[Bioperl-l] linking errors in pod documentation
Heikki Lehvaslaiho
heikki@ebi.ac.uk
Tue, 08 Jan 2002 15:17:19 +0000
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I noticed that there are links in the POD documentation pointing to anchors
that does not exist, so I modified my podchecker script to run pod2html on
all modules.
Before I start going through the modules with errors myself, I'd like people
working on them to have a look first. Not all errors printed are necessary
important.
The modules are:
Bio/AlignIO.pm
Bio/DB/DBFetch.pm
Bio/DB/EMBL.pm
Bio/DB/Fasta.pm
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio/DB/GFF/Adaptor/dbi.pm
Bio/DB/GFF/Featname.pm
Bio/DB/GFF/Feature.pm
Bio/DB/GFF/Homol.pm
Bio/DB/GFF.pm
Bio/DB/GFF/RelSegment.pm
Bio/DB/GFF/Segment.pm
Bio/DB/GFF/Typename.pm
Bio/DB/RefSeq.pm
Bio/Factory/BlastHitFactory.pm
Bio/Factory/BlastResultFactory.pm
Bio/Factory/HitFactoryI.pm
Bio/Factory/ResultFactoryI.pm
Bio/Root/Err.pm
Bio/Root/IOManager.pm
Bio/Root/Object.pm
Bio/Root/RootI.pm
Bio/Root/Utilities.pm
Bio/Root/Vector.pm
Bio/Root/Xref.pm
Bio/Search/BlastUtils.pm
Bio/Search/DatabaseI.pm
Bio/Search/GenericDatabase.pm
Bio/Search/Hit/BlastHit.pm
Bio/Search/HSP/BlastHSP.pm
Bio/Search/HSP/HSPI.pm
Bio/SearchIO/psiblast.pm
Bio/SearchIO/Writer/HitTableWriter.pm
Bio/SearchIO/Writer/HSPTableWriter.pm
Bio/SearchIO/Writer/ResultTableWriter.pm
Bio/Search/Result/BlastResult.pm
Bio/SeqIO.pm
Bio/Structure/IO.pm
Bio/Tools/AnalysisResult.pm
Bio/Tools/Blast/HSP.pm
Bio/Tools/Blast/HTML.pm
Bio/Tools/Blast.pm
Bio/Tools/Blast/Sbjct.pm
Bio/Tools/Fasta.pm
Bio/Tools/RestrictionEnzyme.pm
Bio/Tools/SeqAnal.pm
Bio/Tools/StateMachine/AbstractStateMachine.pm
Bio/Tools/StateMachine/IOStateMachine.pm
Bio/UnivAln.pm
Bio/Variation/IO.pm
Bio/Variation/IO/xml.pm
The more detailed report is here:
Bio/AlignIO.pm: cannot resolve L<perltie> in paragraph 68
Bio/SeqIO.pm: cannot resolve L<perltie> in paragraph 72
Bio/UnivAln.pm: cannot resolve L<INSTALLATION> in paragraph 128
Bio/DB/Fasta.pm: cannot resolve L<bioperl> in paragraph 116
Bio/DB/EMBL.pm: cannot resolve
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 14
Bio/DB/GFF.pm: cannot resolve L<bioperl> in paragraph 521
no title for Bio/DB/GFF/Adaptor/dbi/iterator.pm
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm: cannot resolve L<DBI> in paragraph
52
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm: cannot resolve L<bioperl> in
paragraph 52
Bio/DB/GFF/Adaptor/dbi.pm: cannot resolve L<bioperl> in paragraph 281
no title for Bio/DB/GFF/Adaptor/memory.pm
Bio/DB/GFF/Featname.pm: cannot resolve L<bioperl> in paragraph 44
Bio/DB/GFF/Feature.pm: cannot resolve L<bioperl> in paragraph 196
Bio/DB/GFF/Homol.pm: cannot resolve L<bioperl> in paragraph 27
Bio/DB/GFF/RelSegment.pm: cannot resolve L<bioperl> in paragraph 177
Bio/DB/GFF/Segment.pm: cannot resolve L<bioperl> in paragraph 152
Bio/DB/GFF/Typename.pm: cannot resolve L<bioperl> in paragraph 47
no title for Bio/DB/GFF/Util/Binning.pm
no title for Bio/DB/GFF/Util/Rearrange.pm
Bio/DB/RefSeq.pm: cannot resolve
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 14
Bio/DB/DBFetch.pm: cannot resolve
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 8
Bio/Factory/BlastHitFactory.pm: cannot resolve L<FEEDBACK> in paragraph 21
Bio/Factory/BlastResultFactory.pm: cannot resolve L<FEEDBACK> in paragraph
21
Bio/Factory/HitFactoryI.pm: cannot resolve L<FEEDBACK> in paragraph 18
Bio/Factory/ResultFactoryI.pm: cannot resolve L<FEEDBACK> in paragraph 18
Bio/Root/Err.pm: cannot resolve L<USAGE> in paragraph 20
Bio/Root/Err.pm: cannot resolve L<FEEDBACK> in paragraph 50
Bio/Root/IOManager.pm: cannot resolve L<FEEDBACK> in paragraph 53
Bio/Root/IOManager.pm: cannot resolve L<create_filehandle> in paragraph 144
Bio/Root/Object.pm: cannot resolve L<USAGE> in paragraph 19
Bio/Root/Object.pm: cannot resolve L<_rearrange> in paragraph 28
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 28
Bio/Root/Object.pm: cannot resolve L<warn> in paragraph 28
Bio/Root/Object.pm: cannot resolve L<APPENDIX> in paragraph 28
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 30
Bio/Root/Object.pm: cannot resolve L<INSTALLATION> in paragraph 55
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 62
Bio/Root/Object.pm: cannot resolve L<warn> in paragraph 62
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 66
Bio/Root/Object.pm: cannot resolve L<warn> in paragraph 66
Bio/Root/Object.pm: cannot resolve L<FEEDBACK> in paragraph 81
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 110
Bio/Root/Object.pm: cannot resolve L<warn> in paragraph 110
Bio/Root/Object.pm: cannot resolve L<_rearrange> in paragraph 115
Bio/Root/Object.pm: cannot resolve L<_set_err> in paragraph 195
Bio/Root/Object.pm: cannot resolve L<_set_err_state> in paragraph 201
Bio/Root/Object.pm: cannot resolve L<_set_err> in paragraph 206
Bio/Root/Object.pm: cannot resolve L<_set_err> in paragraph 211
Bio/Root/Object.pm: cannot resolve L<warn> in paragraph 223
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 223
Bio/Root/Object.pm: cannot resolve L<warn> in paragraph 357
Bio/Root/Object.pm: cannot resolve L<throw> in paragraph 357
Bio/Root/RootI.pm: cannot resolve L<_initialize> in paragraph 79
Bio/Root/Utilities.pm: cannot resolve L<FEEDBACK> in paragraph 44
Bio/Root/Vector.pm: cannot resolve L<USAGE> in paragraph 13
Bio/Root/Vector.pm: cannot resolve L<FEEDBACK> in paragraph 39
Bio/Root/Xref.pm: cannot resolve L<FEEDBACK> in paragraph 34
Bio/Search/Hit/BlastHit.pm: cannot resolve L<BUGS> in paragraph 14
Bio/Search/Hit/BlastHit.pm: cannot resolve L<FEEDBACK> in paragraph 42
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_adjust_contigs> in paragraph
149
Bio/Search/Hit/BlastHit.pm: cannot resolve L<BUGS> in paragraph 149
Bio/Search/Hit/BlastHit.pm: cannot resolve L<get_exponent> in paragraph 176
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_set_hsps> in paragraph 195
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_set_hsps> in paragraph 202
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 274
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 282
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 290
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 297
Bio/Search/Hit/BlastHit.pm: cannot resolve L<frac_aligned_hit()> in
paragraph 304
Bio/Search/Hit/BlastHit.pm: cannot resolve L<frac_unaligned_hit()> in
paragraph 308
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 313
Bio/Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 320
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<FEEDBACK> in paragraph 30
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<expect> in paragraph 78
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<expect> in paragraph 88
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<score> in paragraph 208
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<_set_seq> in paragraph 263
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<_set_match_stats> in paragraph
263
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<_set_match_seq> in paragraph
281
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<_set_residues> in paragraph 292
Bio/Search/HSP/BlastHSP.pm: cannot resolve L<collapse_nums> in paragraph 292
Bio/Search/HSP/HSPI.pm: unknown pod directive 'head' in paragraph 20.
ignoring.
no title for Bio/Search/Result/ResultI.pm
Bio/Search/Result/BlastResult.pm: cannot resolve L<FEEDBACK> in paragraph 27
Bio/Search/Result/BlastResult.pm: cannot resolve L<_set_signif> in paragraph
104
Bio/Search/BlastUtils.pm: cannot resolve L<ambiguous_aln> in paragraph 12
Bio/Search/BlastUtils.pm: cannot resolve L<overlap> in paragraph 12
Bio/Search/BlastUtils.pm: cannot resolve L<frac_identical> in paragraph 12
Bio/Search/BlastUtils.pm: cannot resolve L<frac_conserved> in paragraph 12
Bio/Search/BlastUtils.pm: cannot resolve L<frac_aligned_query> in paragraph
12
Bio/Search/BlastUtils.pm: cannot resolve L<frac_aligned_hit> in paragraph 12
Bio/Search/BlastUtils.pm: cannot resolve L<num_unaligned_query> in paragraph
12
Bio/Search/BlastUtils.pm: cannot resolve L<num_unaligned_hit> in paragraph
12
Bio/Search/BlastUtils.pm: cannot resolve L<overlap> in paragraph 34
Bio/Search/BlastUtils.pm: cannot resolve L<_tile_hsps> in paragraph 34
Bio/Search/BlastUtils.pm: cannot resolve L<seq_inds> in paragraph 51
Bio/Search/DatabaseI.pm: cannot resolve L<FEEDBACK> in paragraph 23
Bio/Search/GenericDatabase.pm: cannot resolve L<FEEDBACK> in paragraph 20
Bio/Tools/AnalysisResult.pm: cannot resolve L<parse> in paragraph 10
Bio/Tools/Blast.pm: cannot resolve L<USAGE> in paragraph 24
Bio/Tools/Blast.pm: cannot resolve L<USAGE> in paragraph 32
Bio/Tools/Blast.pm: cannot resolve L<FEEDBACK> in paragraph 44
Bio/Tools/Blast.pm: cannot resolve L<INSTALLATION> in paragraph 56
Bio/Tools/Blast.pm: cannot resolve L<USAGE> in paragraph 59
Bio/Tools/Blast.pm: cannot resolve L<destroy> in paragraph 99
Bio/Tools/Blast.pm: cannot resolve L<INSTALLATION> in paragraph 102
Bio/Tools/Blast.pm: cannot resolve L<INSTALLATION> in paragraph 189
Bio/Tools/Blast.pm: cannot resolve L<SYNOPSIS> in paragraph 209
Bio/Tools/Blast.pm: cannot resolve L<FEEDBACK> in paragraph 271
Bio/Tools/Fasta.pm: cannot resolve L<INSTALLATION> in paragraph 37
Bio/Tools/RestrictionEnzyme.pm: cannot resolve L<_initialize> in paragraph
64
Bio/Tools/RestrictionEnzyme.pm: cannot resolve L<_initialize> in paragraph
73
Bio/Tools/SeqAnal.pm: cannot resolve L<read> in paragraph 42
Bio/Tools/SeqAnal.pm: cannot resolve L<FEEDBACK> in paragraph 63
Bio/Tools/Blast/Sbjct.pm: cannot resolve L<BUGS> in paragraph 26
Bio/Tools/Blast/Sbjct.pm: cannot resolve L<FEEDBACK> in paragraph 61
Bio/Tools/Blast/Sbjct.pm: cannot resolve L<BUGS> in paragraph 165
Bio/Tools/Blast/HSP.pm: cannot resolve L<Links:> in paragraph 22
Bio/Tools/Blast/HTML.pm: cannot resolve L<FEEDBACK> in paragraph 30
no title for Bio/Tools/Blast/Run/postclient.pl
Bio/Tools/StateMachine/AbstractStateMachine.pm: cannot resolve L<FEEDBACK>
in paragraph 59
Bio/Tools/StateMachine/IOStateMachine.pm: cannot resolve L<FEEDBACK> in
paragraph 22
Bio/Variation/IO/xml.pm: cannot resolve
L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>mutationsE<sol>DTDE<sol>seqDiff.dtd>
in paragraph 9
Bio/Variation/IO.pm: cannot resolve L<perltie> in paragraph 66
Bio/SearchIO/Writer/HSPTableWriter.pm: cannot resolve L<SYNOPSIS> in
paragraph 37
Bio/SearchIO/Writer/HitTableWriter.pm: cannot resolve L<SYNOPSIS> in
paragraph 39
no title for Bio/SearchIO/Writer/ResultTableWriter.pm
Bio/SearchIO/Writer/ResultTableWriter.pm: cannot resolve L<SYNOPSIS> in
paragraph 69
Bio/SearchIO/psiblast.pm: cannot resolve L<SYNOPSIS> in paragraph 13
Bio/Structure/IO.pm: cannot resolve L<perltie> in paragraph 43
no title for Bio/StructureI.pm
-Heikki
--
______ _/ _/_____________________________________________________
_/ _/ 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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Bio/AlignIO.pm
Bio/DB/DBFetch.pm
Bio/DB/EMBL.pm
Bio/DB/Fasta.pm
Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio/DB/GFF/Adaptor/dbi.pm
Bio/DB/GFF/Featname.pm
Bio/DB/GFF/Feature.pm
Bio/DB/GFF/Homol.pm
Bio/DB/GFF.pm
Bio/DB/GFF/RelSegment.pm
Bio/DB/GFF/Segment.pm
Bio/DB/GFF/Typename.pm
Bio/DB/RefSeq.pm
Bio/Factory/BlastHitFactory.pm
Bio/Factory/BlastResultFactory.pm
Bio/Factory/HitFactoryI.pm
Bio/Factory/ResultFactoryI.pm
Bio/Root/Err.pm
Bio/Root/IOManager.pm
Bio/Root/Object.pm
Bio/Root/RootI.pm
Bio/Root/Utilities.pm
Bio/Root/Vector.pm
Bio/Root/Xref.pm
Bio/Search/BlastUtils.pm
Bio/Search/DatabaseI.pm
Bio/Search/GenericDatabase.pm
Bio/Search/Hit/BlastHit.pm
Bio/Search/HSP/BlastHSP.pm
Bio/Search/HSP/HSPI.pm
Bio/SearchIO/psiblast.pm
Bio/SearchIO/Writer/HitTableWriter.pm
Bio/SearchIO/Writer/HSPTableWriter.pm
Bio/SearchIO/Writer/ResultTableWriter.pm
Bio/Search/Result/BlastResult.pm
Bio/SeqIO.pm
Bio/Structure/IO.pm
Bio/Tools/AnalysisResult.pm
Bio/Tools/Blast/HSP.pm
Bio/Tools/Blast/HTML.pm
Bio/Tools/Blast.pm
Bio/Tools/Blast/Sbjct.pm
Bio/Tools/Fasta.pm
Bio/Tools/RestrictionEnzyme.pm
Bio/Tools/SeqAnal.pm
Bio/Tools/StateMachine/AbstractStateMachine.pm
Bio/Tools/StateMachine/IOStateMachine.pm
Bio/UnivAln.pm
Bio/Variation/IO.pm
Bio/Variation/IO/xml.pm
/usr/bin/pod2html: ./AlignIO.pm: cannot resolve L<perltie> in paragraph 68
/usr/bin/pod2html: ./SeqIO.pm: cannot resolve L<perltie> in paragraph 72
/usr/bin/pod2html: ./UnivAln.pm: cannot resolve L<INSTALLATION> in paragraph 128
/usr/bin/pod2html: ./DB/Fasta.pm: cannot resolve L<bioperl> in paragraph 116
/usr/bin/pod2html: ./DB/EMBL.pm: cannot resolve L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 14
/usr/bin/pod2html: ./DB/GFF.pm: cannot resolve L<bioperl> in paragraph 521
/usr/bin/pod2html: no title for ./DB/GFF/Adaptor/dbi/iterator.pm
/usr/bin/pod2html: ./DB/GFF/Adaptor/dbi/caching_handle.pm: cannot resolve L<DBI> in paragraph 52
/usr/bin/pod2html: ./DB/GFF/Adaptor/dbi/caching_handle.pm: cannot resolve L<bioperl> in paragraph 52
/usr/bin/pod2html: ./DB/GFF/Adaptor/dbi.pm: cannot resolve L<bioperl> in paragraph 281
/usr/bin/pod2html: no title for ./DB/GFF/Adaptor/memory.pm
/usr/bin/pod2html: ./DB/GFF/Featname.pm: cannot resolve L<bioperl> in paragraph 44
/usr/bin/pod2html: ./DB/GFF/Feature.pm: cannot resolve L<bioperl> in paragraph 196
/usr/bin/pod2html: ./DB/GFF/Homol.pm: cannot resolve L<bioperl> in paragraph 27
/usr/bin/pod2html: ./DB/GFF/RelSegment.pm: cannot resolve L<bioperl> in paragraph 177
/usr/bin/pod2html: ./DB/GFF/Segment.pm: cannot resolve L<bioperl> in paragraph 152
/usr/bin/pod2html: ./DB/GFF/Typename.pm: cannot resolve L<bioperl> in paragraph 47
/usr/bin/pod2html: no title for ./DB/GFF/Util/Binning.pm
/usr/bin/pod2html: no title for ./DB/GFF/Util/Rearrange.pm
/usr/bin/pod2html: ./DB/RefSeq.pm: cannot resolve L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 14
/usr/bin/pod2html: ./DB/DBFetch.pm: cannot resolve L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>cgi-binE<sol>dbfetch> in paragraph 8
/usr/bin/pod2html: ./Factory/BlastHitFactory.pm: cannot resolve L<FEEDBACK> in paragraph 21
/usr/bin/pod2html: ./Factory/BlastResultFactory.pm: cannot resolve L<FEEDBACK> in paragraph 21
/usr/bin/pod2html: ./Factory/HitFactoryI.pm: cannot resolve L<FEEDBACK> in paragraph 18
/usr/bin/pod2html: ./Factory/ResultFactoryI.pm: cannot resolve L<FEEDBACK> in paragraph 18
/usr/bin/pod2html: ./Root/Err.pm: cannot resolve L<USAGE> in paragraph 20
/usr/bin/pod2html: ./Root/Err.pm: cannot resolve L<FEEDBACK> in paragraph 50
/usr/bin/pod2html: ./Root/IOManager.pm: cannot resolve L<FEEDBACK> in paragraph 53
/usr/bin/pod2html: ./Root/IOManager.pm: cannot resolve L<create_filehandle> in paragraph 144
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<USAGE> in paragraph 19
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<_rearrange> in paragraph 28
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 28
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<warn> in paragraph 28
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<APPENDIX> in paragraph 28
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 30
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<INSTALLATION> in paragraph 55
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 62
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<warn> in paragraph 62
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 66
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<warn> in paragraph 66
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<FEEDBACK> in paragraph 81
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 110
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<warn> in paragraph 110
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<_rearrange> in paragraph 115
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<_set_err> in paragraph 195
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<_set_err_state> in paragraph 201
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<_set_err> in paragraph 206
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<_set_err> in paragraph 211
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<warn> in paragraph 223
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 223
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<warn> in paragraph 357
/usr/bin/pod2html: ./Root/Object.pm: cannot resolve L<throw> in paragraph 357
/usr/bin/pod2html: ./Root/RootI.pm: cannot resolve L<_initialize> in paragraph 79
/usr/bin/pod2html: ./Root/Utilities.pm: cannot resolve L<FEEDBACK> in paragraph 44
/usr/bin/pod2html: ./Root/Vector.pm: cannot resolve L<USAGE> in paragraph 13
/usr/bin/pod2html: ./Root/Vector.pm: cannot resolve L<FEEDBACK> in paragraph 39
/usr/bin/pod2html: ./Root/Xref.pm: cannot resolve L<FEEDBACK> in paragraph 34
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<BUGS> in paragraph 14
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<FEEDBACK> in paragraph 42
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_adjust_contigs> in paragraph 149
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<BUGS> in paragraph 149
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<get_exponent> in paragraph 176
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_set_hsps> in paragraph 195
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_set_hsps> in paragraph 202
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 274
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 282
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 290
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 297
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<frac_aligned_hit()> in paragraph 304
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<frac_unaligned_hit()> in paragraph 308
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 313
/usr/bin/pod2html: ./Search/Hit/BlastHit.pm: cannot resolve L<_tile_hsps> in paragraph 320
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<FEEDBACK> in paragraph 30
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<expect> in paragraph 78
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<expect> in paragraph 88
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<score> in paragraph 208
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<_set_seq> in paragraph 263
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<_set_match_stats> in paragraph 263
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<_set_match_seq> in paragraph 281
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<_set_residues> in paragraph 292
/usr/bin/pod2html: ./Search/HSP/BlastHSP.pm: cannot resolve L<collapse_nums> in paragraph 292
/usr/bin/pod2html: ./Search/HSP/HSPI.pm: unknown pod directive 'head' in paragraph 20. ignoring.
/usr/bin/pod2html: no title for ./Search/Result/ResultI.pm
/usr/bin/pod2html: ./Search/Result/BlastResult.pm: cannot resolve L<FEEDBACK> in paragraph 27
/usr/bin/pod2html: ./Search/Result/BlastResult.pm: cannot resolve L<_set_signif> in paragraph 104
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<ambiguous_aln> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<overlap> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<frac_identical> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<frac_conserved> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<frac_aligned_query> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<frac_aligned_hit> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<num_unaligned_query> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<num_unaligned_hit> in paragraph 12
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<overlap> in paragraph 34
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<_tile_hsps> in paragraph 34
/usr/bin/pod2html: ./Search/BlastUtils.pm: cannot resolve L<seq_inds> in paragraph 51
/usr/bin/pod2html: ./Search/DatabaseI.pm: cannot resolve L<FEEDBACK> in paragraph 23
/usr/bin/pod2html: ./Search/GenericDatabase.pm: cannot resolve L<FEEDBACK> in paragraph 20
/usr/bin/pod2html: ./Tools/AnalysisResult.pm: cannot resolve L<parse> in paragraph 10
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<USAGE> in paragraph 24
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<USAGE> in paragraph 32
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<FEEDBACK> in paragraph 44
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<INSTALLATION> in paragraph 56
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<USAGE> in paragraph 59
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<destroy> in paragraph 99
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<INSTALLATION> in paragraph 102
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<INSTALLATION> in paragraph 189
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<SYNOPSIS> in paragraph 209
/usr/bin/pod2html: ./Tools/Blast.pm: cannot resolve L<FEEDBACK> in paragraph 271
/usr/bin/pod2html: ./Tools/Fasta.pm: cannot resolve L<INSTALLATION> in paragraph 37
/usr/bin/pod2html: ./Tools/RestrictionEnzyme.pm: cannot resolve L<_initialize> in paragraph 64
/usr/bin/pod2html: ./Tools/RestrictionEnzyme.pm: cannot resolve L<_initialize> in paragraph 73
/usr/bin/pod2html: ./Tools/SeqAnal.pm: cannot resolve L<read> in paragraph 42
/usr/bin/pod2html: ./Tools/SeqAnal.pm: cannot resolve L<FEEDBACK> in paragraph 63
/usr/bin/pod2html: ./Tools/Blast/Sbjct.pm: cannot resolve L<BUGS> in paragraph 26
/usr/bin/pod2html: ./Tools/Blast/Sbjct.pm: cannot resolve L<FEEDBACK> in paragraph 61
/usr/bin/pod2html: ./Tools/Blast/Sbjct.pm: cannot resolve L<BUGS> in paragraph 165
/usr/bin/pod2html: ./Tools/Blast/HSP.pm: cannot resolve L<Links:> in paragraph 22
/usr/bin/pod2html: ./Tools/Blast/HTML.pm: cannot resolve L<FEEDBACK> in paragraph 30
/usr/bin/pod2html: no title for ./Tools/Blast/Run/postclient.pl
/usr/bin/pod2html: ./Tools/StateMachine/AbstractStateMachine.pm: cannot resolve L<FEEDBACK> in paragraph 59
/usr/bin/pod2html: ./Tools/StateMachine/IOStateMachine.pm: cannot resolve L<FEEDBACK> in paragraph 22
/usr/bin/pod2html: ./Variation/IO/xml.pm: cannot resolve L<http:E<sol>E<sol>www.ebi.ac.ukE<sol>mutationsE<sol>DTDE<sol>seqDiff.dtd> in paragraph 9
/usr/bin/pod2html: ./Variation/IO.pm: cannot resolve L<perltie> in paragraph 66
/usr/bin/pod2html: ./SearchIO/Writer/HSPTableWriter.pm: cannot resolve L<SYNOPSIS> in paragraph 37
/usr/bin/pod2html: ./SearchIO/Writer/HitTableWriter.pm: cannot resolve L<SYNOPSIS> in paragraph 39
/usr/bin/pod2html: no title for ./SearchIO/Writer/ResultTableWriter.pm
/usr/bin/pod2html: ./SearchIO/Writer/ResultTableWriter.pm: cannot resolve L<SYNOPSIS> in paragraph 69
/usr/bin/pod2html: ./SearchIO/psiblast.pm: cannot resolve L<SYNOPSIS> in paragraph 13
/usr/bin/pod2html: ./Structure/IO.pm: cannot resolve L<perltie> in paragraph 43
/usr/bin/pod2html: no title for ./StructureI.pm
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