#4576: [with spkg; needs work] biopython optional package upgrade to 1.49beta
------------------------------------------+---------------------------------
Reporter: mhampton | Owner: mabshoff
Type: enhancement | Status: new
Priority: minor | Milestone: sage-3.2.1
Component: optional packages | Resolution:
Keywords: biopython, optional packages |
------------------------------------------+---------------------------------
Changes (by was):
* summary: [with spkg; needs review] biopython optional package upgrade
to 1.49beta => [with spkg; needs work]
biopython optional package upgrade to 1.49beta
Comment:
REFEREE REPORT:
1. The crap is gone. :-)
2. I tried out some of the things above and it works.
3. It would be good to have an spkg-check script, which would look like
this. This would get run automatically when one does
{{{
export SAGE_CHECK="yes"
}}}
before installing.
Here's spkg-check, probably:
{{{
#!/bin/sh
cd biopython/Tests/
python run_tests.py
}}}
4. However the test suite itself fails 5 tests. Can you comment on this?
{{{
[EMAIL PROTECTED]:~/build/sage-3.2.1.alpha1/biopython-1.49b/biopython/Tests$
python
run_tests.py
test_Ace ... ok
test_AlignIO ... ok
test_BioSQL ... skipping. Enter your settings in Tests/setup_BioSQL.py
(not important if you do not plan to use BioSQL).
ok
test_BioSQL_SeqIO ... skipping. Enter your settings in
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 use 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
important 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.Graphics.
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.Graphics.
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 ... ok
test_ParserSupport ... ok
test_Pathway ... ok
test_Phd ... ok
test_PopGen_FDist ... skipping. Install FDist if you want to use
Bio.PopGen.FDist.
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 ... ok
test_SCOP_Des ... ok
test_SCOP_Dom ... ok
test_SCOP_Hie ... ok
test_SCOP_Raf ... ok
test_SCOP_Residues ... ok
test_SCOP_Scop ... ok
test_SProt ... ok
test_SVDSuperimposer ... ok
test_SeqIO ... `^Hok
test_SeqIO_online ... ok
test_SeqUtils ... ok
test_SubsMat ... ok
test_UniGene ... ok
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
ok
test_align ... ok
test_docstrings ... ok
test_geo ... ok
test_interpro ... ok
test_kNN ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... ok
test_prosite2 ... ok
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
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
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Tests/test_CAPS.py",
line 3, in <module>
from Bio.Restriction import *
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/Restriction/__init__.py",
line 61, in <module>
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/Restriction/Restriction.py",
line 96, in <module>
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/Restriction/PrintFormat.py",
line 14, in <module>
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
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Tests/test_KDTree.py",
line 1, in <module>
from Bio.KDTree.KDTree import _neighbor_test, _test
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/KDTree/__init__.py",
line 10, in <module>
#
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/KDTree/KDTree.py",
line 13, in <module>
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
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Tests/test_Restriction.py",
line 8, in <module>
from Bio.Restriction import *
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/Restriction/__init__.py",
line 61, in <module>
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/Restriction/Restriction.py",
line 96, in <module>
File
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Bio/Restriction/PrintFormat.py",
line 13, in <module>
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
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Tests/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
"/Users/mh/sagestuff/biopython-1.49b/biopython-1.49b/Tests/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'
----------------------------------------------------------------------
Ran 95 tests in 147.466s
FAILED (failures=1, errors=5)
You have new mail in /var/mail/was
}}}
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/4576#comment:6>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
Reinventing the Wheel
--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google Groups
"sage-trac" group.
To post to this group, send email to [email protected]
To unsubscribe from this group, send email to [EMAIL PROTECTED]
For more options, visit this group at
http://groups.google.com/group/sage-trac?hl=en
-~----------~----~----~----~------~----~------~--~---
