[SCM] Perl extension for running and parsing NCBIs BLAST 2.x branch, master, updated. debian/0.66-1-5-g2c90792

Mon Jul 9 16:14:52 UTC 2012

The following commit has been merged in the master branch:
commit 2c90792354d090e6e35ce36aaf04a7c00cf9b24f
Author: Jens Preussner <jenzo at cbv.net>
Date:   Mon Jul 9 16:13:30 2012 +0000

    Fixed major lintian warnings and added a patch for manpage.

diff --git a/Blastall.pm b/Blastall.pm
index 72115e6..ec642f5 100644
--- a/Blastall.pm
+++ b/Blastall.pm
@@ -952,8 +952,6 @@ NHGRI::Blastall - Perl extension for running and parsing NCBI's BLAST 2.x
 
 =head1 SYNOPSIS
 
-=over 4
-
 =head1 DESCRIPTION
 
 If you have NCBI's BLAST2 or WU-BLAST installed locally and your
@@ -970,6 +968,7 @@ like to mask out, you can use the mask method to mask the data against
 these databases. You can then use either the filter or result methods
 to parse the report and access the various elements of the data.
 
+=over 4
 
 =item RUNNING NEW BLASTS
 
diff --git a/debian/control b/debian/control
index c0d10fd..ad1cee4 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: perl
 Priority: optional
 Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
 Uploaders: Laszlo Kajan <lkajan at rostlab.org>, Jens Preussner <jenzo at cbv.net>
-Build-Depends: debhelper (>= 7), perl (>= 5.8.0-7)
+Build-Depends: debhelper (>= 8), perl
 Vcs-Git: git://git.debian.org/pkg-perl/packages/libnhgri-blastall-perl.git
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-perl/packages/libnhgri-blastall-perl.git
 Standards-Version: 3.9.3
@@ -13,7 +13,15 @@ Package: libnhgri-blastall-perl
 Architecture: any
 Depends: ${perl:Depends}, ${shlibs:Depends}, ${misc:Depends}
 Description: Perl extension for running and parsing NCBIs BLAST 2.x
- If you have NCBIs BLAST2 or WU-BLAST installed locally and your environment is already setup you can use Perls object-oriented capabilities to run your BLASTs. Also if you have a blastcl3 binary from the toolkit (or binaries from our
- FTP site) you can run BLAST over the network.  There are also methods to blast single sequences against each other using the bl2seq binaries (also in the toolkit and binaries).  You can blast one sequence against a library of sequences
- using the blast_one_to_many method.  You can format databases with formatdb method.  You can also have NHGRI::Blastall read existing BLAST reports.  If you have a database of repetitive DNA or other DNA you would like to mask out, you can
- use the mask method to mask the data against these databases. You can then use either the filter or result methods to parse the report and access the various elements of the data.
+ If you have NCBI's BLAST2 or WU-BLAST installed locally and your environment 
+ is already setup you can use Perls object-oriented capabilities to run your
+ BLASTs. Also if you have a blastcl3 binary from the toolkit (or binaries
+ from the FTP site) you can run BLAST over the network. There are also methods
+ to blast single sequences against each other using the bl2seq binaries
+ (also in the toolkit and binaries). You can blast one sequence against a
+ library of sequences using the blast_one_to_many method. You can format
+ databases with formatdb method. You can also have NHGRI::Blastall read
+ existing BLAST reports. If you have a database of repetitive DNA or other
+ DNA you would like to mask out, you can use the mask method to mask the
+ data against these databases. You can then use either the filter or result
+ methods to parse the report and access the various elements of the data.
diff --git a/debian/copyright b/debian/copyright
index 3d06b13..254fea7 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -3,17 +3,15 @@ Upstream-Contact: Joseph Ryan <jfryan at nhgri.nih.gov>
 Source: ftp://ftp.nhgri.nih.gov/pub/software/blastall/NHGRI-Blastall-0.66.tar.gz
 
 Files: *
-Copyright: Joseph Ryan
+Copyright: public-domain
 License: public-domain
     PUBLIC DOMAIN NOTICE
-    
     This software/database is ``United States Government Work'' under the 
     terms of the United States Copyright Act. It was written as part of 
     the authors' official duties for the United States Government and thus 
     cannot be copyrighted. This software/database is freely available to 
     the public for use without a copyright notice. Restrictions cannot 
     be placed on its present or future use. 
-    
     Although all reasonable efforts have been taken to ensure the accuracy 
     and reliability of the software and data, the National Human Genome 
     Research Institute (NHGRI) and the U.S. Government does not and cannot 
@@ -21,13 +19,13 @@ License: public-domain
     software or data.  NHGRI and the U.S. Government disclaims all 
     warranties as to performance, merchantability or fitness for any 
     particular purpose. 
-    
     In any work or product derived from this material, proper attribution 
     of the authors as the source of the software or data should be made, 
     using http://genome.nhgri.nih.gov/webblast as the citation. 
 
 Files: debian/*
 Copyright: 2009, Laszlo Kajan <lkajan at rostlab.org>
+	   2012, Jens PreuÃŸner <jenzo at cbv.net>
 License: GPL
-    The Debian packaging is (C) 2009, Laszlo Kajan <lkajan at rostlab.org> and
+    The Debian packaging is (C) Copyright 2009, Laszlo Kajan <lkajan at rostlab.org> and
     is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
diff --git a/debian/patches/manpage-patch b/debian/patches/manpage-patch
new file mode 100644
index 0000000..97f0a20
--- /dev/null
+++ b/debian/patches/manpage-patch
@@ -0,0 +1,22 @@
+Fixes a pod syntax error (=over was not followed by =item). Author: Jens preußner <jenzo at cbv.net>
+Index: libnhgri-blastall-perl-0.66/Blastall.pm
+===================================================================
+--- libnhgri-blastall-perl-0.66.orig/Blastall.pm	2012-07-06 18:45:46.000000000 +0000
++++ libnhgri-blastall-perl-0.66/Blastall.pm	2012-07-09 16:00:26.000000000 +0000
+@@ -952,8 +952,6 @@
+ 
+ =head1 SYNOPSIS
+ 
+-=over 4
+-
+ =head1 DESCRIPTION
+ 
+ If you have NCBI's BLAST2 or WU-BLAST installed locally and your
+@@ -970,6 +968,7 @@
+ these databases. You can then use either the filter or result methods
+ to parse the report and access the various elements of the data.
+ 
++=over 4
+ 
+ =item RUNNING NEW BLASTS
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..953e732
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+manpage-patch
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

-- 
Perl extension for running and parsing NCBIs BLAST 2.x

