[Bioperl-l] Bioperl 1.5.2 RC5

Conrad Halling chhalling at verizon.net
Sun Nov 26 16:00:18 EST 2006

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 

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

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


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


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


-------------------- 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 
does not exist 
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

#   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.

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


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

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