[Bioperl-l] failures on the stable branch
Dave Howorth
dhoworth at mrc-lmb.cam.ac.uk
Wed Apr 21 09:04:45 EDT 2004
On Tue, 20 Apr 2004, Hilmar Lapp wrote:
>>On the latest update of the stable branch if you run the test suite you
>>get a number of failures, some of them looking troubling to the
>>uninitiated.
I was the one having trouble. As previously discussed, I've just
installed bioperl-db/biosql with my existing bioperl 1.4 installation
and am trying to load the GO data. It failed because of problems in 1.4
and Hilmar advised me to get branch-1-4 from cvs.
Yesterday Hilmar very kindly helped me through the process, because I'm
a newbie to it, but it failed with the errors he described. I've just
updated from CVS and unfortunately now get a different set of errors:
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/DB.t 78 9 11.54% 79-87
t/RestrictionIO.t 14 1 7.14% 10
t/TreeIO.t 41 1 2.44% 42
t/cigarstring.t 255 65280 3 6 200.00% 1-3
121 subtests skipped.
make: *** [test_dynamic] Error 11
(the full log is at the end)
What I still don't know is whether the release as it stands will work
for me or not. I don't want to break my existing installation but I
can't get on with my current work until bioperl-db/biosql is working.
Do the DB failures matter?
RestrictionIO didn't fail yesterday. It does now. But I'm pretty sure I
don't need it.
TreeIO didn't fail yesterday. It does now. And I do have existing code
that uses it.
I don't use cigarstring presently, though may do in future (DAS).
I don't know what "make: *** [test_dynamic] Error 11" at the end means.
>>Given that we point people at downloading the current stable branch as
>>a means of getting bug fixes early, in my opinion we should not aim any
>>lower than that on the stable branch *all* tests pass at *any* time,
>>with no exceptions. Also, modules should not be added on the stable
>>branch, let alone an API be altered.
I'd like to second this plea. My work intersects with bioperl - there
are certain specific parts of bioperl that are relevant to my work on
protein structure classification and huge tranches that are irrelevant.
I don't want to have to understand the irrelevant bits of bioperl just
so I can decide whether its safe to install a broken release.
It just adds insult to injury if the broken release is a patch branch
that should be clearing test failures, not introducing new ones!
Jason Stajich wrote:
> I'll take a look at some of these this week. I might have inadvertantly
> caused some of them, not sure.
That would be great; as I say, I'm stuck until I can get a working system.
Thanks, Dave
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
-I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness
qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/AAChange...................ok
... ok snipped
t/Chain......................ok
t/cigarstring................Can't use an undefined value as an ARRAY
reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, <GEN1> line
434.
dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-3
Failed 3/3 tests, 0.00% okay
t/ClusterIO..................ok
...
t/DBCUTG.....................ok
20/22 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/DBFasta....................ok
t/DB.........................
FAILED tests 79-87
Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay,
87.18%)
t/DNAMutation................ok
t/Domcut.....................ok
22/25 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/ECnumber...................ok
...
t/ESEfinder..................ok
10/12 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/est2genome.................ok
...
t/GDB........................ok
t/GeneCoordinateMapper.......
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define
seq_id (at least one sublocation does!)
---------------------------------------------------
-------------------- WARNING ---------------------
MSG: sorted sublocation array requested but root location doesn't define
seq_id (at least one sublocation does!)
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
ok
t/Geneid.....................ok
t/Genewise...................ok
2/51 skipped:
t/Genomewise.................ok
t/Genpred....................ok
t/GFF........................Filehandle Symbol::GEN0 opened only for
output at blib/lib/Bio/Root/IO.pm line 440.
Filehandle Symbol::GEN1 opened only for output at
blib/lib/Bio/Root/IO.pm line 440.
ok
t/GOR4.......................ok
8/11 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/GOterm.....................ok
t/GuessSeqFormat.............ok
t/hmmer......................ok
t/HNN........................ok
10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Index......................ok
...
t/MitoProt...................ok
5/8 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Molphy.....................ok
...
t/RefSeq.....................ok
10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Registry...................DB_File and BerkeleyDB not found. Skipping
DB_File tests
ok
t/Relationship...............ok
t/RelationshipType...........ok
t/RemoteBlast................ok
4/6 skipped: to avoid timeout
t/RepeatMasker...............ok
t/RestrictionAnalysis........ok
t/RestrictionEnzyme..........ok
t/RestrictionIO..............Use of uninitialized value in string eq at
blib/lib/Bio/Restriction/IO/withrefm.pm line 130, <GEN1> line 13.
Use of uninitialized value in string eq at
blib/lib/Bio/Restriction/IO/withrefm.pm line 130, <GEN1> line 24.
FAILED test 10
Failed 1/14 tests, 92.86% okay
t/RNAChange..................ok
...
t/SeqFeature.................ok
6/74 skipped: tests which need the Bio::DB::GenBank module
t/SeqIO......................ok
3/235 skipped:
t/SeqPattern.................ok
...
t/Sopma......................ok
12/15 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Species....................ok
...
t/Taxonomy...................ok
7/8 skipped: to avoid blocking
t/Tempfile...................ok
t/Term.......................ok
t/Tools......................ok
t/TreeIO.....................FAILED test 42
Failed 1/41 tests, 97.56% okay (less 1 skipped test: 39 okay,
95.12%)
t/Tree.......................ok
t/trim.......................ok
t/tutorial...................Use of uninitialized value in print at
blib/lib/bptutorial.pl line 4042, <GEN21> line 934.
ok
t/UCSCParsers................ok
t/Unflattener2...............ok
t/Unflattener................ok
t/UniGene....................ok
t/Variation_IO...............ok
t/WABA.......................ok
t/XEMBL_DB...................ok
Failed 4/180 test scripts, 97.78% okay. -6/8314 subtests failed, 100.07%
okay.
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/DB.t 78 9 11.54% 79-87
t/RestrictionIO.t 14 1 7.14% 10
t/TreeIO.t 41 1 2.44% 42
t/cigarstring.t 255 65280 3 6 200.00% 1-3
121 subtests skipped.
make: *** [test_dynamic] Error 11
--
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960
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