[Bioperl-l] BioPerl 1.6.0 alpha 2 released

[Chris Fields]

And just as quickly, getting back lots indicating more problems from  
CPAN Testers.  Some can be ignored (appear due to the local perl  
testing environment so are local to the tester).  The following are  
the most significant; appears a hard-coded SeqFeature_SQLite.t got  
bundled in somehow, so I'll drop an alpha 3 shortly.

chris

#   Failed test 'use Bio::SeqFeature::Annotated;'
#   at t/Annotation/Annotation.t line 23.
#     Tried to use 'Bio::SeqFeature::Annotated'.
#     Error:  Can't locate URI/Escape.pm in @INC (@INC contains: t/ 
lib . /Users/david/cpantesting/perl-5.10.1/.cpan/build/ 
BioPerl-1.6.0._2-QVXU9n/blib/lib /Users/david/cpantesting/ 
perl-5.10.1/.cpan/build/BioPerl-1.6.0._2-QVXU9n/blib/arch /Users/david/ 
cpantesting/perl-5.10.1/.cpan/build/BioPerl-1.6.0._2-QVXU9n /sw/lib/ 
perl5 /sw/lib/perl5/darwin /Users/david/cpantesting/perl-5.10.1/lib/ 
5.10.1/darwin-thread-multi-2level /Users/david/cpantesting/perl-5.10.1/ 
lib/5.10.1 /Users/david/cpantesting/perl-5.10.1/lib/site_perl/5.10.1/ 
darwin-thread-multi-2level /Users/david/cpantesting/perl-5.10.1/lib/ 
site_perl/5.10.1) at Bio/SeqFeature/Annotated.pm line 100.
# BEGIN failed--compilation aborted at Bio/SeqFeature/Annotated.pm  
line 100.
# Compilation failed in require at (eval 60) line 2.
# BEGIN failed--compilation aborted at (eval 60) line 2.
# Looks like you failed 1 test of 159.
t/Annotation/Annotation.t ....................
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/159 subtests
	(less 12 skipped subtests: 146 okay)


t/LocalDB/SeqFeature.t ....................... ok
DBD::SQLite::db prepare_cached failed: near "INDEXED": syntax error(1)  
at dbdimp.c line 271 at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1678.

-------------------- EXCEPTION --------------------
MSG: near "INDEXED": syntax error(1) at dbdimp.c line 271
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_prepare Bio/DB/ 
SeqFeature/Store/DBI/mysql.pm:1678
STACK Bio::DB::SeqFeature::Store::DBI::SQLite::_features Bio/DB/ 
SeqFeature/Store/DBI/SQLite.pm:665
STACK Bio::DB::SeqFeature::Store::get_features_by_attribute Bio/DB/ 
SeqFeature/Store.pm:961
STACK toplevel t/LocalDB/SeqFeature.t:135
-------------------------------------------
# Looks like you planned 69 tests but only ran 40.
# Looks like your test died just after 40.
t/LocalDB/SeqFeature_SQLite.t ................
Failed 29/69 subtests



On Sep 21, 2009, at 10:56 PM, Chris Fields wrote:

> Just a note that the second alpha is out and propagating it's way  
> around the intertubes:
>
> http://search.cpan.org/~cjfields/BioPerl-1.6.0_2/
>
> Pick your favorite archive here:
>
> http://bioperl.org/DIST/RC/
>
> This should address the bugs reported by Scott from the last  
> release.  Just a note, but I am seeing a warning popping up with 64- 
> bit perl 5.10.1 on Mac with PopGen tests (I think it's a floating  
> point addition issue).  Let me know if this is popping up elsewhere.
>
> Enjoy!
>
> chris
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