Great! I am once again amazed by your speed.
I set SAGE_SERVER as you said, but my attempt at installing fails to
get the package. The output is appended below. I doing this on a PPC
(G4) Apple powerbook, with sage 2.0 upgraded to 2.3.
I had tried to read the documentation you suggested - I was only
volunteering to try this because it seemed relatively simple! I've
installed biopython 1.42 on linux, apple, and windows machines, but I
haven't tried a normal install of 1.43 yet (its quite recent). I am
not sure what mxTextTools is doing; in a python install I just do
'sudo python setup.py install' although I am not sure that the sudo is
necessary.
I'll also give this a try on the Mac Pro (Intel) in my office when I
get in.
Thanks,
Marshall
~/sage-2.0:07:43:42:./sage -i biopython-1.43
Installing biopython-1.43
Calling sage-spkg on biopython-1.43
WARNING: Using SAGE_ROOT variable that was already set to '/Users/mh/
sage-2.0'.
biopython-1.43
Machine:
Darwin medmgmt-3.tajen.edu.tw 8.8.0 Darwin Kernel Version 8.8.0: Fri
Sep 8 17:18:57 PDT 2006; root:xnu-792.12.6.obj~1/RELEASE_PPC Power
Macintosh powerpc
Deleting directories from past builds of previous/current versions of
biopython-1.43
/Users/mh/sage-2.0/local/bin/sage-spkg: file /Users/mh/sage-2.0/
biopython-1.43 does not exist
Attempting to download it.
www.sagemath.org/packages/optional/biopython-1.43.spkg -->
biopython-1.43.spkg
[
Traceback (most recent call last):
File "/Users/mh/sage-2.0/local/bin/sage-download_package", line 53,
in <module>
if not download_file("optional/%s"%F):
File "/Users/mh/sage-2.0/local/bin/sage-download_package", line 45,
in download_file
urllib.urlretrieve(url, file, reporthook)
File "/Users/mh/sage-2.0/local/lib/python2.5/urllib.py", line 89, in
urlretrieve
return _urlopener.retrieve(url, filename, reporthook, data)
File "/Users/mh/sage-2.0/local/lib/python2.5/urllib.py", line 222,
in retrieve
fp = self.open(url, data)
File "/Users/mh/sage-2.0/local/lib/python2.5/urllib.py", line 190,
in open
return getattr(self, name)(url)
File "/Users/mh/sage-2.0/local/lib/python2.5/urllib.py", line 451,
in open_file
return self.open_local_file(url)
File "/Users/mh/sage-2.0/local/lib/python2.5/urllib.py", line 465,
in open_local_file
raise IOError(e.errno, e.strerror, e.filename)
IOError: [Errno 2] No such file or directory: 'www.sagemath.org/
packages/optional/biopython-1.43.spkg'
sage: Failed to download package biopython-1.43 from www.sagemath.org
On Mar 19, 10:52 pm, William Stein <[EMAIL PROTECTED]> wrote:
> On Monday 19 March 2007 8:28 pm, Hamptonio wrote:
>
>
>
> > Hi,
>
> > I became interested in SAGE after I found it to be the easiest way to
> > install cddlib and gmp, and now I am getting hooked. My research is
> > very schizophrenic: besides some computational algebra/geometry coming
> > from dynamical systems, I am also interested in mathematical biology
> > and bioinformatics. There is an open-source project called biopython
> > (http://biopython.org/wiki/Biopython) that I am using in a
> > bioinformatics course right now. It would be very nice if there was a
> > biopython optional package for SAGE. I am willing to try and create
> > one, but I thought I would post here first to see if anyone had any
> > preliminary advice before I waste my time.
>
> > Biopython currently requires Numeric, but all the parts I need seem to
> > work OK using numpy. The developers are currently working on
> > switching over entirely to numpy. It also requires something called
> > mxTextTools, but I think that should be OK since its open source and
> > has a very permissive license.
>
> Adding biopython is a good idea. Prompted by your email, I created
> a package for it, which I've posted here:
>
> http://www.sagemath.org/packages/optional/
>
> If you do
> $ export SAGE_SERVER="www.sagemath.org"
> from bash, you can get it with
> sage -i biopython-1.43
>
> My biophython-1.43 package includes mxTextTools, so it's very easy to install.
> Also, it seems that biophython-1.43 works fine with numpy. If it doesn't,
> Numeric is a well-supported optional sage package: "sage -i numeric-24.2".
>
> One very annoying thing that somebody needs to get to the bottom of, is that
> it seems necessary to hit enter several times half-way through the install,
> or it just pauses forever. This probably has something to do with maybe
> mxTextTools's installing doing something obnoxious. Feedback is appreciated.
>
> By the way, this document gives a basic idea of how spkg's are created:
> http://www.sagemath.com/doc/html/prog/node23.html
>
> In short, an spkg is just a bzip2'd tarball, with a file spkg-install that
> gets run in the environment of SAGE, e.g., "python" is SAGE's Python, etc.,
> and it is supposed to install code to $SAGE_LOCAL.
>
> William
>
> William
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