[Bioperl-l] Package status for 1.5.2

Chris Fields cjfields at uiuc.edu
Sun Sep 24 10:03:46 EDT 2006


Past releases of bioperl-run used to coincide with core, if I  
remember correctly.  For the last release, I think Jason set up tar- 
balls for all of them at roughly the same time; I'm sure there were  
bugs present in them at the time.

If there are any bugs (tests that don't pass) they should probably be  
submitted to bugzilla, unless you can fix them.  The ones in hmmer  
may arise from recent changes in SearchIO.

Chris

On Sep 24, 2006, at 7:08 AM, Sendu Bala wrote:

> 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)?
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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