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

[Lincoln Stein]

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.

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