[med-svn] r769 - in trunk/packages/mummer/trunk/debian: . patches
tille at alioth.debian.org
tille at alioth.debian.org
Wed Nov 7 22:00:41 UTC 2007
Author: tille
Date: 2007-11-07 22:00:41 +0000 (Wed, 07 Nov 2007)
New Revision: 769
Added:
trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff
trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
Removed:
trunk/packages/mummer/trunk/debian/patches/01sm_src.diff
Modified:
trunk/packages/mummer/trunk/debian/changelog
trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff
Log:
Package builds, needs testing
Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog 2007-11-07 21:23:00 UTC (rev 768)
+++ trunk/packages/mummer/trunk/debian/changelog 2007-11-07 22:00:41 UTC (rev 769)
@@ -6,6 +6,7 @@
* Do not autogenerate debian/control
* debian/rules: get-orig-source target that removes non-free docs
* debian/rules: Fixed building docs
+ * Separated patches tigr and kurtz; better Makefile for scripts
-- Andreas Tille <tille at debian.org> Wed, 07 Nov 2007 13:25:34 +0100
Deleted: trunk/packages/mummer/trunk/debian/patches/01sm_src.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src.diff 2007-11-07 21:23:00 UTC (rev 768)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src.diff 2007-11-07 22:00:41 UTC (rev 769)
@@ -1,192 +0,0 @@
-diff -urbN src.orig/kurtz/Makefile src/kurtz/Makefile
---- src.orig/kurtz/Makefile 2006-06-29 19:35:08.000000000 +0200
-+++ src/kurtz/Makefile 2007-04-12 14:20:42.000000000 +0200
-@@ -1,20 +1,21 @@
- all:
-- cd libbasedir; $(MAKE) all
-- cd streesrc; $(MAKE) all
-- cd mm3src; $(MAKE) all
-+ $(MAKE) -C libbasedir all
-+ $(MAKE) -C streesrc all
-+ $(MAKE) BIN_DIR="../../../bin" -C mm3src all
-
- clean:
- rm -f *~
-- cd libbasedir; $(MAKE) clean
-- cd streesrc; $(MAKE) clean
-- cd mm3src; $(MAKE) clean
-+ $(MAKE) -C libbasedir clean
-+ $(MAKE) -C streesrc clean
-+ $(MAKE) -C mm3src clean
-+ rm -rf bin
-
- mummer:
-- cd libbasedir; $(MAKE) libbase.a
-- cd streesrc; $(MAKE) libstree.a
-- cd mm3src; $(MAKE) mummer
-+ $(MAKE) -C libbasedir libbase.a
-+ $(MAKE) -C streesrc libstree.a
-+ $(MAKE) BIN_DIR="../../../bin" -C mm3src mummer
-
- splintall:
-- cd libbasedir; ${MAKE} splintall
-- cd streesrc; ${MAKE} splintall
-- cd mm3src; ${MAKE} splintall
-+ ${MAKE} -C libbasedir splintall
-+ ${MAKE} -C streesrc splintall
-+ ${MAKE} -C mm3src splintall
-diff -urbN src.orig/kurtz/mm3src/Makefile src/kurtz/mm3src/Makefile
---- src.orig/kurtz/mm3src/Makefile 2006-06-29 19:35:08.000000000 +0200
-+++ src/kurtz/mm3src/Makefile 2007-04-12 14:23:55.000000000 +0200
-@@ -3,12 +3,10 @@
-
- ##include ../Makedef
-
--ifndef BIN_DIR
--BIN_DIR := $(CURDIR)
-+ifndef INSTALL_BIN_DIR
-+INSTALL_BIN_DIR=../../bin
- endif
-
--VPATH := $(BIN_DIR)
--
- ALL := maxmat3.x maxmat3.dbg.x
-
- LIBBASEDIR=../libbasedir
-@@ -26,13 +24,13 @@
- LIBSTREE=$(LIBSTREEDIR)/libstree.a
- LIBSTREEDBG=$(LIBSTREEDIR)/libstree.dbg.a
-
--MUM3OBJECTS=maxmat3.o maxmatopt.o maxmatinp.o\
-+MUM3OBJECTS=maxmat3.o maxmatopt.o maxmatinp.o \
- findmumcand.o findmaxmat.o procmaxmat.o
-
--MUM3DBGOBJECTS=maxmat3.dbg.o maxmatopt.dbg.o maxmatinp.dbg.o\
-+MUM3DBGOBJECTS=maxmat3.dbg.o maxmatopt.dbg.o maxmatinp.dbg.o \
- findmumcand.dbg.o findmaxmat.dbg.o procmaxmat.dbg.o
-
--SPLINTALL=maxmat3.splint maxmatopt.splint maxmatinp.splint\
-+SPLINTALL=maxmat3.splint maxmatopt.splint maxmatinp.splint \
- findmumcand.splint findmaxmat.splint procmaxmat.splint
-
- .SUFFIXES: .dbg.o
-@@ -40,22 +38,22 @@
- all: $(ALL)
-
- mummer: $(MUM3OBJECTS) $(LIBSTREE)
-- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE)\
-- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
-+ $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-+ -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
-
- maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
-- $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE)\
-- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
-+ $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
-+ -o $(INSTALL_BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
-
- maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
-- $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG)\
-- -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
-+ $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
-+ -lm -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
-
- include Filegoals.mf
-
- .PHONY:clean
- clean:splintclean
- rm -f *.[ox] shit[123] *~
-- cd $(BIN_DIR); rm -f $(ALL) mummer
-+ rm -f $(BIN_DIR)/mummer*
-
- include Dependencies.mf
-diff -urbN src.orig/tigr/annotate.cc src/tigr/annotate.cc
---- src.orig/tigr/annotate.cc 2006-06-29 19:35:08.000000000 +0200
-+++ src/tigr/annotate.cc 2007-04-12 14:20:42.000000000 +0200
-@@ -10,6 +10,7 @@
- */
-
- #include "tigrinc.hh"
-+#include <assert.h>
-
- #define FIELD_LEN 20
- #define MAX_ALIGN 10000
-@@ -138,19 +139,19 @@
- // Print the alignment between strings A [1 .. M] and B [1 .. N] .
-
- {
-- static int D [MAX_ALIGN] [MAX_ALIGN];
-- static char Op [MAX_ALIGN] [MAX_ALIGN];
-- static char Show_A [2 * MAX_ALIGN];
-- static char Show_B [2 * MAX_ALIGN];
-+ int **D, *D_buf;
-+ char **Op, *Op_buf;
-+ char *Show_A;
-+ char *Show_B;
- int Errors, Tmp;
- long int i, j, Ct;
-
-- if (M >= MAX_ALIGN || N >= MAX_ALIGN)
-- {
-- printf ("\n *** Too long ***\n\n");
-- fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
-- return;
-- }
-+ assert ( D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
-+ D = &D_buf ;
-+ assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
-+ Op = &Op_buf ;
-+ assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
-+ assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
-
- D [0] [0] = 0;
- Op [0] [0] = 'a';
-@@ -229,5 +230,10 @@
- putchar ('\n');
- Ct -= WIDTH;
- } while (Ct > 0);
-+
-+ free ( D_buf ) ;
-+ free ( Op_buf ) ;
-+ free ( Show_A ) ;
-+ free ( Show_B ) ;
- return;
- }
-diff -urbN src.orig/tigr/Makefile src/tigr/Makefile
---- src.orig/tigr/Makefile 2006-06-29 19:35:08.000000000 +0200
-+++ src/tigr/Makefile 2007-04-12 14:20:42.000000000 +0200
-@@ -2,17 +2,15 @@
- # BIN_DIR AUX_BIN_DIR CXX CC CPPFLAGS LDFLAGS
-
- ifndef BIN_DIR
--BIN_DIR := $(CURDIR)
-+BIN_DIR := ../../bin
- endif
- ifndef AUX_BIN_DIR
--AUX_BIN_DIR := $(CURDIR)
-+AUX_BIN_DIR := ../../aux_bin
- endif
-
- OBJ_RULE = $(CXX) $(CPPFLAGS) $< -c -o $@
--BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@; \
-- chmod 755 $(BIN_DIR)/$@
--AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
-- chmod 755 $(AUX_BIN_DIR)/$@
-+BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
-+AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@ && chmod 755 $(AUX_BIN_DIR)/$@
- VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
-
- ALL := annotate combineMUMs delta-filter gaps mgaps \
-@@ -29,10 +27,8 @@
-
- clean:
- rm -f *.o *~
-- cd $(BIN_DIR); rm -f $(ALL)
-- cd $(AUX_BIN_DIR); rm -f $(ALL)
--
--
-+ ( cd $(BIN_DIR) && rm -f $(ALL) )
-+ ( cd $(AUX_BIN_DIR) && rm -f $(ALL) )
-
-
- #-- not so PHONY rules --#
Added: trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff (rev 0)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src_kurtz.diff 2007-11-07 22:00:41 UTC (rev 769)
@@ -0,0 +1,98 @@
+diff -urbN src/kurtz.orig/Makefile src/kurtz/Makefile
+--- src/kurtz.orig/Makefile 2007-07-13 19:06:58.000000000 +0200
++++ src/kurtz/Makefile 2007-11-07 21:47:03.000000000 +0100
+@@ -1,20 +1,21 @@
+ all:
+- cd libbasedir; $(MAKE) all
+- cd streesrc; $(MAKE) all
+- cd mm3src; $(MAKE) all
++ $(MAKE) -C libbasedir all
++ $(MAKE) -C streesrc all
++ $(MAKE) BIN_DIR="../../../bin" -C mm3src all
+
+ clean:
+ rm -f *~
+- cd libbasedir; $(MAKE) clean
+- cd streesrc; $(MAKE) clean
+- cd mm3src; $(MAKE) clean
++ $(MAKE) -C libbasedir clean
++ $(MAKE) -C streesrc clean
++ $(MAKE) -C mm3src clean
++ rm -rf bin
+
+ mummer:
+- cd libbasedir; $(MAKE) libbase.a
+- cd streesrc; $(MAKE) libstree.a
+- cd mm3src; $(MAKE) mummer
++ $(MAKE) -C libbasedir libbase.a
++ $(MAKE) -C streesrc libstree.a
++ $(MAKE) BIN_DIR="../../../bin" -C mm3src mummer
+
+ splintall:
+- cd libbasedir; ${MAKE} splintall
+- cd streesrc; ${MAKE} splintall
+- cd mm3src; ${MAKE} splintall
++ ${MAKE} -C libbasedir splintall
++ ${MAKE} -C streesrc splintall
++ ${MAKE} -C mm3src splintall
+diff -urbN src/kurtz.orig/mm3src/Makefile src/kurtz/mm3src/Makefile
+--- src/kurtz.orig/mm3src/Makefile 2007-07-13 19:06:58.000000000 +0200
++++ src/kurtz/mm3src/Makefile 2007-11-07 21:47:03.000000000 +0100
+@@ -3,12 +3,10 @@
+
+ ##include ../Makedef
+
+-ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
++ifndef INSTALL_BIN_DIR
++INSTALL_BIN_DIR=../../bin
+ endif
+
+-VPATH := $(BIN_DIR)
+-
+ ALL := maxmat3.x maxmat3.dbg.x
+
+ LIBBASEDIR=../libbasedir
+@@ -26,13 +24,13 @@
+ LIBSTREE=$(LIBSTREEDIR)/libstree.a
+ LIBSTREEDBG=$(LIBSTREEDIR)/libstree.dbg.a
+
+-MUM3OBJECTS=maxmat3.o maxmatopt.o maxmatinp.o\
++MUM3OBJECTS=maxmat3.o maxmatopt.o maxmatinp.o \
+ findmumcand.o findmaxmat.o procmaxmat.o
+
+-MUM3DBGOBJECTS=maxmat3.dbg.o maxmatopt.dbg.o maxmatinp.dbg.o\
++MUM3DBGOBJECTS=maxmat3.dbg.o maxmatopt.dbg.o maxmatinp.dbg.o \
+ findmumcand.dbg.o findmaxmat.dbg.o procmaxmat.dbg.o
+
+-SPLINTALL=maxmat3.splint maxmatopt.splint maxmatinp.splint\
++SPLINTALL=maxmat3.splint maxmatopt.splint maxmatinp.splint \
+ findmumcand.splint findmaxmat.splint procmaxmat.splint
+
+ .SUFFIXES: .dbg.o
+@@ -41,21 +39,21 @@
+
+ mummer: $(MUM3OBJECTS) $(LIBSTREE)
+ $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++ -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+
+ maxmat3.x: $(MUM3OBJECTS) $(LIBSTREE)
+ $(LD) $(LDFLAGS) $(MUM3OBJECTS) $(LIBSTREE) $(LIBBASE) \
+- -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++ -o $(INSTALL_BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+
+ maxmat3.dbg.x: ${MUM3DBGOBJECTS} $(LIBSTREEDBG)
+ $(LD) $(LDFLAGS) $(MUM3DBGOBJECTS) $(LIBSTREEDBG) $(LIBBASEDBG) \
+- -lm -o $(BIN_DIR)/$@; chmod 755 $(BIN_DIR)/$@
++ -lm -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
+
+ include Filegoals.mf
+
+ .PHONY:clean
+ clean:splintclean
+ rm -f *.[ox] shit[123] *~
+- cd $(BIN_DIR); rm -f $(ALL) mummer
++ rm -f $(BIN_DIR)/mummer*
+
+ include Dependencies.mf
Added: trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff (rev 0)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff 2007-11-07 22:00:41 UTC (rev 769)
@@ -0,0 +1,103 @@
+diff -urbN src/tigr.orig/annotate.cc src/tigr/annotate.cc
+--- src/tigr.orig/annotate.cc 2007-07-13 19:06:58.000000000 +0200
++++ src/tigr/annotate.cc 2007-11-07 21:47:03.000000000 +0100
+@@ -10,6 +10,7 @@
+ */
+
+ #include "tigrinc.hh"
++#include <assert.h>
+
+ #define FIELD_LEN 20
+ #define MAX_ALIGN 10000
+@@ -138,19 +139,19 @@
+ // Print the alignment between strings A [1 .. M] and B [1 .. N] .
+
+ {
+- static int D [MAX_ALIGN] [MAX_ALIGN];
+- static char Op [MAX_ALIGN] [MAX_ALIGN];
+- static char Show_A [2 * MAX_ALIGN];
+- static char Show_B [2 * MAX_ALIGN];
++ int **D, *D_buf;
++ char **Op, *Op_buf;
++ char *Show_A;
++ char *Show_B;
+ int Errors, Tmp;
+ long int i, j, Ct;
+
+- if (M >= MAX_ALIGN || N >= MAX_ALIGN)
+- {
+- printf ("\n *** Too long ***\n\n");
+- fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
+- return;
+- }
++ assert ( D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
++ D = &D_buf ;
++ assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
++ Op = &Op_buf ;
++ assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
++ assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
+
+ D [0] [0] = 0;
+ Op [0] [0] = 'a';
+@@ -229,5 +230,10 @@
+ putchar ('\n');
+ Ct -= WIDTH;
+ } while (Ct > 0);
++
++ free ( D_buf ) ;
++ free ( Op_buf ) ;
++ free ( Show_A ) ;
++ free ( Show_B ) ;
+ return;
+ }
+diff -urbN src/tigr.orig/Makefile src/tigr/Makefile
+--- src/tigr.orig/Makefile 2007-07-13 19:06:58.000000000 +0200
++++ src/tigr/Makefile 2007-11-07 21:47:03.000000000 +0100
+@@ -2,23 +2,20 @@
+ # BIN_DIR AUX_BIN_DIR CXX CC CPPFLAGS LDFLAGS
+
+ ifndef BIN_DIR
+-BIN_DIR := $(CURDIR)
++BIN_DIR := ../../bin
+ endif
+ ifndef AUX_BIN_DIR
+-AUX_BIN_DIR := $(CURDIR)
++AUX_BIN_DIR := ../../aux_bin
+ endif
+
+ OBJ_RULE = $(CXX) $(CPPFLAGS) $< -c -o $@
+-BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@; \
+- chmod 755 $(BIN_DIR)/$@
+-AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@; \
+- chmod 755 $(AUX_BIN_DIR)/$@
++BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(BIN_DIR)/$@ && chmod 755 $(BIN_DIR)/$@
++AUX_BIN_RULE = $(CXX) $(CPPFLAGS) $^ -o $(AUX_BIN_DIR)/$@ && chmod 755 $(AUX_BIN_DIR)/$@
+ VPATH := $(AUX_BIN_DIR):$(BIN_DIR)
+
+ ALL := annotate combineMUMs delta-filter gaps mgaps \
+ postnuc postpro prenuc prepro repeat-match \
+- show-aligns show-coords show-tiling show-snps \
+- show-diff
++ show-aligns show-coords show-tiling show-snps
+
+
+ #-- PHONY rules --#
+@@ -30,10 +27,8 @@
+
+ clean:
+ rm -f *.o *~
+- cd $(BIN_DIR); rm -f $(ALL)
+- cd $(AUX_BIN_DIR); rm -f $(ALL)
+-
+-
++ ( cd $(BIN_DIR) && rm -f $(ALL) )
++ ( cd $(AUX_BIN_DIR) && rm -f $(ALL) )
+
+
+ #-- not so PHONY rules --#
+@@ -92,5 +87,3 @@
+ show-snps: show-snps.cc tigrinc.o translate.o delta.o
+ $(BIN_RULE)
+
+-show-diff: show-diff.cc tigrinc.o delta.o
+- $(BIN_RULE)
Modified: trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff 2007-11-07 21:23:00 UTC (rev 768)
+++ trunk/packages/mummer/trunk/debian/patches/02at_scripts.diff 2007-11-07 22:00:41 UTC (rev 769)
@@ -131,7 +131,7 @@
- run-mummer3.csh > $(BIN_DIR)/run-mummer3
- chmod 755 $(BIN_DIR)/run-mummer3
-
-+run-mummer1: run-mummer1.cs
++run-mummer1: run-mummer1.sh
+run-mummer3: run-mummer3.sh
nucmer2xfig: nucmer2xfig.pl
- $(SED) -e 's?__PERL_PATH?$(PERL)?g' \
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