[med-svn] [kmc] 04/05: new upstream release
Sascha Steinbiss
sascha at steinbiss.name
Sat Dec 19 22:47:43 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository kmc.
commit b6055973f720dfb78573831eab7b5a9f6a531f5d
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Dec 19 19:14:56 2015 +0000
new upstream release
---
...005-Add-static-library-target-to-makefile.patch | 49 +++++++++---------
...e-standard-compiler-environment-variables.patch | 60 ++++++++++++++--------
debian/patches/disable-asmlib | 37 ++++---------
debian/patches/hardening | 35 ++++++-------
debian/patches/series | 2 -
debian/patches/use-shared-libs | 27 +++-------
6 files changed, 95 insertions(+), 115 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 1b3f12e..186e277 100644
--- a/debian/patches/0005-Add-static-library-target-to-makefile.patch
+++ b/debian/patches/0005-Add-static-library-target-to-makefile.patch
@@ -6,48 +6,45 @@ Subject: Add static library target to makefile
makefile | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
-diff --git a/makefile b/makefile
-index 3e2edc9..bc2ed0f 100644
--- a/makefile
+++ b/makefile
-@@ -1,5 +1,3 @@
--all: kmc
--
- KMC_BIN_DIR = bin
- KMC_MAIN_DIR = kmer_counter
- KMC_API_DIR = kmc_api
-@@ -32,6 +30,8 @@ $(KMC_DUMP_DIR)/kmc_dump.o \
- $(KMC_API_DIR)/kmc_file.o \
- $(KMC_API_DIR)/kmer_api.o
+@@ -56,6 +56,8 @@
+ $(KMC_TOOLS_DIR)/libs/libz.a \
+ $(KMC_TOOLS_DIR)/libs/libbz2.a
+KMC_LIB_OBJS = $(wildcard $(KMC_API_DIR)/*.o)
+
ifeq ($(DISABLE_ASMLIB),true)
CFLAGS += -DDISABLE_ASMLIB
- else
-@@ -39,6 +39,8 @@ else
- $(KMC_MAIN_DIR)/libs/alibelf64.a
- endif
+ KMC_TOOLS_CFLAGS += -DDISABLE_ASMLIB
+@@ -66,6 +68,8 @@
+ $(KMC_TOOLS_DIR)/libs/alibelf64.a
+ endif
-+all: kmc kmc_dump libkmc.a
++all: kmc kmc_dump kmc_tools libkmc.a
+
- .cpp.o:
+ $(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
$(CC) $(CPPFLAGS) $(CFLAGS) -c $< -o $@
-@@ -48,10 +50,15 @@ kmc: $(KMC_OBJS)
- kmc_dump: $(KMC_DUMP_OBJS)
+@@ -75,9 +79,14 @@
+ kmc: $(KMC_OBJS)
-mkdir -p $(KMC_BIN_DIR)
$(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
+
-+libkmc.a: $(KMC_LIB_OBJS)
+ kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
+ -mkdir -p $(KMC_BIN_DIR)
+ $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
++
++libkmc.a: $(KMC_API_OBJS)
+ ar rcs $@ $^
+ ranlib libkmc.a
-+
- clean:
- -rm -f $(KMC_MAIN_DIR)/*.o
- -rm -f $(KMC_API_DIR)/*.o
- -rm -f $(KMC_DUMP_DIR)/*.o
+
+ kmc_tools: $(KMC_TOOLS_OBJS) $(KMC_API_OBJS)
+ -mkdir -p $(KMC_BIN_DIR)
+@@ -89,5 +98,6 @@
+ -rm $(KMC_DUMP_DIR)/*.o
+ -rm $(KMC_TOOLS_DIR)/*.o
-rm -rf bin
+ -rm -f libkmc.a
--all: kmc kmc_dump
+ all: kmc kmc_dump kmc_tools
diff --git a/debian/patches/0007-Use-standard-compiler-environment-variables.patch b/debian/patches/0007-Use-standard-compiler-environment-variables.patch
index ca45b17..9d11df9 100644
--- a/debian/patches/0007-Use-standard-compiler-environment-variables.patch
+++ b/debian/patches/0007-Use-standard-compiler-environment-variables.patch
@@ -9,52 +9,70 @@ Subject: Use standard compiler environment variables
makefile | 22 ++++++++--------------
1 file changed, 8 insertions(+), 14 deletions(-)
-diff --git a/makefile b/makefile
-index ff7357d..55f87ca 100644
--- a/makefile
+++ b/makefile
-@@ -3,11 +3,10 @@ KMC_MAIN_DIR = kmer_counter
- KMC_API_DIR = kmc_api
+@@ -6,14 +6,11 @@
KMC_DUMP_DIR = kmc_dump
+ KMC_TOOLS_DIR = kmc_tools
--CC = g++
--CFLAGS += -Wall -O3 -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
--CLINK = -lm -lz -lbz2 -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
+-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
-
--DISABLE_ASMLIB = true
+-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
+CXX := g++
+CXXFLAGS += -Wall -O3 -fopenmp -std=c++11
++CXXFLAGS_TOOLS := $(CXXFLAGS) -Wall -O3 -fopenmp -std=c++14
+LDFLAGS += -lm -lz -lbz2 -fopenmp -lpthread
+CPPFLAGS += -DDISABLE_ASMLIB
KMC_OBJS = \
$(KMC_MAIN_DIR)/kmer_counter.o \
-@@ -33,24 +32,19 @@ $(KMC_DUMP_DIR)/nc_utils.o \
- $(KMC_DUMP_DIR)/kmc_dump.o \
- $(KMC_LIB_OBJS)
+@@ -58,31 +55,21 @@
+
+ KMC_LIB_OBJS = $(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
--endif
-
- all: kmc kmc_dump libkmc.a
+- $(KMC_MAIN_DIR)/libs/alibelf64.a
+- KMC_TOOLS_LIBS += \
+- $(KMC_TOOLS_DIR)/libs/alibelf64.a
+-endif
+-
+ all: kmc kmc_dump kmc_tools libkmc.a
- .cpp.o:
+ $(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
- $(CC) $(CPPFLAGS) $(CFLAGS) -c $< -o $@
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
+ $(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) -o $(KMC_BIN_DIR)/$@ $^
-+
- kmc_dump: $(KMC_DUMP_OBJS)
++ $(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) -o $(KMC_BIN_DIR)/$@ $^
++ $(CXX) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
- libkmc.a: $(KMC_LIB_OBJS)
+ 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
diff --git a/debian/patches/disable-asmlib b/debian/patches/disable-asmlib
index 109352f..f674f91 100644
--- a/debian/patches/disable-asmlib
+++ b/debian/patches/disable-asmlib
@@ -6,38 +6,21 @@ Subject: disable-asmlib
makefile | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
-diff --git a/makefile b/makefile
-index 8488f72..2858043 100644
--- a/makefile
+++ b/makefile
-@@ -1,15 +1,15 @@
- all: kmc
--
-+
- KMC_BIN_DIR = bin
- KMC_MAIN_DIR = kmer_counter
- KMC_API_DIR = kmc_api
- KMC_DUMP_DIR = kmc_dump
-
- 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
+@@ -13,7 +13,7 @@
+ 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 = false
-+DISABLE_ASMLIB = true
++DISABLE_ASMLIB = true
KMC_OBJS = \
$(KMC_MAIN_DIR)/kmer_counter.o \
-@@ -42,8 +42,8 @@ ifeq ($(DISABLE_ASMLIB),true)
- CFLAGS += -DDISABLE_ASMLIB
- else
- KMC_LIBS += \
-- $(KMC_MAIN_DIR)/libs/alibelf64.a
--endif
-+ $(KMC_MAIN_DIR)/libs/alibelf64.a
-+endif
-
+@@ -95,4 +95,4 @@
+ -rm $(KMC_TOOLS_DIR)/*.o
+ -rm -rf bin
- .cpp.o:
+-all: kmc kmc_dump kmc_tools
+\ No newline at end of file
++all: kmc kmc_dump kmc_tools
diff --git a/debian/patches/hardening b/debian/patches/hardening
index c5f6f6c..bf46e1b 100644
--- a/debian/patches/hardening
+++ b/debian/patches/hardening
@@ -6,36 +6,33 @@ Subject: hardening
makefile | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
-diff --git a/makefile b/makefile
-index 71dd3b2..3e2edc9 100644
--- a/makefile
+++ b/makefile
-@@ -5,8 +5,8 @@ KMC_MAIN_DIR = kmer_counter
- KMC_API_DIR = kmc_api
- KMC_DUMP_DIR = kmc_dump
+@@ -67,22 +67,21 @@
+ endif
--CC = g++
--CFLAGS = -Wall -O3 -m64 -static -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
-+CC = g++
-+CFLAGS += -Wall -O3 -fopenmp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
- CLINK = -lm -lz -lbz2 -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
-
- DISABLE_ASMLIB = true
-@@ -40,14 +40,14 @@ else
- endif
-
- .cpp.o:
+ $(KMC_OBJS) $(KMC_DUMP_OBJS) $(KMC_API_OBJS): %.o: %.cpp
- $(CC) $(CFLAGS) -c $< -o $@
+ $(CC) $(CPPFLAGS) $(CFLAGS) -c $< -o $@
+ $(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 $(KMC_BIN_DIR)/$@ $^
+ $(CC) $(LDFLAGS) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
- kmc_dump: $(KMC_DUMP_OBJS)
+ 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)
+
clean:
- -rm -f $(KMC_MAIN_DIR)/*.o
- -rm -f $(KMC_API_DIR)/*.o
+ -rm $(KMC_MAIN_DIR)/*.o
diff --git a/debian/patches/series b/debian/patches/series
index ec6ced3..b9ba394 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,7 +1,5 @@
disable-asmlib
use-shared-libs
-allow-dry-clean
hardening
0005-Add-static-library-target-to-makefile.patch
-0006-Fix-wildcard-to-define-libkmc-objects.patch
0007-Use-standard-compiler-environment-variables.patch
diff --git a/debian/patches/use-shared-libs b/debian/patches/use-shared-libs
index 7d980b2..c43c6eb 100644
--- a/debian/patches/use-shared-libs
+++ b/debian/patches/use-shared-libs
@@ -7,8 +7,6 @@ Subject: use-shared-libs
makefile | 8 ++------
2 files changed, 6 insertions(+), 10 deletions(-)
-diff --git a/kmer_counter/fastq_reader.h b/kmer_counter/fastq_reader.h
-index 5132d23..bad1243 100644
--- a/kmer_counter/fastq_reader.h
+++ b/kmer_counter/fastq_reader.h
@@ -16,8 +16,8 @@
@@ -22,7 +20,7 @@ index 5132d23..bad1243 100644
using namespace std;
-@@ -42,10 +42,10 @@ class CFastqReader {
+@@ -42,10 +42,10 @@
int bzerror;
uint64 part_size;
@@ -35,22 +33,11 @@ index 5132d23..bad1243 100644
uint32 gzip_buffer_size;
uint32 bzip2_buffer_size;
-diff --git a/makefile b/makefile
-index 2858043..0706eb3 100644
--- a/makefile
+++ b/makefile
-@@ -7,7 +7,7 @@ KMC_DUMP_DIR = kmc_dump
-
- 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
-+CLINK = -lm -lz -lbz2 -fopenmp -O3 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=c++11
-
- DISABLE_ASMLIB = true
-
-@@ -25,10 +25,6 @@ $(KMC_MAIN_DIR)/kb_completer.o \
- $(KMC_MAIN_DIR)/kb_storer.o \
- $(KMC_MAIN_DIR)/kmer.o
+@@ -30,10 +30,6 @@
+ $(KMC_MAIN_DIR)/kmer.o \
+ $(KMC_MAIN_DIR)/prob_qual.o
-KMC_LIBS = \
-$(KMC_MAIN_DIR)/libs/libz.a \
@@ -59,12 +46,12 @@ index 2858043..0706eb3 100644
KMC_DUMP_OBJS = \
$(KMC_DUMP_DIR)/nc_utils.o \
$(KMC_API_DIR)/mmer.o \
-@@ -51,7 +47,7 @@ endif
-
+@@ -79,7 +75,7 @@
+
kmc: $(KMC_OBJS)
-mkdir -p $(KMC_BIN_DIR)
- $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^ $(KMC_LIBS)
+ $(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
- kmc_dump: $(KMC_DUMP_OBJS)
+ kmc_dump: $(KMC_DUMP_OBJS) $(KMC_API_OBJS)
-mkdir -p $(KMC_BIN_DIR)
$(CC) $(CLINK) -o $(KMC_BIN_DIR)/$@ $^
--
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