[Bioperl-l] test failures on main trunk

[Ewan Birney]

perl 5.004_04 is failing again. Some I can fix, others Peter/Jason might
want to take a peek at. They are

Failed Test  Status Wstat Total Fail  Failed  List of failed
-------------------------------------------------------------------------------
t/Clustalw.t                  9    1  11.11%  4
t/DB.t            0    11    ??   ??       %  ??
t/Index.t         2   512     8    3  37.50%  6-8
t/SeqFeature.t               21   ??       %  ??
t/TCoffee.t                   9    1  11.11%  4
Failed 5/48 test scripts, 89.58% okay. -1/594 subtests failed, 100.17%
okay.
make: *** [test_dynamic] Error 29
riker:~/src/bioperl-live> perl t/DB/



riker:~/src/bioperl-live> perl t/DB.t
IO::String not installed. This means the Bio::DB::* modules are not
usable. Skipping tests.
1..1
ok 1
Segmentation fault
riker:~/src/bioperl-live> perl t/Clustalw.t
1..9
Clustalw program not found as /clustalw or not executable.
  Clustalw can be obtained from eg-
http://corba.ebi.ac.uk/Biocatalog/Alignment_Search_software.html/
ok 1

-------------------- EXCEPTION --------------------
MSG: Unallowed parameter: NEW !
CONTEXT: Error in uNKNOWN CONTEXT
SCRIPT: t/Clustalw.t
STACK:
Bio::Tools::Run::Alignment::Clustalw::AUTOLOAD(308)
main::t/Clustalw.t(52)
---------------------------------------------------


riker:~/src/bioperl-live> perl t/SeqFeature.t
1..21
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
ok 13
ok 14
ok 15
ok 16
ok 17
not ok 18
ok 19
not ok 20
ok 21
ok 22
ok 23
ok 24
ok 25
ok 26
ok 27


riker:~/src/bioperl-live> perl t/TCoffee.t
1..9
TCoffee program not found as /t_coffee or not executable.
  TCoffee can be obtained from eg-
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
ok 1

-------------------- EXCEPTION --------------------
MSG: Unallowed parameter: NEW !
CONTEXT: Error in uNKNOWN CONTEXT
SCRIPT: t/TCoffee.t
STACK:
Bio::Tools::Run::Alignment::TCoffee::AUTOLOAD(561)
main::t/TCoffee.t(55)
---------------------------------------------------





I'll start to work on TCoffee/Clustalw...






-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------