[Bioperl-l] Bioperl 1.5.2 RC5

[Chris Fields]

On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote:

> 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
> ...

There is an eval{} block set up to catch that error but apparently it  
doesn't work.  I'll have a look at it.

Like the warning states, XML::SAX::Expat is not supported for  
BLASTXML parsing unless you have the NCBI DTDs installed as well  
(blame this on NCBI since their BLAST DTDs don't have the explicit  
web address).  Saying that I don't recommend using XML::SAX::Expat at  
all (it is no longer actively maintained).  Pretty much any other  
XML::SAX backend works; I recommend using XML::SAX::ExpatXS or  
XML::LibXML for speedier parsing, though XML::SAX::PurePerl also works.

Chris


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