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 from www.sagemath.org'
error, so I manually downloaded the spkg from www.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/ -~----------~----~----~----~------~----~------~--~---