On Tuesday 20 March 2007 9:30 am, Hamptonio wrote: > 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.
Sorry, you have to do this (note the http://) -- I forgot to mention this before -- my mistake. export SAGE_SERVER="http://www.sagemath.org"; sage -optional ... > > -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 > > -- William Stein Associate Professor of Mathematics University of Washington --~--~---------~--~----~------------~-------~--~----~ 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/ -~----------~----~----~----~------~----~------~--~---
