Errors About Biopython 1.61 Installation

Question

[l0o0]

I downloaded the tar file from the biopython website, extracted and intalled it as the readme told.

python setup.py build
python setup.py test

when i did the second command, there came some errors, the errors are above:

======================================================================
FAIL: Test an input file containing a single sequence.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Clustalw_tool.py", line 166, in test_single_sequence
    self.assertTrue(str(err) == "No records found in handle")
AssertionError

======================================================================
ERROR: Test Entrez.read from URL
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Entrez_online.py", line 34, in test_read_from_url
    rec = Entrez.read(einfo)
  File "/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/__init__.py", line 362, in read
    record = handler.read(handle)
  File "/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/Parser.py", line 184, in read
    self.parser.ParseFile(handle)
  File "/share/fg2/Linxzh/biopython-1.61/build/lib.linux-x86_64-2.6/Bio/Entrez/Parser.py", line 322, in endElementHandler
    raise RuntimeError(value)
RuntimeError: Unable to open connection to #DbInfo?dbaf=

======================================================================
ERROR: Run tutorial doctests.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Tutorial.py", line 152, in test_doctests
ValueError: 4 Tutorial doctests failed: test_from_line_05671, test_from_line_06030, test_from_line_06190, test_from_line_06479

----------------------------------------------------------------------
Ran 213 tests in 1621.002 seconds

FAILED (failures = 3)

How can i solve these errors?

[Michael Schubert]

are you using python>=3?

[l0o0]

i have python 3 installed in my machine, but i also have python 2.65 installed. python = python 2.6.5 by default.

[David W]

You may well get help here, but it's probably also a good idea to send a message to the Biopython mailing list with details of your setup (OS/Python version and version of Clustal you have installed in your $PATH) along with this information. List details are here: http://biopython.org/wiki/Mailing_lists.

[l0o0]

Thanks for your advice. I will try this way.

Answer 1

[Peter]

The author's mailing list post is here (and I have replied there): http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010597.html