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 <ti...@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 <m...@ubuntu.com>, Andreas Tille <ti...@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 <m...@ubuntu.com> -Switched to quilt: Andreas Tille <ti...@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 <m...@bioxray.dk> -Switched to quilt: Andreas Tille <ti...@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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit