[med-svn] r6250 - in trunk/packages/mafft/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Fri Mar 11 23:53:08 UTC 2011 

Author: tille
Date: 2011-03-11 23:53:07 +0000 (Fri, 11 Mar 2011)
New Revision: 6250

Modified:
   trunk/packages/mafft/trunk/debian/changelog
   trunk/packages/mafft/trunk/debian/compat
   trunk/packages/mafft/trunk/debian/control
   trunk/packages/mafft/trunk/debian/links
   trunk/packages/mafft/trunk/debian/patches/20_manpages_are_no_binaries.patch
   trunk/packages/mafft/trunk/debian/rules
Log:
New upstream version and the needed changes, debhelper 8, switched to dh


Modified: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog	2011-03-11 22:53:30 UTC (rev 6249)
+++ trunk/packages/mafft/trunk/debian/changelog	2011-03-11 23:53:07 UTC (rev 6250)
@@ -1,3 +1,13 @@
+mafft (6.850-1) unstable; urgency=low
+
+  * New upstream version
+  * Adapted patch to new upstream
+  * Debhelper 8 (control + compat)
+  * debian/rules: Switch to dh
+  * debian/links: override broken symlinks created in Makefile
+
+ -- Andreas Tille <tille at debian.org>  Sat, 12 Mar 2011 00:02:43 +0100
+
 mafft (6.833-1) unstable; urgency=low
 
   * New upstream version

Modified: trunk/packages/mafft/trunk/debian/compat
===================================================================
--- trunk/packages/mafft/trunk/debian/compat	2011-03-11 22:53:30 UTC (rev 6249)
+++ trunk/packages/mafft/trunk/debian/compat	2011-03-11 23:53:07 UTC (rev 6250)
@@ -1 +1 @@
-7
+8

Modified: trunk/packages/mafft/trunk/debian/control
===================================================================
--- trunk/packages/mafft/trunk/debian/control	2011-03-11 22:53:30 UTC (rev 6249)
+++ trunk/packages/mafft/trunk/debian/control	2011-03-11 23:53:07 UTC (rev 6250)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>,
  Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.1), quilt
+Build-Depends: debhelper (>= 8), quilt (>= 0.47)
 Standards-Version: 3.9.1
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mafft/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mafft/trunk/

Modified: trunk/packages/mafft/trunk/debian/links
===================================================================
--- trunk/packages/mafft/trunk/debian/links	2011-03-11 22:53:30 UTC (rev 6249)
+++ trunk/packages/mafft/trunk/debian/links	2011-03-11 23:53:07 UTC (rev 6250)
@@ -12,3 +12,7 @@
 
 usr/lib/mafft/bin/mafft-homologs.rb usr/bin/mafft-homologs
 usr/lib/mafft/bin/mafft             usr/bin/mafft
+
+# override broken symlinks created in Makefile
+usr/lib/mafft/lib/mafft/mafft-distance usr/lib/mafft/bin/mafft-distance
+usr/lib/mafft/lib/mafft/mafft-profile  usr/lib/mafft/bin/mafft-profile

Modified: trunk/packages/mafft/trunk/debian/patches/20_manpages_are_no_binaries.patch
===================================================================
--- trunk/packages/mafft/trunk/debian/patches/20_manpages_are_no_binaries.patch	2011-03-11 22:53:30 UTC (rev 6249)
+++ trunk/packages/mafft/trunk/debian/patches/20_manpages_are_no_binaries.patch	2011-03-11 23:53:07 UTC (rev 6250)
@@ -1,28 +1,18 @@
-Author: Andreas Tille <tille at debian.org>
-Description: Prevent upstream Makefile from handling manpages as binaries
---- mafft-6.713-without-extensions.orig/core/Makefile
-+++ mafft-6.713-without-extensions/core/Makefile
-@@ -107,7 +107,7 @@
- all : $(PROGS) $(SCRIPTS)
- 	cp $(SCRIPTS) ../scripts
+--- mafft-6.850-without-extensions.orig/core/Makefile
++++ mafft-6.850-without-extensions/core/Makefile
+@@ -113,7 +113,6 @@
  	chmod 755 ../scripts/*
--	cp $(PROGS) $(MANPAGES) ../binaries
-+	cp $(PROGS) ../binaries
+ 	cp $(PROGS) ../binaries
  	chmod 755 ../binaries/*
+-	cp $(MANPAGES) ../binaries
  	@echo done.
  
-@@ -484,7 +484,7 @@
- 	chmod 755 $(SCRIPTS)
+ univscript: univscript.tmpl Makefile
+@@ -490,7 +489,6 @@
  	$(INSTALL) $(SCRIPTS)  $(BINDIR)
  	chmod 755 $(PROGS)
--	$(INSTALL) $(PROGS) $(MANPAGES) $(LIBDIR)
-+	$(INSTALL) $(PROGS) $(LIBDIR)
+ 	$(INSTALL) $(PROGS) $(LIBDIR)
+-	$(INSTALL) --mode=644 $(MANPAGES) $(LIBDIR)
+ 
  	( cd $(BINDIR); \
  rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
- rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
-@@ -499,4 +499,4 @@
- 
- 	mkdir -p $(MANDIR)
- 	chmod 755 $(MANDIR)
--	$(INSTALL) $(MANPAGES) $(MANDIR)
-+	$(INSTALL) --mode=644 $(MANPAGES) $(MANDIR)

Modified: trunk/packages/mafft/trunk/debian/rules
===================================================================
--- trunk/packages/mafft/trunk/debian/rules	2011-03-11 22:53:30 UTC (rev 6249)
+++ trunk/packages/mafft/trunk/debian/rules	2011-03-11 23:53:07 UTC (rev 6250)
@@ -5,25 +5,14 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
-include /usr/share/quilt/quilt.make
+%:
+	dh $@ --with quilt
 
-CFLAGS = -Wall -g
-
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
-	CFLAGS += -O0
-else
-	CFLAGS += -O2
-endif
-
-build: patch build-stamp
-build-stamp:
-	dh_testdir
+override_dh_build:
 	$(MAKE) -C core PREFIX=/usr/lib/mafft
-	touch $@
 
 MAFFT = MAFFT_BINARIES=$(CURDIR)/binaries scripts/mafft
-
-test: build-stamp
+override_dh_auto_test:
 	-$(MAFFT) 				test/sample | diff test/sample.fftns2 -
 	-$(MAFFT) --maxiterate 100 		test/sample | diff test/sample.fftnsi -
 	-$(MAFFT) --globalpair 			test/sample | diff test/sample.gins1 -
@@ -31,37 +20,10 @@
 	-$(MAFFT) --localpair			test/sample | diff test/sample.lins1 -
 	-$(MAFFT) --localpair --maxiterate 100	test/sample | diff test/sample.linsi -
 
-clean: unpatch
-	dh_testdir
-	dh_testroot
+override_dh_clean:
 	[ ! -f core/Makefile ] || $(MAKE) -C core clean
 	rm -rf binaries/* scripts/*
-	dh_clean build-stamp
-
-install: build-stamp test
-	dh_testdir
-	dh_testroot
 	dh_clean
-	dh_installdirs
-	$(MAKE) -C core PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft MANDIR=$(CURDIR)/debian/mafft/usr/share/man/man1 install
 
-binary-indep: build install
-binary-arch: build install
-	dh_testdir
-	dh_testroot
-	dh_installchangelogs 
-	dh_installdocs
-	dh_install
-	dh_installman
-	dh_link
-	dh_strip
-	dh_compress
-	dh_fixperms
-	dh_installdeb
-	dh_shlibdeps
-	dh_gencontrol
-	dh_md5sums
-	dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+override_dh_install:
+	$(MAKE) -C core PREFIX=$(CURDIR)/debian/mafft/usr/lib/mafft MANDIR=$(CURDIR)/debian/mafft/usr/share/man/man1 install

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