[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

[Chris Fields]

On Jan 19, 2009, at 8:32 PM, Martin MOKREJŠ wrote:

> Chris Fields wrote:
>
>> The RC is currently being uploaded to CPAN and should be available in
>> the next 24-48 hours under authorname CJFIELDS.  In the meantime, the
>> release candidates can be directly downloaded here:
>>
>> http://bioperl.org/DIST/BioPerl-1.5.9_3.tar.bz2
>
>> Known Issues:
>>
>> 1) Warnings for Bio::Assembly tests are for incomplete phrap parsing.
>> These modules will be a focus of BioPerl 1.7; in the meantime I'll  
>> see
>> about quenching the tests.
>> 2) Warnings for Bio::Annotation tests can be fixed by an upgrade to  
>> the
>> latest Data::Stag (this is NOT a required upgrade).
>
> Chris,
>  you mean all of these?
>
> t/Annotation/Annotation......................116/155 Use of  
> uninitialized value in concatenation (.) or string at /usr/lib/perl5/ 
> site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in concatenation (.) or string at /usr/ 
> lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in concatenation (.) or string at /usr/ 
> lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in concatenation (.) or string at /usr/ 
> lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in concatenation (.) or string at /usr/ 
> lib/perl5/site_perl/5.8.8/Data/Stag/ITextWriter.pm line 51.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.
> Use of uninitialized value in string eq at /usr/lib/perl5/site_perl/ 
> 5.8.8/Data/Stag/ITextWriter.pm line 64.

 From Data::Stag 0.10.  I've bumped the required version to 0.11 to  
get rid of these (should upgrade your local installation).

> t/Annotation/Annotation......................ok
> t/Annotation/AnnotationAdaptor...............ok
> t/Assembly/Assembly..........................2/50 # If there are  
> warnings here, it's because the phrap parser doesn't include the  
> sequence string in the sequence objects.
>
> --------------------- WARNING ---------------------
> MSG: Adding non-nucleotidic sequence ML4922R
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: Adding non-nucleotidic sequence ML4947F
> ---------------------------------------------------
> t/Assembly/Assembly..........................ok
>
>
>
> Why doesn't it say something like the other tests?, e.g.:
>
> t/PodSyntax..................................skipped: Test::Pod 1.00  
> required for testing POD

That's a diagnostic response, it's probably best to change that to a  
TODO (fixed now).

> t/Root/Utilities.............................1/50
> --------------------- WARNING ---------------------
> MSG: find_exe: Multiple paths to 'gunzip' found. Using first.
> ---------------------------------------------------
>
> $ whereis gunzip
> gunzip: /bin/gunzip /usr/bin/gunzip /usr/X11R6/bin/gunzip /usr/bin/ 
> X11/gunzip
> $ :-((
>
> In my case all the other gzunzips are soflinks to /bin/gunzip.

File this as a bug.  The check should make sure the others are not  
soft links.  Won't be fixed in time for 1.6, though, but I remember  
this popping up sporadically elsewhere.

>> 4) Small warning for t/Tree/TreeIO/svggraph.t due to an issue with  
>> SVG::Graph.
>
> t/Tree/TreeIO/svggraph.......................1/4 Use of  
> uninitialized value in join or string at /usr/lib/perl5/vendor_perl/ 
> 5.8.8/SVG/Element.pm line 1195, <GEN0> line 1.
> t/Tree/TreeIO/svggraph.......................ok
>
> Right.

This one has been discussed before and is a bug within SVG::Graph.

> Very good. Chris! Congratulations to all devs!
> Martin


Thanks!

chris