[med-svn] r5714 - in trunk/packages/theseus/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2011-01-27 09:03:54 +0000 (Thu, 27 Jan 2011)
New Revision: 5714

Removed:
   trunk/packages/theseus/trunk/debian/patches/00-makefile.patch
   trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch
Modified:
   trunk/packages/theseus/trunk/debian/changelog
   trunk/packages/theseus/trunk/debian/control
   trunk/packages/theseus/trunk/debian/patches/series
Log:
New upstream version, removed several patches which are either applied upstream or non-functional (break the build - the latter might harm performance, thus further optimisation should be considered)


Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog	2011-01-26 12:19:33 UTC (rev 5713)
+++ trunk/packages/theseus/trunk/debian/changelog	2011-01-27 09:03:54 UTC (rev 5714)
@@ -1,7 +1,5 @@
-theseus (1.6.0-1) UNRELEASED; urgency=low
+theseus (1.6.1-1) unstable; urgency=low
 
-UNRELEASED because of segfaulting example
-
   * New upstream version
   * debian/patches:
     - 99-theseus_align.sh.patch:
@@ -10,6 +8,16 @@
     - use_muscle_instead_of_clustalw.patch:
       Removed because clustalw is no in main and we do not need
       to actively replace it by muscle
+    - 00-makefile.patch:
+      Removed because applied upstream
+    - 200-make.inc.patch:
+      Removed
+      + One purpose was to replace not working libtool call by ar
+        which was applied upstream
+      + Other purpose was to enable liblapack (patch by Morten
+        Kjeldgaard) which was discussed with upstream and seems to
+        cause problems.  So it was deactivated for now and might be
+        tested later for enabling higher performance if needed.
 
  -- Andreas Tille <tille at debian.org>  Wed, 26 Jan 2011 11:39:36 +0100
 

Modified: trunk/packages/theseus/trunk/debian/control
===================================================================
--- trunk/packages/theseus/trunk/debian/control	2011-01-26 12:19:33 UTC (rev 5713)
+++ trunk/packages/theseus/trunk/debian/control	2011-01-27 09:03:54 UTC (rev 5714)
@@ -5,7 +5,7 @@
 Uploaders: Morten Kjeldgaard <mok0 at ubuntu.com>,
  Andreas Tille <tille at debian.org>
 DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), libgsl0-dev, liblapack-dev, libtool
+Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), libgsl0-dev
 Standards-Version: 3.9.1
 Homepage: http://www.theseus3d.org
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/theseus/trunk/

Deleted: trunk/packages/theseus/trunk/debian/patches/00-makefile.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00-makefile.patch	2011-01-26 12:19:33 UTC (rev 5713)
+++ trunk/packages/theseus/trunk/debian/patches/00-makefile.patch	2011-01-27 09:03:54 UTC (rev 5714)
@@ -1,15 +0,0 @@
-Fix clean target of original Makefile
-Author: Morten Kjeldgaard <mok0 at ubuntu.com>
-Switched to quilt: Andreas Tille <tille at debian.org>
-
---- theseus_src.orig/Makefile
-+++ theseus_src/Makefile
-@@ -149,6 +149,6 @@
- 					cp lib/*.a ${LOCALLIBDIR}
- 
- clean:
--					find . -name '*.[oa]' -exec rm {} \;	
--					rm theseus &> /dev/null
-+					find . -name '*.[oa]' -exec rm -f {} \;	
-+					rm -f theseus &> /dev/null
- 

Deleted: trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch	2011-01-26 12:19:33 UTC (rev 5713)
+++ trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch	2011-01-27 09:03:54 UTC (rev 5714)
@@ -1,50 +0,0 @@
-1. Use ar instead of libtool because of "libtool: unrecognized option `-o'" error
-   when using libtool (Andreas Tille)
-2. Remove -arch options which let gcc fail (Andreas Tille)
-3. Add Ubuntu specific build options which work for Debian as well (Morten Kjeldgaard)
-Author: Morten Kjeldgaard <mok at bioxray.dk>
-Switched to quilt: Andreas Tille <tille at debian.org>
-
---- theseus_src.orig/make.inc
-+++ theseus_src/make.inc
-@@ -2,10 +2,10 @@
- #  The archiver and the flag(s) to use when building archive (library)
- #  If you system has no ranlib, set RANLIB = echo.
- #
--#ARCH     = ar
--ARCH = libtool
--ARCHFLAGS = -o
--#ARCHFLAGS= -rvs
-+ARCH     = ar
-+#ARCH = libtool
-+#ARCHFLAGS = -o
-+ARCHFLAGS= -rvs
- RANLIB   = ranlib
- 
- #MACOSX_DEPLOYMENT_TARGET=10.4
-@@ -22,7 +22,7 @@
- #OPT = -O0 -ggdb
- OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer 
- WARN = -Werror -Wall -pedantic -std=c99 #-Wstrict-aliasing=2
--CFLAGS = $(WARN) #-force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch ppc -arch i386 #-DNDEBUG
-+CFLAGS = $(WARN) -DNDEBUG
- CC = /usr/bin/gcc
- 
- # Intel Xeon Mac OSX
-@@ -243,3 +243,16 @@
- # CFLAGS = $(WARN)
- # CC = cc
- 
-+
-+# Ubuntu Linux x86 & amd64
-+SYSLIBS = -lpthread -lm -lc
-+LIBS = -Llib -ldistfit -lgsl -lmsa -ldssplite -ldltmath -lDLTutils
-+BLASLIB = -L/usr/lib/atlas -llapack
-+BLASLIBDIR =
-+LAPACKLIB =
-+LAPACKLIBDIR =
-+INSTALLDIR =
-+OPT = -g -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer -ftree-vectorize
-+WARN = -Wall -pedantic -std=c99
-+CFLAGS += $(WARN) 
-+CC = gcc

Modified: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series	2011-01-26 12:19:33 UTC (rev 5713)
+++ trunk/packages/theseus/trunk/debian/patches/series	2011-01-27 09:03:54 UTC (rev 5714)
@@ -1,3 +1 @@
-00-makefile.patch
-200-make.inc.patch
 10_kbsd.patch