[Bioperl-l] Bioperl 1.5.2 RC5

[Sendu Bala]

Chris Fields wrote:
> On Nov 26, 2006, at 3:00 PM, Conrad Halling wrote:
[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

[snip]

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

The test script has nothing to catch in the eval because blastxml.pm 
catches the error and emits a warning. You'll either have to make 
blastxml.pm throw (instead of returning undef + warn), or figure 
something else out.

It's a behaviour change, but would anyone care if it threw thanks to 
this problem?