diff -Nru mustang-3.2.2/COPYING mustang-3.2.3/COPYING --- mustang-3.2.2/COPYING 2014-07-08 06:45:58.000000000 +0000 +++ mustang-3.2.3/COPYING 2017-01-04 13:24:30.000000000 +0000 @@ -1,6 +1,6 @@ Copyright (c) 2005-, Arun Konagurthu, Monash University. .@monash.edu -http://www.csse.monash.edu.au/~karun/Site/mustang.html +http://lcb.infotech.monash.edu.au/mustang All rights reserved. Redistribution and use in source and binary forms, with or without modification, Binary files /tmp/tmpCszSc6/j_jd1A1h9d/mustang-3.2.2/data/test/.test_zf-CCHH.swp and /tmp/tmpCszSc6/6wk1bzgyKI/mustang-3.2.3/data/test/.test_zf-CCHH.swp differ diff -Nru mustang-3.2.2/debian/changelog mustang-3.2.3/debian/changelog --- mustang-3.2.2/debian/changelog 2014-08-13 13:39:09.000000000 +0000 +++ mustang-3.2.3/debian/changelog 2017-03-23 09:12:35.000000000 +0000 @@ -1,3 +1,29 @@ +mustang (3.2.3-1ubuntu1) zesty; urgency=medium + + * Update existing hardening patch to rebuild app with -fPIC. + + -- Bhavani Shankar Thu, 23 Mar 2017 14:41:45 +0530 + +mustang (3.2.3-1) unstable; urgency=medium + + * New upstream version + * New homepage + * New watch location + + -- Andreas Tille Thu, 05 Jan 2017 08:32:16 +0100 + +mustang (3.2.2-2) unstable; urgency=medium + + * Homepage with code vanished - use the publication page as next best URL + to link to + * Create fake watch file indicating that there is no upstream site any more + * cme fix dpkg-control + * debhelper 10 + * DEP5 fixes + * hardening=+all + + -- Andreas Tille Tue, 06 Dec 2016 16:17:04 +0100 + mustang (3.2.2-1) unstable; urgency=medium * New upstream version diff -Nru mustang-3.2.2/debian/compat mustang-3.2.3/debian/compat --- mustang-3.2.2/debian/compat 2013-09-12 08:58:18.000000000 +0000 +++ mustang-3.2.3/debian/compat 2016-12-06 15:15:10.000000000 +0000 @@ -1 +1 @@ -9 +10 diff -Nru mustang-3.2.2/debian/control mustang-3.2.3/debian/control --- mustang-3.2.2/debian/control 2014-08-13 13:37:19.000000000 +0000 +++ mustang-3.2.3/debian/control 2017-03-23 09:12:45.000000000 +0000 @@ -1,14 +1,14 @@ Source: mustang -Maintainer: Debian Med Packaging Team +Maintainer: Ubuntu Developers +XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: science Priority: optional -Testsuite: autopkgtest -Build-Depends: debhelper (>= 9) -Standards-Version: 3.9.5 -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mustang/trunk/ +Build-Depends: debhelper (>= 10) +Standards-Version: 3.9.8 +Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/mustang/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mustang/trunk/ -Homepage: http://www.csse.monash.edu.au/~karun/Site/mustang.html +Homepage: http://lcb.infotech.monash.edu.au/mustang/ Package: mustang Architecture: any diff -Nru mustang-3.2.2/debian/copyright mustang-3.2.3/debian/copyright --- mustang-3.2.2/debian/copyright 2013-09-12 08:58:18.000000000 +0000 +++ mustang-3.2.3/debian/copyright 2016-12-06 17:14:26.000000000 +0000 @@ -1,21 +1,21 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: MUSTANG Upstream-Contact: Arun S Konagurthu Source: http://www.csse.monash.edu.au/~karun/Site/mustang.html -Files: Makefile src/* data/test/test_zf-CCHH +Files: * Copyright: 2005-2009 Arun S Konagurthu The University of Melbourne. -License: BSD-like +License: BSD-3-clause Files: debian/* Copyright: 2007-2009 Morten Kjeldgaard 2008 Steffen Möller 2010 Charles Plessy - 2008-2012 Andreas Tille -License: BSD-like + 2008-2016 Andreas Tille +License: BSD-3-clause -Files: data/test/pdbs: +Files: data/test/pdbs/* Copyright: PD License: PD ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE @@ -57,7 +57,7 @@ no representation that these resources will not infringe any patent or other proprietary right. -License: BSD-like +License: BSD-3-clause Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . diff -Nru mustang-3.2.2/debian/patches/hardening.patch mustang-3.2.3/debian/patches/hardening.patch --- mustang-3.2.2/debian/patches/hardening.patch 2014-06-29 13:50:03.000000000 +0000 +++ mustang-3.2.3/debian/patches/hardening.patch 2017-03-23 09:11:38.000000000 +0000 @@ -4,12 +4,15 @@ --- a/Makefile +++ b/Makefile -@@ -13,7 +13,7 @@ BIN = $(MUSTANG)/bin +@@ -12,8 +12,8 @@ + #compiler options CPP = g++ - CPPFLAGS = -traditional -Wall -O3 +-CPPFLAGS = -traditional -Wall -O3 -LDFLAGS = -+LDFLAGS := $(LDFLAGS) ++CPPFLAGS = -traditional -Wall -O3 -fPIC ++LDFLAGS := $(LDFLAGS) .cpp.o: $(CPP) $(CPPFLAGS) -c -o $@ $< + diff -Nru mustang-3.2.2/debian/rules mustang-3.2.3/debian/rules --- mustang-3.2.2/debian/rules 2013-09-12 08:58:18.000000000 +0000 +++ mustang-3.2.3/debian/rules 2016-12-06 17:15:40.000000000 +0000 @@ -1,6 +1,8 @@ #!/usr/bin/make -f # -*- mode: makefile; mode: font-lock -*- +export DEB_BUILD_MAINT_OPTIONS = hardening=+all + %: dh $@ diff -Nru mustang-3.2.2/debian/upstream/metadata mustang-3.2.3/debian/upstream/metadata --- mustang-3.2.2/debian/upstream/metadata 2014-02-23 17:40:55.000000000 +0000 +++ mustang-3.2.3/debian/upstream/metadata 2016-12-06 15:11:23.000000000 +0000 @@ -1,6 +1,3 @@ -Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun) -Homepage: http://www.cs.mu.oz.au/~arun/mustang/ -Name: MUSTANG Reference: Author: Arun S. Konagurthu and James C. Whisstock and Peter J. Stuckey and Arthur M. Lesk Title: > diff -Nru mustang-3.2.2/debian/watch mustang-3.2.3/debian/watch --- mustang-3.2.2/debian/watch 2014-06-29 13:20:05.000000000 +0000 +++ mustang-3.2.3/debian/watch 2017-01-05 07:28:08.000000000 +0000 @@ -1,2 +1,3 @@ -version=3 -http://www.csse.monash.edu.au/~karun/Site/mustang.html http://www.csse.monash.edu.au/~karun/mustang/mustang_v([.\d]*)\.tgz +version=4 + +http://lcb.infotech.monash.edu.au/mustang/ mustang_v(\d[\d.]+)\.tgz diff -Nru mustang-3.2.2/Makefile mustang-3.2.3/Makefile --- mustang-3.2.2/Makefile 2009-10-15 02:10:33.000000000 +0000 +++ mustang-3.2.3/Makefile 2017-01-04 12:21:05.000000000 +0000 @@ -1,5 +1,5 @@ #****************************************************************************** -# TARGETS : ./bin/mustang-3.2.1 +# TARGETS : ./bin/mustang-3.2.3 # AUTHOR : ARUN S KONAGURTHU #****************************************************************************** #directories @@ -28,14 +28,14 @@ $(OBJ)/upgma.o \ $(OBJ)/superpose_on_core.o $(OBJ)/multiple_superposition.o \ $(OBJ)/output_algn.o $(OBJ)/main.o -ALL = $(BIN)/mustang-3.2.1 +ALL = $(BIN)/mustang-3.2.3 #targets all: $(ALL) #------------------------------------------------------------------------------ -$(BIN)/mustang-3.2.1: $(OBJECTS) +$(BIN)/mustang-3.2.3: $(OBJECTS) $(CPP) $(CPPFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(OBJ)/globals.o: $(SRC)/globals.h $(SRC)/macros.h $(SRC)/globals.cpp diff -Nru mustang-3.2.2/man/mustang.1 mustang-3.2.3/man/mustang.1 --- mustang-3.2.2/man/mustang.1 2009-10-15 02:06:35.000000000 +0000 +++ mustang-3.2.3/man/mustang.1 2017-01-04 14:30:35.000000000 +0000 @@ -98,7 +98,7 @@ multiple structural alignment algorithm, \fBProteins, 64(3) 559-574 (2006).\fR .SH BUG REPORT -arun AT csse DOT unimelb DOT edu DOT au +arun DOT konagurthu AT monash DOT edu .SH SEE ALSO -\fBMustang\fR's homepage: http://www.csse.unimelb.edu.au/~arun/mustang/ +\fBMustang\fR's homepage: http://lcb.infotech.monash.edu.au/mustang diff -Nru mustang-3.2.2/README mustang-3.2.3/README --- mustang-3.2.2/README 2014-07-08 06:39:35.000000000 +0000 +++ mustang-3.2.3/README 2017-01-04 13:32:12.000000000 +0000 @@ -1,13 +1,13 @@ INSTALLATION ON LINUX (or other Unix-based systems with GCC): * Extract the tarball using: - tar -zxvf MUSTANG_v3.2.2.tgz + tar -zxvf MUSTANG_v3.2.3.tgz * then: - cd MUSTANG_v3.2.2 + cd MUSTANG_v3.2.3 * run: make * Test the installation using: - ./bin/mustang-3.2.2 -f ./data/test/test_zf-CCHH + ./bin/mustang-3.2.3 -f ./data/test/test_zf-CCHH This should produce the following files: -- results.html diff -Nru mustang-3.2.2/src/macros.h mustang-3.2.3/src/macros.h --- mustang-3.2.2/src/macros.h 2014-07-08 06:48:20.000000000 +0000 +++ mustang-3.2.3/src/macros.h 2017-01-04 12:22:47.000000000 +0000 @@ -29,7 +29,7 @@ #ifndef MACROS_H #define MACROS_H -#define VERSION "v3.2.2" +#define VERSION "v3.2.3" /* OUTPUT CONTROLS*/ #define TRUE 1 diff -Nru mustang-3.2.2/src/main.cpp mustang-3.2.3/src/main.cpp --- mustang-3.2.2/src/main.cpp 2014-07-08 06:48:20.000000000 +0000 +++ mustang-3.2.3/src/main.cpp 2017-01-04 13:12:47.000000000 +0000 @@ -370,7 +370,15 @@ cout << "\nAll Done! Thank you for using " << "\033[1m" << "MUSTANG" << "\033[0m.\n" ; clock_t ends = clock(); cout.setf(ios::fixed) ; - cout << "Running Time : " << setprecision(2) << (double) (ends - start) / CLOCKS_PER_SEC << " s." << endl; + cout << "Running Time : " << setprecision(2) << (double) (ends - start) / CLOCKS_PER_SEC << " s." << endl; + cout << "\033[36;4m. -=o0o=- .\033[0m\n" ; + cout << "\033[36;3m| Visit \033[0m\033[33;3mhttp://lcb.infotech.monash.edu.au\033[0m\033[36;3m for other supporting programs |\033[0m\n" ; + cout << "\033[34;3m| Some suggested utilities for you to try out: |\n"; + cout << "\033[33;3m| SST\033[0m\033[36;3m: A Bayesian approach to assigning secondary structures. \033[0m\033[33;3m|\033[0m\n"; + cout << "\033[33;3m| MMLigner\033[0m\033[36;3m: Pairwise structural alignment using information & compression.\033[0m\033[33;3m|\033[0m\n"; + cout << "\033[33;3m| Super\033[0m\033[36;3m: Rapidly screen entire PDB for well-superposable fragments. \033[0m\033[33;3m|\033[0m\n"; + cout << "\033[36;4m. -=o0o=- .\033[0m\n" ; + return 0; }