Merge pull request #28 from mklarqvist/dev

Fix build for OSX-based machines.

.travis.yml

@@ -1,6 +1,7 @@
 # Control file for continuous integration testing at http://travis-ci.org/
 language: cpp
 dist: trusty
+
 matrix:
   include:
     # works on Precise and Trusty
@@ -20,7 +21,7 @@ matrix:
             - libcurl4-openssl-dev 
             - liblz-dev
             - libbz2-dev
-- liblzma-dev
+            - liblzma-dev
       env:
          - MATRIX_EVAL="CC=gcc-4.9 && CXX=g++-4.9"
       compiler: gcc
@@ -66,6 +67,50 @@ matrix:
       env:
         - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6"
       compiler: gcc
+
+    # works on Precise and Trusty
+    - os: linux
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-7
+            - pkg-config
+            - libncurses5-dev
+            - libncursesw5-dev
+            - zlib1g-dev 
+            - libssl-dev
+            - liblz4-dev
+            - libcurl4-openssl-dev 
+            - liblz-dev
+            - libbz2-dev
+            - liblzma-dev
+      env:
+        - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+      compiler: gcc
+
+    # works on Precise and Trusty
+    - os: linux
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+          packages:
+            - g++-8
+            - pkg-config
+            - libncurses5-dev
+            - libncursesw5-dev
+            - zlib1g-dev 
+            - libssl-dev
+            - liblz4-dev
+            - libcurl4-openssl-dev 
+            - liblz-dev
+            - libbz2-dev
+            - liblzma-dev
+      env:
+        - MATRIX_EVAL="CC=gcc-8 && CXX=g++-8"
+      compiler: gcc
 
     # works on Precise and Trusty
     - os: linux
@@ -196,26 +241,74 @@ matrix:
         - MATRIX_EVAL="CC=clang-5.0 && CXX=clang++-5.0"
       compiler: clang
 
+    # works on Trusty
+    - os: linux
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+            - llvm-toolchain-trusty-6.0
+          packages:
+            - clang-6.0
+            - libstdc++-6-dev
+            - pkg-config
+            - libncurses5-dev
+            - libncursesw5-dev
+            - zlib1g-dev 
+            - libssl-dev
+            - liblz4-dev
+            - libcurl4-openssl-dev 
+            - liblz-dev
+            - libbz2-dev
+            - liblzma-dev
+      env:
+        - MATRIX_EVAL="CC=clang-6.0 && CXX=clang++-6.0"
+      compiler: clang
+
+    # works on Trusty
+    - os: linux
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test
+            - llvm-toolchain-trusty-7
+          packages:
+            - clang-7
+            - libstdc++-7-dev
+            - pkg-config
+            - libncurses5-dev
+            - libncursesw5-dev
+            - zlib1g-dev 
+            - libssl-dev
+            - liblz4-dev
+            - libcurl4-openssl-dev 
+            - liblz-dev
+            - libbz2-dev
+            - liblzma-dev
+      env:
+        - MATRIX_EVAL="CC=clang-7 && CXX=clang++-7"
+      compiler: clang
+
     # OSX begin
     - os: osx
-      osx_image: xcode8
+      osx_image: xcode10
       env:
-        - MATRIX_EVAL="CC=gcc-4.9 && CXX=g++-4.9"
+        - MATRIX_EVAL="brew update && brew install gcc@5 && CC=gcc-5 && CXX=g++-5"
 
     - os: osx
-      osx_image: xcode8
+      osx_image: xcode10
       env:
-        - MATRIX_EVAL="brew update && brew install gcc5 && CC=gcc-5 && CXX=g++-5"
+        - MATRIX_EVAL="brew update && brew install gcc@6 && CC=gcc-6 && CXX=g++-6"
 
     - os: osx
-      osx_image: xcode8
+      osx_image: xcode10
       env:
-        - MATRIX_EVAL="brew update && brew install gcc6 && CC=gcc-6 && CXX=g++-6"
+        - MATRIX_EVAL="brew update && brew install gcc@7 && CC=gcc-7 && CXX=g++-7"
 
     - os: osx
-      osx_image: xcode8
+      osx_image: xcode10
       env:
-        - MATRIX_EVAL="brew update && brew install gcc && CC=gcc-7 && CXX=g++-7"
+        - MATRIX_EVAL="brew update && brew install gcc@8 && CC=gcc-8 && CXX=g++-8"
 
 
 before_install:
@@ -227,5 +320,5 @@ before_install:
 
 script:
   - git submodule update --recursive
-  - make -j4
-
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then make -j 4 2>/dev/null; fi
+  - if [[ "$TRAVIS_OS_NAME" != "osx" ]]; then make -j 4; fi

lib/aggregation.h

@@ -38,7 +38,7 @@ struct twk_agg_slave {
 
 		if(stream.good()) stream.close();
 
-		stream = std::ifstream(filename,std::ios::binary | std::ios::in);
+		stream.open(filename,std::ios::binary | std::ios::in);
 		if(stream.good() == false){
 			std::cerr << utility::timestamp("ERROR","THREAD") << "Failed to open \"" << filename << "\"..." << std::endl;
 			return nullptr;
@@ -94,7 +94,7 @@ struct twk_agg_slave {
 
 		if(stream.good()) stream.close();
 
-		stream = std::ifstream(filename,std::ios::binary | std::ios::in);
+		stream.open(filename,std::ios::binary | std::ios::in);
 		if(stream.good() == false){
 			std::cerr << utility::timestamp("ERROR","THREAD") << "Failed to open \"" << filename << "\"..." << std::endl;
 			return nullptr;

lib/importer.cpp

@@ -1,6 +1,5 @@
 #include "importer.h"
 
-#include <omp.h>
 #include <thread>
 
 #include "zstd.h"

lib/two_sorter_structs.cpp

@@ -8,7 +8,7 @@ std::thread* twk_sort_slave::Start(IndexOutput& rdr){
 	if(t - f == 0) return nullptr;
 	//delete thread;
 
-	stream = std::ifstream(filename,std::ios::binary | std::ios::in);
+	stream.open(filename,std::ios::binary | std::ios::in);
 	if(stream.good() == false){
 		std::cerr << utility::timestamp("ERROR","THREAD") << "Failed to open \"" << filename << "\"..." << std::endl;
 		return nullptr;
@@ -25,7 +25,7 @@ std::thread* twk_sort_slave::Start(IndexOutput& rdr){
 	blk->resize((m_limit*1e9)/sizeof(twk1_two_t));
 	it->stream = &stream;
 
-	ostream = std::ofstream(tmp_filename, std::ios::binary | std::ios::out);
+	ostream.open(tmp_filename, std::ios::binary | std::ios::out);
 	if(ostream.good() == false){
 		std::cerr << utility::timestamp("ERROR","THREAD") << "Failed to open temp output file \"" << tmp_filename << "\"..." << std::endl;
 		return nullptr;
@@ -191,7 +191,7 @@ bool twk_two_stream_iterator::Open(const std::string file,
 		const uint32_t n_uncompressed,
 		const uint32_t n_compressed)
 {
-	stream = std::ifstream(file, std::ios::binary);
+	stream.open(file, std::ios::binary);
 	if(stream.good() == false){
 		std::cerr << utility::timestamp("ERROR") << "Could not open \"" << file << "\"..." << std::endl;
 		return false;

makefile

@@ -111,18 +111,24 @@ endif
 
 # OS X linker doesn't support -soname, and use different extension
 # see : https://developer.apple.com/library/mac/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html
+# Use LDFLAGS for passing additional flags. Avoid using LD_LIB_FLAGS.
 ifneq ($(shell uname), Darwin)
 SHARED_EXT   = so
-LD_LIB_FLAGS = -shared '-Wl,-rpath-link,$$ORIGIN/,-rpath-link,$(PWD),-rpath-link,$$ORIGIN/zstd/lib,-rpath-link,$$ORIGIN/htslib,-soname,libtomahawk.$(SHARED_EXT)'
+LD_LIB_FLAGS = -shared '-Wl,-rpath-link,$$ORIGIN/,-rpath-link,$(PWD),-rpath-link,$$ORIGIN/zstd/lib,-rpath-link,$$ORIGIN/htslib,-soname,libtomahawk.$(SHARED_EXT)' $(LDFLAGS)
 else
 SHARED_EXT   = dylib
-LD_LIB_FLAGS = -dynamiclib -install_name libtomahawk.$(SHARED_EXT) '-Wl,-rpath-link,$$ORIGIN/,-rpath-link,$(PWD),-rpath-link,$$ORIGIN/zstd/lib,-rpath-link,$$ORIGIN/htslib'
+LD_LIB_FLAGS = -dynamiclib -install_name "@rpath/libtomahawk.$(SHARED_EXT)" '-Wl,-rpath,@loader_path/,-rpath,$(PWD),-rpath,@loader_path/zstd/lib,-rpath,@loader_path/htslib' $(LDFLAGS) 
 endif
 
 CXXFLAGS      = -std=c++0x $(OPTFLAGS) $(DEBUG_FLAGS)
 CFLAGS        = -std=c99   $(OPTFLAGS) $(DEBUG_FLAGS)
 CFLAGS_VENDOR = -std=c99   $(OPTFLAGS)
+
+ifneq ($(shell uname), Darwin)
 BINARY_RPATHS = '-Wl,-rpath,$$ORIGIN/,-rpath,$(PWD),-rpath,$$ORIGIN/zstd/lib,-rpath,$$ORIGIN/htslib'
+else
+BINARY_RPATHS = '-Wl,-rpath,@loader_path/,-rpath,$(PWD),-rpath,@loader_path/zstd/lib,-rpath,@loader_path/htslib'
+endif
 
 LIBS := -lzstd -lhts
 CXX_SOURCE = $(wildcard lib/*.cpp) \
@@ -146,23 +152,27 @@ all: tomahawk
 
 # Generic rules
 %.o: %.cpp
-	g++ $(CXXFLAGS) $(INCLUDE_PATH) -c -DVERSION=\"$(GIT_VERSION)\" -o $@ $<
+	$(CXX) $(CXXFLAGS) $(INCLUDE_PATH) -c -DVERSION=\"$(GIT_VERSION)\" -o $@ $<
 
 tomahawk: $(OBJECTS)
-	g++ $(BINARY_RPATHS) $(LIBRARY_PATHS) -pthread $(OBJECTS) $(LIBS) -o tomahawk
+	$(CXX) $(BINARY_RPATHS) $(LIBRARY_PATHS) -pthread $(OBJECTS) $(LIBS) -o tomahawk
 	$(MAKE) cleanmost
 	$(MAKE) library library=true
 
 library: $(OBJECTS)
 	@echo 'Building dynamic library...'
-	g++ $(LD_LIB_FLAGS) $(LIBRARY_PATHS) -pthread $(OBJECTS) $(LIBS) -o libtomahawk.$(SHARED_EXT).$(LIBVER)
+	$(CXX) $(LD_LIB_FLAGS) $(LIBRARY_PATHS) -pthread $(OBJECTS) $(LIBS) -o libtomahawk.$(SHARED_EXT).$(LIBVER)
 	@echo 'Building static library...'
-	ar crs libtomahawk.a $(OBJECTS)
+	$(AR) crs libtomahawk.a $(OBJECTS)
 	@echo 'Symlinking library...'
 	ln -sf libtomahawk.$(SHARED_EXT).$(LIBVER) libtomahawk.$(SHARED_EXT)
 	ln -sf libtomahawk.$(SHARED_EXT).$(LIBVER) ltomahawk.$(SHARED_EXT)
 
-install: $(PROGRAMS)
+install_deps:
+	@$(MAKE) tomahawk
+	@$(MAKE) library library=true
+
+install: install_deps
 	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir)/tomahawk $(DESTDIR)$(libdir)
 	$(INSTALL_DATA) include/*.h $(DESTDIR)$(includedir)/tomahawk
 	$(INSTALL_PROGRAM) tomahawk $(DESTDIR)$(bindir)
@@ -177,6 +187,6 @@ cleanmost:
 	rm -f $(OBJECTS) $(CPP_DEPS)
 
 clean: cleanmost clean_examples
-	rm -f tomahawk libtomahawk.so libtomahawk.so.* ltomahawk.so libtomahawk.a
+	rm -f tomahawk libtomahawk.so libtomahawk.so.* ltomahawk.so libtomahawk.a libtomahawk.dylib* ltomahawk.dylib
 
-.PHONY: all clean clean_examples cleanmost library install
+.PHONY: all clean clean_examples cleanmost library install install_deps