Slightly OT: A SAGE Review

[Martin Albrecht]

This might be a bit off topic, but someone wrote a nice review of SAGE at

http://georgm.blogspot.com/2007/03/sage-computer-algebra-system.html

Sorry for any inconvenience caused,
Martin

--
name: Martin Albrecht
_pgp: http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x8EF0DC99
_www: http://www.informatik.uni-bremen.de/~malb
_jab: martinr...@jabber.ccc.de

[David Joyner]

Thank you for posting that Martin.

[William Stein]

On 4/5/07, Martin Albrecht <ma...@informatik.uni-bremen.de> wrote:
> This might be a bit off topic, but someone wrote a nice review of SAGE at
>
> http://georgm.blogspot.com/2007/03/sage-computer-algebra-system.html
>
> Sorry for any inconvenience caused,

I think this is very on topic. It's very useful feedback from a SAGE end user,
and I strongly encourage all SAGE developers to read it. Also, if anybody
else notices something like this online, I encourage them to post it
to sage-devel.

Thanks Martin!

-- William

[William Stein]

Hi,

Regarding the review, which mentions the stats package R, a lot of people have
written me off list about creating an interface to R. Note that there
has been a Python <--> R
interface since before SAGE was ever written:

http://rpy.sourceforge.net/

I haven't used it, but imagine it would be easy to install into SAGE.
(??) If somebody
investigates, please post their experiences.

William

[Hamptonio]

My current bioinformatics textbook uses R for all its coding examples,
and since I wanted to use python/biopython for my course, I tried to
install the R-python interface. As is often the case with such
things, it turned out to be far from self-contained, and I needed a
whole bunch of libraries I didn't have (this was on OS X 10.4). Since
I am impatient and low on time, I gave up after about 1/2 hour, since
there is a very nice R.app for OS X available already and I didn't
have any specific connection in mind. However, it looks like I will
often have statistics grad students in that course and they might use
such an interface. So I will give another vote in favor of getting R
into sage. Currently I think sage should appeal to everyone in math
except perhaps math ed and stats folks, and having R included would
win over the stats people.

-Marshall Hampton

[Robert Miller]

> > Regarding the review, which mentions the stats package R, a lot of people have
> > written me off list about creating an interface to R. Note that there
> > has been a Python <--> R
> > interface since before SAGE was ever written:
>
> > http://rpy.sourceforge.net/
>
> > I haven't used it, but imagine it would be easy to install into SAGE.
> > (??) If somebody
> > investigates, please post their experiences.
>
> > William

>From the installation instructions for rpy:

...(b) Then, configure the path to the R library. You have several
ways to do
this (substitute RHOME with the path where R is installed, usually
/usr/local/lib/R):

o make a link to RHOME/bin/libR.so in /usr/local/lib or /usr/
lib, then
run 'ldconfig',

o or, put the following line in your .bashrc (or equivalent):

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:RHOME/bin

o or, edit the file /etc/ld.so.conf and add the following
line:

RHOME/bin

and then, run 'ldconfig'.

To accomplish this in the spkg-install script, should I do the first
option
in SAGE_ROOT/local/lib?

[mabshoff]

> ...(b) Then, configure the path to the R library. You have several
> ways to do
> this (substitute RHOME with the path where R is installed, usually
> /usr/local/lib/R):
>
> o make a link to RHOME/bin/libR.so in /usr/local/lib or /usr/
> lib, then
> run 'ldconfig',
>
> o or, put the following line in your .bashrc (or equivalent):
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:RHOME/bin
>
> o or, edit the file /etc/ld.so.conf and add the following
> line:
>
> RHOME/bin
>
> and then, run 'ldconfig'.
>
> To accomplish this in the spkg-install script, should I do the first
> option
> in SAGE_ROOT/local/lib?

No, SAGE_ROOT/local/lib is in LD_LIBRARY_PATH anyway. libR.so should
go in there. Then it is automatically found when requested by SAGE. To
run ldconfig one needs root, so that is not an option. Why a lib
should end up in $RHOME/bin seems rather odd to me.

Cheers,

Michael

[fgk]

I've used R quite extensively as well as the rpy interface. R is by
far the best open-source statistics package out there, with an
excellent supporting community and predictable six-month release
cycles. If that could be plugged into SAGE, it would be an enormous
boon to anyone wanting to do statistical numerics. In my limited
experience with rpy itself, the interface is solid although
occassionally flaky. The new version of R (2.5) will be coming out in
a couple of weeks, so it may be worth revisiting the question then.

Sincerely,
Finny Kuruvilla