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sascha-guest pushed a commit to branch master
in repository kmc.
commit dd888358864ec9355745c23260618316c1ef8205
Author: Sascha Steinbiss <sas...@steinbiss.name>
Date: Wed Dec 23 16:45:31 2015 +0000
adjust patches to removed directories
---
...005-Add-static-library-target-to-makefile.patch | 35 ++++++--------
...e-standard-compiler-environment-variables.patch | 40 ++++++----------
debian/patches/hardening | 53 ++++++++++++++++++----
debian/patches/spelling | 11 -----
debian/patches/use-shared-libs | 52 ++++++++++++++++++++-
5 files changed, 124 insertions(+), 67 deletions(-)
diff --git a/debian/patches/0005-Add-static-library-target-to-makefile.patch
b/debian/patches/0005-Add-static-library-target-to-makefile.patch
index 186e277..5ab8854 100644
--- a/debian/patches/0005-Add-static-library-target-to-makefile.patch
+++ b/debian/patches/0005-Add-static-library-target-to-makefile.patch
@@ -8,40 +8,31 @@ Subject: Add static library target to makefile
--- a/makefile
+++ b/makefile
-@@ -56,6 +56,8 @@
- $(KMC_TOOLS_DIR)/libs/libz.a \
- $(KMC_TOOLS_DIR)/libs/libbz2.a
+@@ -52,9 +52,13 @@
+ $(KMC_TOOLS_DIR)/fastq_writer.o \
+ $(KMC_TOOLS_DIR)/percent_progress.o
-+KMC_LIB_OBJS = $(wildcard $(KMC_API_DIR)/*.o)
++KMC_LIB_OBJS = $(sort $(wildcard $(KMC_API_DIR)/*.o))
+
- ifeq ($(DISABLE_ASMLIB),true)
- CFLAGS += -DDISABLE_ASMLIB
- KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
-@@ -66,6 +68,8 @@
- $(KMC_TOOLS_DIR)/libs/alibelf64.a
- endif
+ CFLAGS += -DDISABLE_ASMLIB
+ KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
+all: kmc kmc_dump kmc_tools libkmc.a
+
$(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
$(CC) $(CPPFLAGS) $(CFLAGS) -c $< -o $@
-@@ -75,9 +79,14 @@
- kmc: $(KMC_OBJS)
+@@ -73,11 +77,16 @@
-mkdir -p $(KMC_BIN_DIR)
- $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
-+
- kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
- -mkdir -p $(KMC_BIN_DIR)
- $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
-+
+ $(CC) $(LDFLAGS) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
+
+libkmc.a: $(KMC_API_OBJS)
+ ar rcs $@ $^
+ ranlib libkmc.a
-
- kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS)
- -mkdir -p $(KMC_BIN_DIR)
-@@ -89,5 +98,6 @@
++
+ clean:
+ -rm $(KMC_MAIN_DIR)/*.o
+ -rm $(KMC_API_DIR)/*.o
-rm $(KMC_DUMP_DIR)/*.o
-rm $(KMC_TOOLS_DIR)/*.o
-rm -rf bin
diff --git
a/debian/patches/0007-Use-standard-compiler-environment-variables.patch
b/debian/patches/0007-Use-standard-compiler-environment-variables.patch
index 9d11df9..9c6d8b6 100644
--- a/debian/patches/0007-Use-standard-compiler-environment-variables.patch
+++ b/debian/patches/0007-Use-standard-compiler-environment-variables.patch
@@ -16,13 +16,13 @@ Subject: Use standard compiler environment variables
KMC_TOOLS_DIR = kmc_tools
-CC = g++
--CFLAGS = -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
--CLINK = -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
+-CFLAGS = -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
+-CLINK = -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
-
-KMC_TOOLS_CFLAGS = -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++14
-KMC_TOOLS_CLINK = -lm -static -O3 -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++14
-
--DISABLE_ASMLIB = true
+-DISABLE_ASMLIB = true
+CXX := g++
+CXXFLAGS += -Wall -O3 -fopenmp -std=c++11
+CXXFLAGS_TOOLS := $(CXXFLAGS) -Wall -O3 -fopenmp -std=c++14
@@ -31,19 +31,12 @@ Subject: Use standard compiler environment variables
KMC_OBJS = \
$(KMC_MAIN_DIR)/kmer_counter.o \
-@@ -58,31 +55,21 @@
+@@ -54,28 +51,26 @@
- KMC_LIB_OBJS = $(wildcard $(KMC_API_DIR)/*.o)
+ KMC_LIB_OBJS = $(sort $(wildcard $(KMC_API_DIR)/*.o))
--ifeq ($(DISABLE_ASMLIB),true)
-- CFLAGS += -DDISABLE_ASMLIB
-- KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
--else
-- KMC_LIBS += \
-- $(KMC_MAIN_DIR)/libs/alibelf64.a
-- KMC_TOOLS_LIBS += \
-- $(KMC_TOOLS_DIR)/libs/alibelf64.a
--endif
+-CFLAGS += -DDISABLE_ASMLIB
+-KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
-
all: kmc kmc_dump kmc_tools libkmc.a
@@ -54,25 +47,22 @@ Subject: Use standard compiler environment variables
$(KMC_TOOLS_OBJS): %.o: %.cpp
- $(CC) $(CPPFLAGS) $(KMC_TOOLS_CFLAGS) -c $< -o $@
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS_TOOLS) -c $< -o $@
-
+
+
kmc: $(KMC_OBJS)
-mkdir -p $(KMC_BIN_DIR)
- $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
+ $(CXX) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
-
++
kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
-mkdir -p $(KMC_BIN_DIR)
- $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
+ $(CXX) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
- libkmc.a: $(KMC_API_OBJS)
- ar rcs $@ $^
-@@ -90,7 +77,7 @@
-
kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS)
-mkdir -p $(KMC_BIN_DIR)
-- $(CC) $(LDFLAGS) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
$(KMC_TOOLS_LIBS)
-+ $(CXX) $(LDFLAGS) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
$(KMC_TOOLS_LIBS)
-
- clean:
- -rm $(KMC_MAIN_DIR)/*.o
+- $(CC) $(LDFLAGS) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
++ $(CXX) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
+
+ libkmc.a: $(KMC_API_OBJS)
+ ar rcs $@ $^
diff --git a/debian/patches/hardening b/debian/patches/hardening
index bf46e1b..575df97 100644
--- a/debian/patches/hardening
+++ b/debian/patches/hardening
@@ -8,8 +8,41 @@ Subject: hardening
--- a/makefile
+++ b/makefile
-@@ -67,22 +67,21 @@
- endif
+@@ -1,5 +1,5 @@
+ all: kmc
+-
++
+ KMC_BIN_DIR = bin
+ KMC_MAIN_DIR = kmer_counter
+ KMC_API_DIR = kmc_api
+@@ -7,13 +7,13 @@
+ KMC_TOOLS_DIR = kmc_tools
+
+ CC = g++
+-CFLAGS = -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
+-CLINK = -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
++CFLAGS = -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
++CLINK = -lm -static -fopenmp -O3 -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++11
+
+ KMC_TOOLS_CFLAGS = -Wall -O3 -m64 -static -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++14
+ KMC_TOOLS_CLINK = -lm -static -O3 -Wl,--whole-archive -lpthread
-Wl,--no-whole-archive -std=c++14
+
+-DISABLE_ASMLIB = true
++DISABLE_ASMLIB = true
+
+ KMC_OBJS = \
+ $(KMC_MAIN_DIR)/kmer_counter.o \
+@@ -33,7 +33,7 @@
+ KMC_DUMP_OBJS = \
+ $(KMC_DUMP_DIR)/nc_utils.o \
+ $(KMC_API_DIR)/mmer.o \
+-$(KMC_DUMP_DIR)/kmc_dump.o
++$(KMC_DUMP_DIR)/kmc_dump.o
+
+ KMC_API_OBJS = \
+ $(KMC_API_DIR)/mmer.o \
+@@ -56,23 +56,23 @@
+ KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
$(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
- $(CC) $(CFLAGS) -c $< -o $@
@@ -17,9 +50,10 @@ Subject: hardening
$(KMC_TOOLS_OBJS): %.o: %.cpp
- $(CC) $(KMC_TOOLS_CFLAGS) -c $< -o $@
--
+ $(CC) $(CPPFLAGS) $(KMC_TOOLS_CFLAGS) -c $< -o $@
-
++
+
+-
kmc: $(KMC_OBJS)
-mkdir -p $(KMC_BIN_DIR)
- $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
@@ -27,12 +61,15 @@ Subject: hardening
kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
-mkdir -p $(KMC_BIN_DIR)
- $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
+-
+ $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
-
++
kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS)
-mkdir -p $(KMC_BIN_DIR)
-- $(CC) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^ $(KMC_TOOLS_LIBS)
-+ $(CC) $(LDFLAGS) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
$(KMC_TOOLS_LIBS)
-
+- $(CC) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
+-
++ $(CC) $(LDFLAGS) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
++
clean:
-rm $(KMC_MAIN_DIR)/*.o
+ -rm $(KMC_API_DIR)/*.o
diff --git a/debian/patches/spelling b/debian/patches/spelling
index 0f05044..e2b6a7b 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -37,17 +37,6 @@ Applied-Upstream: https://github.com/marekkokot/KMC/pull/8
-// ***** EOF
\ No newline at end of file
+// ***** EOF
---- a/kmc_tools/libs/zlib.h
-+++ b/kmc_tools/libs/zlib.h
-@@ -846,7 +846,7 @@
- available input is skipped. No output is provided.
-
- inflateSync searches for a 00 00 FF FF pattern in the compressed data.
-- All full flush points have this pattern, but not all occurences of this
-+ All full flush points have this pattern, but not all occurrences of this
- pattern are full flush points.
-
- inflateSync returns Z_OK if a possible full flush point has been found,
--- a/kmer_counter/bkb_sorter.h
+++ b/kmer_counter/bkb_sorter.h
@@ -367,7 +367,7 @@
diff --git a/debian/patches/use-shared-libs b/debian/patches/use-shared-libs
index c43c6eb..490d749 100644
--- a/debian/patches/use-shared-libs
+++ b/debian/patches/use-shared-libs
@@ -46,7 +46,29 @@ Subject: use-shared-libs
KMC_DUMP_OBJS = \
$(KMC_DUMP_DIR)/nc_utils.o \
$(KMC_API_DIR)/mmer.o \
-@@ -79,7 +75,7 @@
+@@ -56,19 +52,8 @@
+ $(KMC_TOOLS_DIR)/fastq_writer.o \
+ $(KMC_TOOLS_DIR)/percent_progress.o
+
+-KMC_TOOLS_LIBS = \
+-$(KMC_TOOLS_DIR)/libs/libz.a \
+-$(KMC_TOOLS_DIR)/libs/libbz2.a
+-
+-ifeq ($(DISABLE_ASMLIB),true)
+- CFLAGS += -DDISABLE_ASMLIB
+- KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
+-else
+- KMC_LIBS += \
+- $(KMC_MAIN_DIR)/libs/alibelf64.a
+- KMC_TOOLS_LIBS += \
+- $(KMC_TOOLS_DIR)/libs/alibelf64.a
+-endif
++CFLAGS += -DDISABLE_ASMLIB
++KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
+
+ $(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
+ $(CC) $(CFLAGS) -c $< -o $@
+@@ -79,14 +64,14 @@
kmc: $(KMC_OBJS)
-mkdir -p $(KMC_BIN_DIR)
@@ -55,3 +77,31 @@ Subject: use-shared-libs
kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
-mkdir -p $(KMC_BIN_DIR)
$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
+
+ kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS)
+ -mkdir -p $(KMC_BIN_DIR)
+- $(CC) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^ $(KMC_TOOLS_LIBS)
++ $(CC) $(KMC_TOOLS_CLINK) -o $(KMC_BIN_DIR)/$@ $^
+
+ clean:
+ -rm $(KMC_MAIN_DIR)/*.o
+--- a/kmc_tools/fastq_reader.h
++++ b/kmc_tools/fastq_reader.h
+@@ -17,8 +17,8 @@
+ #include <stdio.h>
+ #include <iostream>
+
+-#include "libs/zlib.h"
+-#include "libs/bzlib.h"
++#include <zlib.h>
++#include <bzlib.h>
+
+
+ using namespace std;
+@@ -93,4 +93,4 @@
+
+ #endif
+
+-// ***** EOF
+\ No newline at end of file
++// ***** EOF
--
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