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

[Ewan Birney]

On Mon, 23 Sep 2002, 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.
>
> How does end of the week sound.

Fine by me...



>
> 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
>