Stupid of me not to try that - i.e. the 'http://'. Ah well. I have written to the biopython dev list to let them know of the SAGE- biopython connection.
I tried to take a look at what was causing those installation hangups. It looks like its not the mxTextTools, but rather the components that immediately follow - namely the lack of Reportlab (optional, I've never used its functionality) and the compilation of part of Bio.PDB (basically a parser for molecular structure files). I cut out the relevant section and pasted it below. If I have time, I will try to figure out a workaround for this in the installation script. I am now spending a great deal of time working in the SAGE notebook environment, which should inspire me eventually to do more development work on SAGE. Here's the installation snippet of interest: *** Reportlab *** is either not installed or out of date. This package is optional, which means it is only used in a few specialized modules in Biopython. You probably don't need this if you are unsure. You can ignore this requirement, and install it later if you see ImportErrors. You can find Reportlab at http://www.reportlab.org/downloads.html. Do you want to continue this installation? (Y/n) *** Bio.KDTree *** NOT built by default The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module, which in turn, depends on C++ code that does not compile cleanly on all platforms. Hence, Bio.KDTree is not built by default. Would you like to build Bio.KDTree ? (y/N) running build On Mar 20, 12:39 pm, William Stein <[EMAIL PROTECTED]> wrote: > 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 fromwww.sagemath.orgthrough 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/ -~----------~----~----~----~------~----~------~--~---
