[Bioperl-l] Package status for 1.5.2

[Sendu Bala]

To what extent do we want a unified release for all the various 
packages? As I see it, here is the current status:

Core
----
P1 and P2 bugs remain in bugzilla, but nothing that need prevent the 
release. These only need to be resolved before 1.6.

Test suite passes satisfactorily, though see 
http://www.bioperl.org/wiki/Release_1.5.2 for some minor issues (again, 
nothing that prevents release).

Installation issues (ie. PPM, Windows) are being investigated by Nathan 
and Chris. Are they serious enough to prevent release? (Minimal Perl 
version will be 5.6.1)

Conclusion: ok to be tagged bioperl-release-1-5-2-rc1 and released for 
testing.


Run
---
Has no INSTALL file.

I don't have most of the programs installed, so I skip most tests. 
However I still manage to fail 2 tests:

Failed Test       Stat Wstat Total Fail  Failed  List of Failed
t/Analysis_soap.t               17    1   5.88%  17
t/Hmmer.t                       20    8  40.00%  5-8 12-15

Should an attempt be made to get things in the Run package to work? Does 
anyone have a comprehensive selection of programs installed for better 
testing?

Conclusion: NOT ok to be tagged.


Ext
---
Has no INSTALL file.

I can't install the staden stuff, so can't even run the test suite.

Conclusion: ??


GUI
---
Has no INSTALL file.

Passes its single test.

Conclusion: ok to tag, but do we want to? (It doesn't seem to have been 
part of a unified release in the past.)


DB
--
Test suite passes first time, but subsequently warnings and failures 
seem to arrise due to things stored in DB by test scritps not being 
removed from DB (even though the test script tries to).

eg. perl t/04swiss.t
1..52
ok 1
[...]
ok 51
not ok 52
# Test 52 got: <UNDEF> (t/04swiss.t at line 119)
#    Expected: '1'

This may be a problem particular to me.

Conclusion: ??, do we even want a unified release with this (haven't in 
the past)?


Pedigree
--------
Has no README or INSTALL file.

Test suite passes, though t/PedIO.t warns about uninitialized values in 
ped.pm line 291.

Conclusion: ok to tag, but do we want to? (It doesn't seem to have been 
part of a unified release in the past.)


Microarray
----------
Has no README or INSTALL file.

All tests fail because they can't find Bio/Expression/FeatureSet.pm. I 
can't find it either.

Conclusion: NOT ok to tag, do we even want a unified release with this 
(haven't in the past)?


Network
-------
Has no README.

Test suite has big problems:

Failed Test            Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/Graph-Articulation.t    9  2304    47    0   0.00%  ??
t/Graph-MD5.t             2   512    19    0   0.00%  ??
t/Graph-Seq.t           255 65280    18    0   0.00%  ??
t/IO_dip_tab.t            9  2304    16    0   0.00%  ??
t/IO_psi.t              255 65280    21    0   0.00%  ??
t/Interaction.t         255 65280    17    0   0.00%  ??
t/ProteinNet.t            9  2304   168    0   0.00%  ??
297 subtests skipped.
Failed 7/9 test scripts, 22.22% okay. 0/343 subtests failed, 100.00% okay.

eg.
t/Graph-Articulation....ok 1/47Can't locate object method 
"get_nodes_by_id" via package "Graph::Undirected" at 
[...]Bio/Network/IO/dip_tab.pm line 141, <GEN1>
line 1.

t/Graph-MD5.............Can't locate object method "new" via package 
"Graph::Undirected" (perhaps you forgot to load "Graph::Undirected"?) at 
t/Graph-MD5.t line 44.

Conclusion: NOT ok to tag, do we even want a unified release with this 
(haven't in the past)?


Pipeline
--------
Is there a config file? Many tests fail for me because they try a 
database connection with user root, but with no password this fails.

Conclusion: ??, do we even want a unified release with this (haven't in 
the past)?