[Bioperl-l] About to tag the last RC...

Tue Jan 13 19:18:59 UTC 2009

On Jan 13, 2009, at 12:49 PM, Dave Messina wrote:

> Hey Chris,
> I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6.
>
> When I skip install of optional modules, BioPerl scripts, and  
> network tests,
> everything goes fine.
>
> All tests successful, 58 tests and 319 subtests skipped.
> Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys  
> = 97.83
> CPU)
>
>
> However, when I request installation of all optional modules, all  
> BioPerl
> scripts, and the network tests, I run into some minor problems. Note  
> that
> I'm building and testing on the command line, not via the CPAN shell.
>
> Test output is below (minus the 'copying script' stuff at the  
> beginning).
>
> Dave
>
> ...
> t/Biblio/eutils..............................1/4
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded
> Exception Can't locate XML/Twig.pm in @INC (@INC contains:
> /Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib .
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch
> /Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess
> /System/Library/Perl/5.8.8/darwin-thread-multi-2level
> /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- 
> multi-2level
> /Library/Perl/5.8.8 /Library/Perl
> /Network/Library/Perl/5.8.8/darwin-thread-multi-2level
> /Network/Library/Perl/5.8.8 /Network/Library/Perl
> /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
> /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/ 
> 5.8.1)
> at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm  
> line
> 122.
> BEGIN failed--compilation aborted at
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm  
> line 122.
> Compilation failed in require at
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315.
>
> For more information about the Biblio system please see the  
> Bio::Biblio
> docs.
>
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357
> STACK: Bio::Biblio::_load_access_module
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319
> STACK: Bio::Biblio::new
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280
> STACK: t/Biblio/eutils.t:22
> -----------------------------------------------------------
> # Looks like you planned 4 tests but only ran 1.
> t/Biblio/eutils.............................. Dubious, test returned  
> 255
> (wstat 65280, 0xff00)
> Failed 3/4 subtests

Fixed on main trunk (missing a dependency).

> t/RemoteDB/DB................................104/116
> #   Failed test in t/RemoteDB/DB.t at line 352.
> #          got: 'unknown'
> #     expected: 'GDB:188393'
> t/RemoteDB/DB................................114/116 # Looks like  
> you failed
> 1 test of 116.
> t/RemoteDB/DB................................ Dubious, test returned 1
> (wstat 256, 0x100)
> Failed 1/116 subtests
> (less 8 skipped subtests: 107 okay)

...

> t/RemoteDB/GDB...............................2/12
> #   Failed test 'info was unknown'
> #   in t/RemoteDB/GDB.t at line 40.
> #          got: 'unknown'
> #     expected: 'GDB:188296'
> ...
> Failed 8/12 subtests

These pass for me but skips the GDB tests due to lack of server  
connection.  The server does indeed appear to be down.

I thought GDB was supposed to be maintained by ORNL past July 31?  If  
it is indeed down for good we'll need to (unfortunately) deprecate  
this module.  There is an article about that here:

http://www.sciencemag.org/cgi/content/full/279/5357/1611d?ck=nck (req.  
subscription)
http://en.wikipedia.org/wiki/GDB_Human_Genome_Database

> t/RemoteDB/HIV/HIV...........................21/29 # Error:
> # ------------- EXCEPTION: Bio::WebError::Exception -------------
> # MSG: Unparsed failure at
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line  
> 275.
> #
> # VALUE: An empty string ("")
> # STACK: Error::throw
> # STACK: Bio::Root::Root::throw
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357
> # STACK: Bio::DB::HIV::get_request
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277
> # STACK: Bio::DB::HIV::get_seq_stream
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396
> # STACK: Bio::DB::HIV::get_Stream_by_acc
> /Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491
> # STACK: t/RemoteDB/HIV/HIV.t:78
> # ---------------------------------------------------------------
> t/RemoteDB/HIV/HIV...........................22/29 # Looks like you  
> planned
> 29 tests but ran 1 extra.
> t/RemoteDB/HIV/HIV........................... Dubious, test returned  
> 255
> (wstat 65280, 0xff00)
> All 29 subtests passed
> (less 9 skipped subtests: 20 okay)

Test count can off when batch-eval tests.  Fixed on main trunk.

> t/Root/RootIO................................30/31
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: request failed: HTTP/1.0 400 Bad Request
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
> STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234
> STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279
> STACK: Bio::Root::IO::new Bio/Root/IO.pm:223
> STACK: t/Root/RootIO.t:107
> -----------------------------------------------------------
> # Looks like you planned 31 tests but only ran 30.
> t/Root/RootIO................................ Dubious, test returned  
> 255
> (wstat 65280, 0xff00)
> Failed 1/31 subtests

Odd one, will have to look into that; it may be a problem specifically  
with using Bio::Root::HTTPget (I think this defaults to LWP if it is  
installed).

Thanks for the tests!

chris