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

[Lincoln Stein]

I feel pretty happy with the graphics HOWTO, POD fixes and with the new 
Bio::Graphics layout algorithm, so no more stalling from my end on the 1.1.1 
release.

Lincoln


On Tuesday 24 September 2002 04:20 am, Heikki Lehvaslaiho wrote:
> 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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-- 
Lincoln Stein
lstein@cshl.org