[Biopython-dev] Running Biopython tests on windows xp
Bruce Southey
bsouthey at gmail.com
Wed Jan 14 20:24:29 UTC 2009
Hi,
I decided to install windows on a virtual system part to have a windows
test system. I installed Python 2.5, numpy 1.2 and biopython 1.49 using
binary installers. I am aiming to get add the optional software like
Reportlab and a C compiler.
Is there a way to run the Biopython tests within Python rather than
using the system command line?
When I run the tests from the command like I get a number a failures
that I think are due to a lack of a C compiler.
Are these expected or do you want bug reports?
Bruce
C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.49>c:\Pyt
hon25\python.exe setup.py test
running test
test_Ace ... ok
test_AlignIO ... ok
test_BioSQL ... skipping. Install MySQLdb or correct
Tests/setup_BioSQL.py (not
important if you do not plan to use BioSQL).
ok
test_BioSQL_SeqIO ... skipping. Install MySQLdb or correct
Tests/setup_BioSQL.py
(not important if you do not plan to use BioSQL).
ok
test_CAPS ... ERROR
test_Clustalw ... ok
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you
want to us
e Bio.Clustalw.
ok
test_Cluster ... FAIL
test_CodonTable ... ok
test_CodonUsage ... ok
test_Compass ... ok
test_Crystal ... ok
test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
ok
test_EmbossPrimer ... ok
test_Entrez ... ok
test_Enzyme ... ok
test_FSSP ... ok
test_Fasta ... ok
test_Fasta2 ... ok
test_File ... ok
test_GACrossover ... ok
test_GAMutation ... ok
test_GAOrganism ... ok
test_GAQueens ... ok
test_GARepair ... ok
test_GASelection ... ok
test_GFF ... skipping. Environment is not configured for this test (not
importan
t if you do not plan to use Bio.GFF).
ok
test_GFF2 ... skipping. Install MySQLdb if you want to use Bio.GFF.
ok
test_GenBank ... ok
test_GraphicsChromosome ... skipping. Install reportlab if you want to
use Bio.G
raphics.
ok
test_GraphicsDistribution ... skipping. Install reportlab if you want to
use Bio
.Graphics.
ok
test_GraphicsGeneral ... skipping. Install reportlab if you want to use
Bio.Grap
hics.
ok
test_HMMCasino ... ok
test_HMMGeneral ... ok
test_HotRand ... ok
test_IsoelectricPoint ... ok
test_KDTree ... ERROR
test_KEGG ... ok
test_KeyWList ... ok
test_Location ... ok
test_LocationParser ... ok
test_LogisticRegression ... ok
test_MEME ... ok
test_MarkovModel ... ok
test_Medline ... ok
test_NCBIStandalone ... ok
test_NCBIXML ... ok
test_NCBI_qblast ... ok
test_NNExclusiveOr ... ok
test_NNGene ... ok
test_NNGeneral ... ok
test_Nexus ... ok
test_PDB ... ERROR
test_ParserSupport ... ok
test_Pathway ... ok
test_Phd ... ok
test_PopGen_FDist ... skipping. Install FDist if you want to use
Bio.PopGen.FDis
t.
ok
test_PopGen_FDist_nodepend ... ok
test_PopGen_GenePop ... ok
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use
Bio.PopGen
.SimCoal.
ok
test_PopGen_SimCoal_nodepend ... ok
test_ProtParam ... ok
test_Registry ... ok
test_Restriction ... ERROR
test_SCOP_Astral ... ok
test_SCOP_Cla ... FAIL
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... FAIL
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SProt ... ok
test_SVDSuperimposer ... ok
test_SeqIO ... ok
test_SeqIO_online ... ok
test_SeqUtils ... ok
test_SubsMat ... ok
test_UniGene ... ok
test_Wise ... skipping. Don't know how to find the Wise2 tool dnal on
Windows.
ok
test_align ... ok
test_docstrings ... ok
test_geo ... ok
test_interpro ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... ok
test_prosite2 ... ok
test_psw ... skipping. Don't know how to find the Wise2 tool dnal on
Windows.
ok
test_seq ... ok
test_translate ... ok
test_trie ... ERROR
test_triefind ... ERROR
======================================================================
ERROR: test_CAPS
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 138, in runSafeTest
cur_test = __import__(self.test_name)
File "test_CAPS.py", line 3, in <module>
from Bio.Restriction import *
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\Restriction\__init__.py", line 61, in <module>
from Bio.Restriction.Restriction import *
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\Restriction\Restriction.py", line 96, in <module>
from Bio.Restriction.PrintFormat import PrintFormat
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\Restriction\PrintFormat.py", line 14, in <module>
from Bio.Restriction.DNAUtils import complement
ImportError: No module named DNAUtils
======================================================================
ERROR: test_KDTree
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 138, in runSafeTest
cur_test = __import__(self.test_name)
File "test_KDTree.py", line 10, in <module>
from Bio.KDTree.KDTree import _neighbor_test, _test
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\KDTree\__init__.py", line 10, in <module>
from KDTree import KDTree
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\KDTree\KDTree.py", line 20, in <module>
from Bio.KDTree import _CKDTree
ImportError: cannot import name _CKDTree
======================================================================
ERROR: test_PDB
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 138, in runSafeTest
cur_test = __import__(self.test_name)
File "test_PDB.py", line 98, in <module>
run_test()
File "test_PDB.py", line 90, in run_test
quick_neighbor_search_test()
File "test_PDB.py", line 19, in quick_neighbor_search_test
from Bio.PDB.NeighborSearch import NeighborSearch
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\PDB\NeighborSearch.py", line 8, in <module>
from Bio.KDTree import *
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\KDTree\__init__.py", line 10, in <module>
from KDTree import KDTree
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\KDTree\KDTree.py", line 20, in <module>
from Bio.KDTree import _CKDTree
ImportError: cannot import name _CKDTree
======================================================================
ERROR: test_Restriction
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 138, in runSafeTest
cur_test = __import__(self.test_name)
File "test_Restriction.py", line 8, in <module>
from Bio.Restriction import *
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\Restriction\__init__.py", line 61, in <module>
from Bio.Restriction.Restriction import *
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\Restriction\Restriction.py", line 96, in <module>
from Bio.Restriction.PrintFormat import PrintFormat
File "C:\Documents and
Settings\virtualme\Desktop\biopython-1.49\biopython-1.4
9\Bio\Restriction\PrintFormat.py", line 13, in <module>
from Bio.Restriction import RanaConfig as RanaConf
ImportError: cannot import name RanaConfig
======================================================================
ERROR: test_trie
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 138, in runSafeTest
cur_test = __import__(self.test_name)
File "test_trie.py", line 6, in <module>
from Bio import trie
ImportError: cannot import name trie
======================================================================
ERROR: test_triefind
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 138, in runSafeTest
cur_test = __import__(self.test_name)
File "test_triefind.py", line 6, in <module>
from Bio import trie
ImportError: cannot import name trie
======================================================================
FAIL: test_Cluster
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 162, in runSafeTest
expected_handle)
File "run_tests.py", line 263, in compare_output
% (repr(output_line), repr(expected_line))
AssertionError:
Output : 'test_clusterdistance (test_Cluster.TestCluster) ... ERROR\n'
Expected: 'test_clusterdistance (test_Cluster.TestCluster) ... ok\n'
======================================================================
FAIL: test_SCOP_Cla
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 162, in runSafeTest
expected_handle)
File "run_tests.py", line 263, in compare_output
% (repr(output_line), repr(expected_line))
AssertionError:
Output : 'testIndex (test_SCOP_Cla.ClaTests) ... ERROR\n'
Expected: 'testIndex (test_SCOP_Cla.ClaTests) ... ok\n'
======================================================================
FAIL: test_SCOP_Raf
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 125, in runTest
self.runSafeTest()
File "run_tests.py", line 162, in runSafeTest
expected_handle)
File "run_tests.py", line 263, in compare_output
% (repr(output_line), repr(expected_line))
AssertionError:
Output : 'testSeqMapIndex (test_SCOP_Raf.RafTests) ... ERROR\n'
Expected: 'testSeqMapIndex (test_SCOP_Raf.RafTests) ... ok\n'
----------------------------------------------------------------------
Ran 96 tests in 86.153s
FAILED (failures=3, errors=6)
C:\Documents and Settings\virtualme\Desktop\biopython-1.49\biopython-1.49>
More information about the Biopython-dev
mailing list