build.sh breaks on unit tests in svn 48

What steps will reproduce the problem?

Run build.sh in my environment ;-)
ah@bioinfws19:~/Downloads/weblogo/svn$ ./build.sh

## Build WebLogo release
Create sequence logos from biological sequence alignments.

## Check Subversion status (Working copy checked in and up to date?)
?      tmp
?      logo8.eps

## Lines of code
  3431 total

## Code Tags
test_weblogo.py:    # FIXME: The version of python used by Popen may not be the
test_weblogo.py:        # TODO: Don't actually know if this is correct
weblogolib/__init__.py:    # TODO: Raise ArgumentErrors instead of
ValueError and document
weblogolib/__init__.py:        # FIXME: More validation
weblogolib/__init__.py:        # FIXME: Validate here. Move from eps_formatter
weblogolib/__init__.py:    # TODO: Document this method and enviroment variable
weblogolib/__init__.py:#TODO: Move to seq_io?
weblogolib/__init__.py:                #FIXME: fixup
corebio.moremath.entropy()?
weblogolib/__init__.py:        # FIXME: Check seqs.alphabet?
weblogolib/__init__.py:    # FIXME Add test?
weblogolib/__init__.py:    # TODO: Future Feature
weblogolib/__init__.py:        # TODO: Check that alphas are positive
weblogolib/__init__.py:        #TODO : what if alpha's not one dimensional?
weblogolib/__init__.py:        # TODO: Optimize
weblogolib/__init__.py:            if a>0 : ent += - 1.0 * a * digamma(
1.0+a) # FIXME: Check
weblogolib/_cgi.py:# TODO: Check units
weblogolib/_cgi.py:# TODO: In WebLogo2: why slash create.cgi? I think this
was a workaround
weblogolib/_cgi.py:    # FIXME: Ugly fix: Must check that sequence_file key
exists
weblogolib/_cgi.py:    # FIXME: Sending malformed or missing form keys
should not cause a crash
weblogolib/_cgi.py:    html =
Template(template).safe_substitute(subsitutions) #FIXME

# Cleaning previous
rm: cannot remove `dist/_extract_/': No such file or directory

## Rebuild API docs :

## Rebuild examples :
........

## PYTHON 2.4 ##
## CoreBio version
0.6b170

## Build source distribution :

## Extract source distribution
## Change directory to source
## Run unit tests  :
.........................FE.E...........
======================================================================
ERROR: test_parse_prior_equiprobable (__main__.test_parse_prior)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test_weblogo.py", line 93, in test_parse_prior_equiprobable
    self.assertTrue(
  File
"/home/bioinf/ah/Downloads/weblogo/svn/dist/_extract_/weblogo-3.0b14/weblogolib/
__init__.py",
line 957, in parse_prior
    raise ValueError("Unknown or malformed composition: %s"%composition)
ValueError: Unknown or malformed composition:  equiprobablE

======================================================================
ERROR: test_parse_prior_none (__main__.test_parse_prior)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test_weblogo.py", line 87, in test_parse_prior_none
    parse_prior( 'noNe', None) )
  File
"/home/bioinf/ah/Downloads/weblogo/svn/dist/_extract_/weblogo-3.0b14/weblogolib/
__init__.py",
line 914, in parse_prior
    if weight is None: weight = float(len(alphabet))
TypeError: len() of unsized object

======================================================================
FAIL: test_explicit (__main__.test_parse_prior)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "./test_weblogo.py", line 133, in test_explicit
    self.assertTrue( all(
  File "./test_weblogo.py", line 79, in assertTrue
    self.assertEquals( bool, True)
AssertionError: False != True

----------------------------------------------------------------------
Ran 40 tests in 7.135s

FAILED (failures=1, errors=2)

What is the expected output? What do you see instead?

What version of the product are you using? On what operating system?
OS: Debian Linux
Version: SVN revision 48 (Thu, 04 Jan 2007)

Please provide any additional information below.
It's not clear to me if the build.sh is the primary installation script or
setup.py.
Btw., It should be mentioned that epydoc is required.

Best, Andreas
Original issue reported on code.google.com by ahensc...@gmail.com on 2 May 2007 at 10:37
gecrooks / weblogo

build.sh breaks on unit tests in svn 48 #15
