On Apr 29, 2009, at 8:55 AM, Giovanni Marco Dall'Olio wrote:
> >>>> m = pygr.Data.Bio.MSA.UCSC.bosTau2ToBostau3() > TypeError Traceback (most recent > call last) > (see the second log file attached for details, > pygr_XMLRPCSequenceDB.error) > TypeError: object.__new__(XMLRPCSequenceDB) is not safe, use > dict.__new__() Yes, this is an incompatibility between the new 0.8 server being accessed from an 0.7 client, which we were about to fix. Hopefully we can insert the fix and restart the server today. The fix has to be made in the 0.8 server, to make it backwards compatible with older (0.7) clients. > > Traceback (most recent call last): > File "protest.py", line 107, in <module> > if do_test(sys.argv[2],sys.argv[3],sys.argv[4]): > File "protest.py", line 21, in do_test > m() > File "/home/gioby/Local_Repository/pygr/tests/sequence_test.py", > line 93, in blast_test > assert approximate_cmp(result,correct,.0001)==0, 'blast results > should match' > AssertionError: blast results should match This is not a real bug, but simply the unfortunate fact that your BLAST program returned slightly different results than the version on my machine, whose results were saved and used as the gold standard for all subsequent tests. We've seen this problem that BLAST results on different machines differ slightly. We are going to recast the BLAST tests to separate the correctness of running BLAST and getting results back from it, vs. using canned BLAST output files to test that the parsing etc. routines produce an exact match to the expected results. --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to pygr-dev@googlegroups.com To unsubscribe from this group, send email to pygr-dev+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
