POD fixes Re: [Bioperl-l] Push for 1.1.1 developer's release this week

[Heikki Lehvaslaiho]

On Mon, 2002-09-23 at 3:05, Lincoln Stein wrote:
> I'd like to finish my Graphics HOWTO document, and do some rearrangement in 
> the scripts directory, which is a mess.  I will add skeleton POD 
> documentation to the modules that are missing them, but these are *all* 
> internal modules that contain only utility code.

Thanks Lincoln, 

Skeleton code stating that they are internal modules, and pointing to
the main module with more documentation is exactly what is needed.

	-Heikki



> How does end of the week sound.
> 
> Lincoln
> 
> 
> On Monday 23 September 2002 5:35 am, Heikki Lehvaslaiho wrote:
> > On Sun, 2002-09-22 at 17:26, Ewan Birney wrote:
> > > Hilmar/Elia/Heikki/Chris - is there anything I should wait for for the
> > > 1.1.1 before letting it get out there? Any thoughts by anyone?
> >
> > I did my POD checking routine yesterday and fixed dozens of files.
> >
> > Most of the errors are caused by POD = lines not separated by empty
> > lines or badly structured SYNOPSIS section. Here are the basic rules for
> > SYNOPSIS:
> >
> > - make sure code is runnable
> > - indent lines by two spaces
> > - empty lines should NOT contain white space
> >
> >
> > After my fixing, these are the outstanding files to fix:
> >
> >
> > The following modules does not contain any POD documentation:
> >
> >
> > ./DB/Flat/BDB/fasta.pm			Lincoln
> > ./DB/Flat/BDB/embl.pm			Lincoln
> > ./DB/GFF/Adaptor/dbi/iterator.pm	Lincoln
> > ./DB/GFF/Adaptor/memory_iterator.pm	Lincoln
> > ./DB/GFF/Util/Binning.pm		Lincoln
> > ./DB/GFF/Util/Rearrange.pm		Lincoln
> > ./Graphics/Glyph/Factory.pm		Lincoln
> > ./Tools/Prints.pm			savikalpa
> > ./Tools/Seg.pm				savikalpa
> > ./Tools/Tmhmm.pm			savikalpa
> >
> > jason
> >
> > *** ERROR: unresolved internal link 'HSP Tiling and Ambiguous Alignments'
> > at line 876 in file ./Search/Hit/GenericHit.pm *** ERROR: unresolved
> > internal link 'HSP Tiling and Ambiguous Alignments' at line 925 in file
> > ./Search/Hit/GenericHit.pm ./Search/Hit/GenericHit.pm has 2 pod syntax
> > errors.
> >
> > Chad
> >
> > *** WARNING: multiple occurence of link target 'Bio::RangeI methods' at
> > line - in file ./Seq/PrimedSeq.pm *** WARNING: multiple occurence of link
> > target 'start' at line - in file ./Seq/PrimedSeq.pm
> >
> > *** WARNING: empty section in previous paragraph at line 18 in file
> > ./SeqFeature/Primer.pm *** WARNING: empty section in previous paragraph at
> > line 20 in file ./SeqFeature/Primer.pm *** WARNING: empty section in
> > previous paragraph at line 46 in file ./SeqFeature/Primer.pm
> >
> > *** WARNING: 2 unescaped <> in paragraph at line 18 in file
> > ./Tools/Primer3.pm *** WARNING: empty section in previous paragraph at line
> > 52 in file ./Tools/Primer3.pm *** ERROR: empty =head2 at line 92 in file
> > ./Tools/Primer3.pm
> > *** WARNING: line containing nothing but whitespace in paragraph at line
> > 271 in file ./Tools/Primer3.pm *** WARNING: multiple occurence of link
> > target 'null' at line - in file ./Tools/Primer3.pm ./Tools/Primer3.pm has 1
> > pod syntax error.
> >
> >
> > "Fugu Team"
> >
> > *** WARNING: empty section in previous paragraph at line 15 in file
> > ./Tools/Genewise.pm *** WARNING: empty section in previous paragraph at
> > line 17 in file ./Tools/Genewise.pm *** WARNING: empty section in previous
> > paragraph at line 15 in file ./Tools/Pseudowise.pm *** WARNING: empty
> > section in previous paragraph at line 17 in file ./Tools/Pseudowise.pm
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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