[Bioperl-l] [ANNOUCEMENT] BioPerl 1.6 RC3

Martin MOKREJŠ mmokrejs at ribosome.natur.cuni.cz
Mon Jan 19 21:32:15 EST 2009


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.
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




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.


> 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.


Very good. Chris! Congratulations to all devs!
Martin


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