[Bioperl-l] Bioperl 1.5.2 RC5

[Conrad Halling]

I attempted to use CPAN to install BioPerl 1.5.2 RC5 into a fresh 
installation of Perl 5.8.8 under Mac OS X 10.4.8 with all dependencies 
installed.

The tests fail for t/SearchIO. An edited record of the output is shown 
below.


cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz

[*snip*]

*** Optional dependencies section ***
All dependencies are installed

[*snip*]

Running make test
PERL_DL_NONLAZY=1 /test/perl/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t

[*snip*]

t/SearchIO...................ok 
1/1340                                      
-------------------- WARNING ---------------------
MSG: XML::SAX::Expat not currently supported; must have local copies of 
NCBI DTD docs!
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: error in parsing a report:
 
404 File 
`/Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd' 
does not exist 
file:///Users/challing/.cpan/build/bioperl-1.5.2_005-RC/NCBI_BlastOutput.dtd
Handler couldn't resolve external entity at line 2, column 82, byte 104
error in processing external entity reference at line 2, column 82, byte 
104 at /test/perl/lib/site_perl/5.8.8/darwin-2level/XML/Parser.pm line 187

---------------------------------------------------
t/SearchIO...................NOK 
5/1340                                     
#   Failed test 'The object isa Bio::Search::Result::ResultI'
#   in t/SearchIO.t at line 65.
#     The object isn't defined
Can't call method "database_name" on an undefined value at t/SearchIO.t 
line 66.
# Looks like you planned 1340 tests but only ran 5.
# Looks like you failed 1 test of 5 run.
# Looks like your test died just after 5.
t/SearchIO...................dubious                                         

        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-1340
        Failed 1336/1340 tests, 0.30% okay

[*snip*]

Failed Test  Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/SearchIO.t  255 65280  1340 2671  5-1340
2 tests and 126 subtests skipped.
Failed 1/235 test scripts. 1336/11940 subtests failed.
Files=235, Tests=11940, 321 wallclock secs (154.44 cusr + 24.28 csys = 
178.72 CPU)
Failed 1/235 test programs. 1336/11940 subtests failed.
make: *** [test_dynamic] Error 255
  /usr/bin/make test -- NOT OK
Running make install
  make test had returned bad status, won't install without force



Sendu Bala wrote:
> Bioperl 1.5.2 Release Candidate 5 is ready and available for testing.
> See http://www.bioperl.org/wiki/Release_1.5.2 for
> instructions on getting and testing this RC.
>
> Everyone:
>    Even though 1.5.2 is a 'developer' release, we consider it the most
>    stable and capable version of Bioperl, and recommend that you use
>    it in all but the most critical production environments. Please
>    try it out and let us know of any problems or difficulties you run
>    into.
>
>    Please try the new Build.PL installation script and report back how
>    you get on. Also try installing using CPAN. Your CPAN mirrors may
>    not be current enough, so you may have delete all entries in your
>    urllist first.
>
>
> Developers:
>    Please experiment with installation, especially via CPAN. If you
>    already have all/most prerequisite external modules installed,
>    try uninstalling some and report how effective the system is at
>    reinstalling them for you.
>
>    RC5 may form the final release for some of the packages (probably
>    all except for bioperl-run), so any further commits made, even to
>    branch-1-5-2, may not make final release. If you think you've
>    committed an important bug fix that should be part of final release,
>    let me know.
>
>
> Thank you,
> Sendu.
>
>
> PS. What happened to RC4? I didn't announce it, but it was available on 
> CPAN where I did some testing on it.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   

-- 
Conrad Halling
chhalling at verizon.net