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strip out -w flag (see perllexwarn as to why setting this is not a go…

…od thing); also refs #3215
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1 parent af91f5f commit 53b05a72e54e9c858554b21c0f28f991d0df5638 Chris Fields committed May 9, 2011
Showing with 65 additions and 65 deletions.
  1. +1 −1 doc/Deobfuscator/bin/deob_index.pl
  2. +1 −1 doc/Deobfuscator/cgi-bin/deob_detail.cgi
  3. +1 −1 doc/Deobfuscator/cgi-bin/deob_interface.cgi
  4. +1 −1 examples/align/align_on_codons.pl
  5. +1 −1 examples/align/aligntutorial.pl
  6. +1 −1 examples/biblio/biblio-eutils-example.pl
  7. +1 −1 examples/biblio/biblio-soap-example.pl
  8. +1 −1 examples/biblio/biblio_soap.pl
  9. +1 −1 examples/contributed/nmrpdb_parse.pl
  10. +1 −1 examples/contributed/prosite2perl.pl
  11. +1 −1 examples/db/est_tissue_query.pl
  12. +1 −1 examples/db/gb2features.pl
  13. +1 −1 examples/db/getGenBank.pl
  14. +1 −1 examples/db/get_seqs.pl
  15. +1 −1 examples/db/use_registry.pl
  16. +1 −1 examples/generate_random_seq.pl
  17. +1 −1 examples/longorf.pl
  18. +1 −1 examples/make_primers.pl
  19. +1 −1 examples/popgen/parse_calc_stats.pl
  20. +1 −1 examples/revcom_dir.pl
  21. +1 −1 examples/searchio/blast_example.pl
  22. +1 −1 examples/searchio/waba2gff.pl
  23. +1 −1 examples/searchio/waba2gff3.pl
  24. +1 −1 examples/sirna/rnai_finder.cgi
  25. +1 −1 examples/structure/structure-io.pl
  26. +1 −1 examples/tk/gsequence.pl
  27. +1 −1 examples/tk/hitdisplay.pl
  28. +1 −1 examples/tools/extract_genes.pl
  29. +1 −1 examples/tools/gb_to_gff.pl
  30. +1 −1 examples/tools/parse_codeml.pl
  31. +1 −1 examples/tools/reverse-translate.pl
  32. +1 −1 examples/tools/run_primer3.pl
  33. +1 −1 maintenance/authors.pl
  34. +1 −1 maintenance/check_NAME.pl
  35. +1 −1 maintenance/check_URLs.pl
  36. +1 −1 maintenance/dependencies.pl
  37. +1 −1 maintenance/deprecated.pl
  38. +1 −1 maintenance/module_usage.pl
  39. +1 −1 maintenance/modules.pl
  40. +1 −1 maintenance/ncbi_blast_switches.pl
  41. +1 −1 maintenance/pod.pl
  42. +1 −1 maintenance/version.pl
  43. +1 −1 scripts/Bio-DB-GFF/genbank2gff.PLS
  44. +1 −1 scripts/Bio-DB-GFF/genbank2gff3.PLS
  45. +1 −1 scripts/Bio-DB-GFF/process_sgd.PLS
  46. +1 −1 scripts/DB/bioflat_index.PLS
  47. +1 −1 scripts/index/bp_index.PLS
  48. +1 −1 scripts/index/bp_seqret.PLS
  49. +1 −1 scripts/popgen/composite_LD.PLS
  50. +1 −1 scripts/popgen/heterogeneity_test.PLS
  51. +1 −1 scripts/searchio/fastam9_to_table.PLS
  52. +1 −1 scripts/searchio/parse_hmmsearch.PLS
  53. +1 −1 scripts/searchio/search2table.PLS
  54. +1 −1 scripts/seq/seqretsplit.PLS
  55. +1 −1 scripts/taxa/classify_hits_kingdom.PLS
  56. +1 −1 scripts/taxa/local_taxonomydb_query.PLS
  57. +1 −1 scripts/taxa/query_entrez_taxa.PLS
  58. +1 −1 scripts/taxa/taxonomy2tree.PLS
  59. +1 −1 scripts/tree/blast2tree.PLS
  60. +1 −1 scripts/utilities/download_query_genbank.PLS
  61. +1 −1 scripts/utilities/mutate.PLS
  62. +1 −1 scripts/utilities/remote_blast.PLS
  63. +1 −1 t/Align/Graphics.t
  64. +1 −1 t/SeqIO/mbsout.t
  65. +1 −1 t/SeqIO/msout.t
View
2 doc/Deobfuscator/bin/deob_index.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# deob_index.pl
# part of the Deobfuscator package
View
2 doc/Deobfuscator/cgi-bin/deob_detail.cgi
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Deob_detail.cgi
# part of the Deobfuscator package
View
2 doc/Deobfuscator/cgi-bin/deob_interface.cgi
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Deob_interface.cgi
# part of the Deobfuscator package
View
2 examples/align/align_on_codons.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use vars qw($USAGE %VALIDALIGN $CODONSIZE);
View
2 examples/align/aligntutorial.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# An example of how to use the different alignment tools in bioperl
# to align some sequences
View
2 examples/biblio/biblio-eutils-example.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
biblio-eutils-example.pl
View
2 examples/biblio/biblio-soap-example.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
biblio-soap-example.pl
View
2 examples/biblio/biblio_soap.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
# This was actually a part of the test suite - but because it starts
# an external process it was safer not to use it as a test (the process
View
2 examples/contributed/nmrpdb_parse.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
# This program will read in an NMR derived PDB file containing
View
2 examples/contributed/prosite2perl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# prosite2perl -- convert Prosite patterns to Perl regular expressions
#
# Jordan Dimov (jdimov@cis.clarion.edu)
View
2 examples/db/est_tissue_query.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# This script will report the names of the tissues which were seen
# in a BLAST/FASTA report against an EST (or cDNA possibly) library.
View
2 examples/db/gb2features.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Author: Damien Mattei C.N.R.S / U.N.S.A - UMR 6549
# example: ./idfetch.pl AP001266
View
2 examples/db/getGenBank.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/local/bin/perl
#
# How to retrieve GenBank entries over the Web
#
View
2 examples/db/get_seqs.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/local/bin/perl
use strict;
use vars qw($USAGE);
use Carp;
View
2 examples/db/use_registry.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use Bio::DB::Registry;
View
2 examples/generate_random_seq.pl
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/bin/perl
use strict;
use vars qw($USAGE);
View
2 examples/longorf.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# longorf.pl v0208020920
# (c) Dan Kortschak 2002
View
2 examples/make_primers.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Author: cckim@stanford.edu
# Description: This program designs primers for constructing knockouts
View
2 examples/popgen/parse_calc_stats.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Author: Jason Stajich, jason@bioperl.org
# $Revision: 6576 $
View
2 examples/revcom_dir.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
################################################################################
#11-17-2001
View
2 examples/searchio/blast_example.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Example that shows values returned by Bio::SearchIO::Blast.
# Note that some methods will return objects or arrays, not text.
# For example, $hsp->get_aln will return a Bio::SimpleAlign object,
View
2 examples/searchio/waba2gff.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use Bio::SearchIO;
use Getopt::Long;
View
2 examples/searchio/waba2gff3.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 examples/sirna/rnai_finder.cgi
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=pod
View
2 examples/structure/structure-io.pl
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/bin/perl
# Getting Entry, Chain, Residue, and Atom objects given a PDB file
use Bio::Structure::IO;
View
2 examples/tk/gsequence.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# gSequence - Protein Sequence Control Panel
# by Lorenz Pollsk
#
View
2 examples/tk/hitdisplay.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/local/bin/perl
#
# PROGRAM : hitdisplay.pl
# PURPOSE : Demonstrate Bio::Tk::HitDisplay
View
2 examples/tools/extract_genes.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=pod
=head1 NAME
View
2 examples/tools/gb_to_gff.pl
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/local/bin/perl
use strict;
use Bio::Tools::GFF;
View
2 examples/tools/parse_codeml.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use Bio::Tools::Phylo::PAML;
View
2 examples/tools/reverse-translate.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 examples/tools/run_primer3.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 maintenance/authors.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
=head1 NAME
View
2 maintenance/check_NAME.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 maintenance/check_URLs.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 maintenance/dependencies.pl
@@ -1,6 +1,6 @@
# $Id: dependencies.pl 10084 2006-07-04 22:23:29Z cjfields $
#
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use warnings;
View
2 maintenance/deprecated.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use warnings;
View
2 maintenance/module_usage.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
# Counts up all the used and inherited modules in a directory of modules to
# help indicate which the most important modules are, graphs it also
View
2 maintenance/modules.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
=head1 NAME
View
2 maintenance/ncbi_blast_switches.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# This script determines all the valid command line switches
# from the four main NCBI BLAST tools, and produces Perl code
View
2 maintenance/pod.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
=head1 NAME
View
2 maintenance/version.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
=head1 version
View
2 scripts/Bio-DB-GFF/genbank2gff.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use lib '.';
View
2 scripts/Bio-DB-GFF/genbank2gff3.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#$Id$;
View
2 scripts/Bio-DB-GFF/process_sgd.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# This script will convert from SGD format to GFF format
# See http://db.yeastgenome.org/schema/Schema.html
View
2 scripts/DB/bioflat_index.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#$Id$
=head1 NAME
View
2 scripts/index/bp_index.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 scripts/index/bp_seqret.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# -*-Perl-*- mode (for emacs)
=head1 NAME
View
2 scripts/popgen/composite_LD.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# -*-Perl-*-
=head1 NAME
View
2 scripts/popgen/heterogeneity_test.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# -*-Perl-*- (for my emacs)
use strict;
View
2 scripts/searchio/fastam9_to_table.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 scripts/searchio/parse_hmmsearch.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
View
2 scripts/searchio/search2table.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 scripts/seq/seqretsplit.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
=head1 NAME
View
2 scripts/taxa/classify_hits_kingdom.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 scripts/taxa/local_taxonomydb_query.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use strict;
use Bio::DB::Taxonomy;
View
2 scripts/taxa/query_entrez_taxa.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# This is a -*-Perl-* file (make my emacs happy)
=head1 NAME
View
2 scripts/taxa/taxonomy2tree.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 scripts/tree/blast2tree.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
# Author: Jason Stajich <jason@bioperl.org>
# Purpose: Blast Report -> MSA -> Tree
View
2 scripts/utilities/download_query_genbank.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#$Id$
=head1 NAME
View
2 scripts/utilities/mutate.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
=head1 NAME
View
2 scripts/utilities/remote_blast.PLS
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
#
# BioPerl module for remote_blast.pl
#
View
2 t/Align/Graphics.t
@@ -1,4 +1,4 @@
-#!usr/bin/perl -w
+#!usr/bin/perl
use strict;
use Bio::Root::Test;
View
2 t/SeqIO/mbsout.t
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use version;
our $API_VERSION = qv('1.1.3');
View
2 t/SeqIO/msout.t
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/perl
use version;
our $API_VERSION = qv('1.1.6');

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