[med-svn] r10942 - in trunk/packages/paml/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Tue May 22 12:27:58 UTC 2012 

Author: tille
Date: 2012-05-22 12:27:58 +0000 (Tue, 22 May 2012)
New Revision: 10942

Added:
   trunk/packages/paml/trunk/debian/patches/hardening.patch
Modified:
   trunk/packages/paml/trunk/debian/README.Debian
   trunk/packages/paml/trunk/debian/changelog
   trunk/packages/paml/trunk/debian/compat
   trunk/packages/paml/trunk/debian/control
   trunk/packages/paml/trunk/debian/paml.docs
   trunk/packages/paml/trunk/debian/patches/makefile.patch
   trunk/packages/paml/trunk/debian/patches/series
Log:
Enable hardening using debhelper 9 + Makefile patch; upload to unstable


Modified: trunk/packages/paml/trunk/debian/README.Debian
===================================================================
--- trunk/packages/paml/trunk/debian/README.Debian	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/README.Debian	2012-05-22 12:27:58 UTC (rev 10942)
@@ -9,4 +9,22 @@
 description of the documentation has not yet been addressed. Help
 from the community would be much appreciated on those issues.
 
- -- Pjotr Prins <pjotr.debian at thebird.nl>  Wed, 08 Sep 2010 09:44:46 +0200
+
+Renamed executable: evolver
+---------------------------
+
+A different package in Debian (namely evolver) ships a binary with the
+very same name and to avoid name space pollution the binary from the
+paml package needed to be renamed to /usr/bin/paml-evolver (if you
+disagree with this choice of name please help us to make Debian better
+and make a more appropriate suggestion.)
+
+If you are using this exectuable in scripts and you need to relay on the
+original name there is another option:  Copy the directory
+/usr/share/doc/paml/profile.d to /etc/profile.d and by doing so enable
+setting the PATH variable to prefer the PATH /usr/lib/debian-med/bin
+over /usr/bin.  There the original name is conserved.  Please note that
+this might hide the binary contained in the evolver package from all
+users of your computer.
+
+ -- Andreas Tille <tille at debian.org>  Tue, 15 May 2012 11:10:59 +0200

Modified: trunk/packages/paml/trunk/debian/changelog
===================================================================
--- trunk/packages/paml/trunk/debian/changelog	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/changelog	2012-05-22 12:27:58 UTC (rev 10942)
@@ -1,4 +1,4 @@
-paml (4.5-1) UNRELEASED; urgency=low
+paml (4.5-1) unstable; urgency=low
 
   [ Pjotr Prins ]
   * Improved long description.
@@ -20,7 +20,11 @@
        paml-doc)
   * debian/profile.d/paml: Set PATH to find paml executables under
     their expected names
+  * debian/README.Debian: Document the name space conflict solution
   * debian/upstream: Citation information
+  * debhelper 9 (control+compat)
+  * debian/patches/hardening.patch: Enable propagation of hardening
+    flags
 
  -- Andreas Tille <tille at debian.org>  Tue, 15 May 2012 11:10:59 +0200
 

Modified: trunk/packages/paml/trunk/debian/compat
===================================================================
--- trunk/packages/paml/trunk/debian/compat	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/compat	2012-05-22 12:27:58 UTC (rev 10942)
@@ -1 +1 @@
-8
+9

Modified: trunk/packages/paml/trunk/debian/control
===================================================================
--- trunk/packages/paml/trunk/debian/control	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/control	2012-05-22 12:27:58 UTC (rev 10942)
@@ -6,7 +6,7 @@
  Steffen Moeller <moeller at debian.org>,
  Andreas Tille <tille at debian.org>
 DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 8)
+Build-Depends: debhelper (>= 9)
 Standards-Version: 3.9.3
 Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/paml/trunk

Modified: trunk/packages/paml/trunk/debian/paml.docs
===================================================================
--- trunk/packages/paml/trunk/debian/paml.docs	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/paml.docs	2012-05-22 12:27:58 UTC (rev 10942)
@@ -1,2 +1,3 @@
 GeneticCode.txt
 README.txt
+debian/profile.d

Added: trunk/packages/paml/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/paml/trunk/debian/patches/hardening.patch	                        (rev 0)
+++ trunk/packages/paml/trunk/debian/patches/hardening.patch	2012-05-22 12:27:58 UTC (rev 10942)
@@ -0,0 +1,45 @@
+Description: Enable propagation of hardening flags
+Author: Andreas Tille <tille at debian.org>
+Date: Tue, 15 May 2012 11:10:59 +0200
+
+--- paml4.5.orig/src/Makefile
++++ paml4.5/src/Makefile
+@@ -1,7 +1,7 @@
+ PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2 
+ CC = cc # cc, gcc, cl
+ 
+-CFLAGS = -O4 -funroll-loops -fomit-frame-pointer -finline-functions
++CFLAGS += -O4 -funroll-loops -fomit-frame-pointer -finline-functions
+ 
+ #MAC OSX G5:
+ #CFLAGS = -mcpu=G5 -O4 -funroll-loops -fomit-frame-pointer -finline-functions
+@@ -20,21 +20,21 @@
+ all : $(PRGS)
+ 
+ baseml : baseml.c tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.c tools.c $(LIBS)
+ basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.c tools.c $(LIBS)
+ codeml : codeml.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.c tools.c $(LIBS)
+ evolver : evolver.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.c tools.c $(LIBS)
+ pamp : pamp.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.c tools.c $(LIBS)
+ mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 
+-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.c $(LIBS)
+ yn00: yn00.c tools.c paml.h
+-	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.c tools.c $(LIBS)
+ chi2 : chi2.c
+-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
+ 
+ PREFIX=/usr
+ DESTDIR=/

Modified: trunk/packages/paml/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/paml/trunk/debian/patches/makefile.patch	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/patches/makefile.patch	2012-05-22 12:27:58 UTC (rev 10942)
@@ -1,7 +1,9 @@
-Index: paml-4.4c/Makefile
-===================================================================
---- /dev/null	1970-01-01 00:00:00.000000000 +0000
-+++ paml-4.4c/Makefile	2010-09-11 17:33:04.957524695 +0200
+Description: Simplify building by creating main Makefile and install target for src/Makefile
+Author: Pjotr Prins <pjotr.debian at thebird.nl>
+Date: Tue, 07 Sep 2010 21:09:02 +0200
+
+--- /dev/null
++++ paml4.5/Makefile
 @@ -0,0 +1,9 @@
 +
 +all install build:
@@ -12,10 +14,8 @@
 +	echo "Cleaning binaries"
 +	rm -f $(find src -name "*.c" | sed -e 's/.c$//')
 +
-Index: paml-4.4c/src/Makefile
-===================================================================
---- paml-4.4c.orig/src/Makefile	2010-09-08 09:29:29.810248323 +0200
-+++ paml-4.4c/src/Makefile	2010-09-11 18:01:01.116529194 +0200
+--- paml4.5.orig/src/Makefile
++++ paml4.5/src/Makefile
 @@ -35,3 +35,11 @@
  	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)
  chi2 : chi2.c

Modified: trunk/packages/paml/trunk/debian/patches/series
===================================================================
--- trunk/packages/paml/trunk/debian/patches/series	2012-05-22 11:37:31 UTC (rev 10941)
+++ trunk/packages/paml/trunk/debian/patches/series	2012-05-22 12:27:58 UTC (rev 10942)
@@ -1 +1,2 @@
 makefile.patch
+hardening.patch

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