debian/changelog

-bioperl (1.7.4-1) UNRELEASED; urgency=medium
+bioperl (1.7.4-1) unstable; urgency=medium
 
   * New upstream version
   * Drop broken uversionmangle from watch file
   * debhelper 12
   * Standards-Version: 4.3.0
   * Build-Depends: libyaml-perl, libtest-requiresinternet-perl
+  * Drop manual renaming and permission fixes which are not needed
+    any more
+  * More fixes to Perl path in examples
 
- -- Andreas Tille <tille@debian.org>  Tue, 05 Feb 2019 21:51:10 +0100
+ -- Andreas Tille <tille@debian.org>  Tue, 05 Feb 2019 22:17:53 +0100
 
 bioperl (1.7.2-3) unstable; urgency=medium
 

debian/copyright

@@ -148,56 +148,15 @@ Comment:
     the toolkit.
 URL: see http://www.bioperl.org/wiki/Licensing_BioPerl
 
-Files: t/lib/Error.pm
-Copyright: © 1997-8 Graham Barr <gbarr@ti.com>
-License: Perl
-
-Files: Bio/SeqIO/bsml.pm
-Copyright: © 2001 Charles Tilford <tilfordc@bms.com>
-License: LGPL-2.1+
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- Lesser General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-Comment: On Debian systems, the complete text of the GNU Lesser General Public
- License version 2.1 can be found in ‘/usr/share/common-licenses/LGPL-2.1’.
-
-Files: Bio/SeqIO/msout.pm Bio/SeqIO/mbsout.pm
-Copyright: Public Domain work
-License: public-domain
- 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
- warrant the performance or results that may be obtained by using this
- software or data.  NHGRI and the U.S. Government disclaims all
- warranties as to performance, merchantability or fitness for any
- particular purpose.
-
 Files: debian/*
 Copyright: © 1999 Stéphane Bortzmeyer <bortzmeyer@debian.org>
            © 2001 Dr. Guenter Bechly <gbechly@debian.org>
            © 2001 Adrian Bunk <bunk@fs.tum.de>
-           © 2001—2004 Matt Hope <dopey@debian.org>
-           © 2007—2011 Charles Plessy <charles-debian-nospam@plessy.org>
+           © 2001-2004 Matt Hope <dopey@debian.org>
+           © 2007-2011 Charles Plessy <charles-debian-nospam@plessy.org>
            © 2008 David Paleino <d.paleino@gmail.com>
            © 2008 Nelson A. de Oliveira <naoliv@debian.org>
-           © 2015-2017 Andreas Tille <tille@debian.org>
+           © 2015-2019 Andreas Tille <tille@debian.org>
 License: unclear
  The license under which is placed the work of the earlier contributors is
  unknown. The work of Charles Plessy can be treated as if it were public

debian/docs

 README.md 
-DEPRECATED
-BUGS
 AUTHORS

debian/rules

@@ -14,13 +14,6 @@ override_dh_clean:
 	dh_clean build-stamp install-stamp bioperl.conf biodatabases.pod \
 	biodesign.pod bioperl.pod bioscripts.pod
 
-override_dh_install:
-	dh_install
-	# prename is the rename utility written in perl usually available as /usr/bin/rename in Debian.
-	prename s/.pl$$// debian/bioperl/usr/bin/*pl
-	prename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p
-	chmod 644 debian/libbio-perl-perl/usr/share/perl5/Bio/DB/HIV/lanl-schema.xml
-
 override_dh_installchangelogs:
 	dh_installchangelogs Changes
 
@@ -29,3 +22,6 @@ override_dh_installexamples:
 	for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
 	    sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
 	done
+	for pl in `grep -Rl '#![[:space:]]*/usr/local/bin/perl' debian/*/usr/*` ; do \
+	    sed -i '1s?^#![[:space:]]*/usr/local/bin/[[:space:]]*perl?#!/usr/bin/perl?' $${pl} ; \
+	done