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

[Heikki Lehvaslaiho]

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