmol
(Continue reading)

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François Bissey | 14 Jun 2010 22:52
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Re: sage-notebook & jmol

> Hello,
> 
> I believe Jmol is the default Sage 3D viewer. However, it seems to be
> broken from the notebook. A
> 
> 	sphere()
> 
> from the sage prompt works as expected but not so from the notebook.
> Here I get that the problem is in locating the JmolApplet class. It
> appears that sagenb is coded to look in the data directory under sagenb
> for package data, i.e. relative to the python tree in
> site-packages/sagenb/data. After opening the notebook the contents of
> the directory can be viewed by pointing one's browser to
> 
> 	http://localhost:8000/java/
> 
> In particular the notebook seems to look in
> site-packages/sagenb/data/jmol for the JmolApplet class data which was
> removed with the advent of the sage-on-gentoo package,
> sci-chemistry/jmol. Now here I'm able to get Jmol to work from the
> notebook if I create either of the symlinks,
> 
> 	site-packages/sagenb/data/jmol ->
> /usr/share/webapps/jmol/11.6.16/htdocs
> or
> 	site-packages/sagenb/data/jmol -> /var/www/localhost/htdocs/jmol
> 
> There should be a better way to do this but I'm unable to find a way to
> get the sagenb package to access external data other than through a
> symlink. If the first of the above is done then a version bump of jmol
(Continue reading)

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François Bissey | 15 Jun 2010 12:51
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Re: sage-notebook & jmol


> sci-chemistry/jmol. Now here I'm able to get Jmol to work from the
> notebook if I create either of the symlinks,
> 
> 	site-packages/sagenb/data/jmol ->
> /usr/share/webapps/jmol/11.6.16/htdocs
> or
> 	site-packages/sagenb/data/jmol -> /var/www/localhost/htdocs/jmol
> 
> There should be a better way to do this but I'm unable to find a way to
> get the sagenb package to access external data other than through a
> symlink. If the first of the above is done then a version bump of jmol
> will require a new sage-notebook install! There is also an "appletweb"
> directory that's present under sagenb/data/jmol and I was curious as to
> whether it's needed? Is it perhaps a carry-over from the older
> Sage-provided jmol stuff?
> 
A bit more details on this. First the cli it is enough to install jmol with
the flag client-only which just install the binary.
The next problem is that to get the web-applet we need either 
-client-only or vhost use flags. Which require the gentoo web-app 
framework. We don't want that. 
*sage uses twisted as its server, this is not supported by web-app.

We basically need a lot of the stuff that is provided for the web-app
without the requirements of the web-app framework.

I can say you have installed jmol as a web-app Steve. The stuff provided
in the appletweb folder could be provided by jmol. At first I was trying
to provide some stuff from jmol and keeping some stuff from sagenb.
(Continue reading)

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Steven Trogdon | 15 Jun 2010 17:11
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Re: sage-notebook & jmol

Hi François,

On   06/15/10 - 05:51:23, François Bissey wrote:
> 
> A bit more details on this. First the cli it is enough to install  
> jmol with
> the flag client-only which just install the binary.
> The next problem is that to get the web-applet we need either
> -client-only or vhost use flags. Which require the gentoo web-app
> framework. We don't want that.
> *sage uses twisted as its server, this is not supported by web-app.
> 
> We basically need a lot of the stuff that is provided for the web-app
> without the requirements of the web-app framework.

I believe you are correct here and installing the web-app framework  
with the provided ebuild was the only way I could get the JmolApplet  
class installed.

> 
> I can say you have installed jmol as a web-app Steve. The stuff  
> provided
> in the appletweb folder could be provided by jmol. At first I was  
> trying
> to provide some stuff from jmol and keeping some stuff from sagenb.
> This one has tough requirements.

Yes, tough is what I thought as well. Or, at the least, not  
straightforward.
(Continue reading)

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justin | 16 Jun 2010 09:16
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sci-chemistry/ccp4-6.1.3* testing request

Hi all,

I just updated a couple of ccp4 related packages and keyworded them for
linux prefix.

I like to ask all of you, who can test the installation in real life, to
unmask sci-chemistry/ccp4-6.1.3-r1 and test it. Please report all issues
to me or on http://bugs.gentoo.org. If there are no major regressions I
will ask for stabilization at the end of July and remove all old versions.

justin
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justin | 16 Jun 2010 10:46
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Re: sci-chemistry/ccp4-6.1.3* testing request

On 16/06/10 09:16, justin wrote:
> Hi all,
> 
> I just updated a couple of ccp4 related packages and keyworded them for
> linux prefix.
> 
> I like to ask all of you, who can test the installation in real life, to
> unmask sci-chemistry/ccp4-6.1.3-r1 and test it. Please report all issues
> to me or on http://bugs.gentoo.org. If there are no major regressions I
> will ask for stabilization at the end of July and remove all old versions.
> 
> 
> justin
> 

I am really sorry, but there was a big typo in the last version so it is
necessary to bump to sci-chemistry/ccp4-apps-6.1.3-r4 , otherwise many
apps aren't installed.

Thanks justin
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François Bissey | 17 Jun 2010 13:09
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Re: sage-notebook & jmol

Hi all,

So I committed some changes that makes jmol works
at least on my computer.
At the moment it requires the version of jmol from
the sage-on-gentoo overlay, but it probably would work
with the one in the portage tree.
I required the "vhosts" useflag for jmol so people don't
have to deal with web-app configuration, but it would
also works with "-client-only". So it may end up being
a recommendation.
It has quite a nasty structure as, while there is no link
involved as in Steve's first message, the path is explicit
in the sage-notebook code. A real clean solution to
this will require some changes to the jmol ebuild to
install a simple stripped down web applet not requiring
web-applet.

Happy testing!!!

Francois
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Auke Booij | 25 Jun 2010 18:46

G-CRAN: time for cake, packages are building

Just pushed to my git repository: a fallible commit containing an
ebuild which builds some CRAN-style packages (hopefully).

As some of you might incidentally know, I'm working on getting Gentoo
to build CRAN package as a Google Summer of Code project. That means
I'm supposed to do something impressive, but I'm leaving that part to
you guys. What I /am/ doing is writing some clever code which
hopefully will build most CRAN-style packages from within package
managers. That would mean automatic dependency resolving (most
importantly, this must also work for external (non-CRAN)
dependencies), proper installation of documentation, and hopefully a
whole lot more clean package handling (perhaps there are dependencies
between Bioconductor and CRAN? what about cross-platform building? i
am doing my own research regarding this but would love to hear what
problems you're expecting and what you'd like to see fixed).

Alright, back to e7265e5bfce8a7e39a6cbbb14814bec5e1c3ffc9. No, there
is no ebuild for G-CRAN itself, there is no integration with layman,
no intelligent documentation installer, no friendly interface, no
quick database for fast package searches and/or caching, but at least
the darned thing actually builds and installs some CRAN-style
packages. If you're desperate to give this Grendel a spin, feel free
to clone the git repository and do the following:

-modify cran.ebuild to reflect the right location of g-cran.py - there
are two instances where you'll need to update it (eventually g-cran.py
and friends should just be installed to the right directory, of
course)
-create or open up a local overlay (let's say you created /usr/local/portage)
-execute:
(Continue reading)

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Gmane