On Tue, 6 Mar 2012 09:48:58 -0500, Alexander Hansen
<[email protected]> wrote:
Package manager version: 0.32.99.git
> Distribution version: selfupdate-cvs Tue Mar 6 09:18:52 2012, 10.7, x86_64
> Trees: local/main stable/main local/injected
> Xcode: 4.3
> Max. Fink build jobs: 4
>
> I happened to be building in maintainer mode and found the following:
For comparison, here are some differences I notice on 10.6/i38/xcode4.2
> test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you
> want to use it from Biopython.
test_Clustalw_tool ... ERROR
I have the "clustalw" package installed (1.83-3) but not "clustalw2".
> test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
[...]
> test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_Wise ... ok
[...]
test_psw ... ok
I have wise2-2.2.0-3 installed.
Here's the meat of the clustalw error:
======================================================================
ERROR: test_Clustalw_tool
----------------------------------------------------------------------
Traceback (most recent call last):
File "./run_tests.py", line 317, in runTest
suite = unittest.TestLoader().loadTestsFromName(name)
File "/sw/lib/python2.7/unittest/loader.py", line 91, in loadTestsFromName
module = __import__('.'.join(parts_copy))
File
"/sw/build.build/biopython-py27-1.58-1/biopython-1.58/Tests/test_Clustalw_tool.py",
line 112, in
<module>
assert str(err) == "No records found in handle", str(err)
AssertionError: Command 'clustalw -infile=Fasta/f001' returned non-zero
exit status 4
Then I have the same error backtraces as akh for these:
> ERROR: test_nuccore_X52960 (test_SeqIO_online.EntrezTests)
> Bio.Entrez.efetch(nuccore, X52960, ...)
> ERROR: test_nucleotide_6273291 (test_SeqIO_online.EntrezTests)
> Bio.Entrez.efetch(nucleotide, 6273291, ...)
> ERROR: test_protein_16130152 (test_SeqIO_online.EntrezTests)
> Bio.Entrez.efetch(protein, 16130152, ...)
dan
--
Daniel Macks
[email protected]
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