Just to clarify: the downloading problem isn't biopython-specific - I
can't get anything from www.sagemath.org through sage, only from a
browser. For example, 'sage -optional' fails as well.
-MH
On Mar 20, 10:31 am, "Hamptonio" <[EMAIL PROTECTED]> wrote:
> Woo-hoo! Thank you!!!
>
> I had the same error as before on my Mac Pro - the
> '...
> 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 fromwww.sagemath.org'
>
> error, so I manually downloaded the spkg fromwww.sagemath.org, and it
> installed fine apart from the weird need for 'enter' commands that
> you warned me about. I have tested a few of my more commonly used
> tasks and it seems to work.
>
> I can tell the biopython developers about this once the package
> download problems get a little sorted out.
>
> Thanks again,
> Marshall
>
> On Mar 20, 7:53 am, "Hamptonio" <[EMAIL PROTECTED]> wrote:
>
> > 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 fromwww.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
--~--~---------~--~----~------------~-------~--~----~
To post to this group, send email to sage-devel@googlegroups.com
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at http://groups.google.com/group/sage-devel
URLs: http://sage.scipy.org/sage/ and http://modular.math.washington.edu/sage/
-~----------~----~----~----~------~----~------~--~---
