From ff1252fe3db1ba639fe148f45b0408a4f182da0d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 14 Aug 2017 07:43:07 +0000
Subject: Tests and fixes
 https://github.com/genetics-statistics/GEMMA/issues/26

---
 Makefile | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

(limited to 'Makefile')

diff --git a/Makefile b/Makefile
index 1983148..875573c 100644
--- a/Makefile
+++ b/Makefile
@@ -16,7 +16,9 @@ WITH_OPENBLAS   =
 NO_INTEL_COMPAT =
 FORCE_32BIT     =
 FORCE_DYNAMIC   =
+GCC_FLAGS       = -O3 # extra flags -Wl,--allow-multiple-definition
 DIST_NAME       = gemma-0.97.1
+TRAVIS_CI       =
 
 # --------------------------------------------------------------------
 # Edit below this line with caution
@@ -36,11 +38,10 @@ else
 endif
 
 ifdef DEBUG
-  # development mode
-  CPPFLAGS = -g -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
+  CPPFLAGS = -g $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
 else
-  # release
-  CPPFLAGS = -DNDEBUG -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
+  # release mode
+  CPPFLAGS = -DNDEBUG $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
 endif
 
 ifdef SHOW_COMPILER_WARNINGS
@@ -50,7 +51,9 @@ endif
 ifdef FORCE_DYNAMIC
   LIBS = -lgsl -lgslcblas -pthread -lz
 else
-  LIBS = -lgsl -lgslcblas -pthread -lz
+  ifndef TRAVIS_CI # Travis static compile we cheat a little
+    CPPFLAGS += -static
+  endif
 endif
 
 OUTPUT = $(BIN_DIR)/gemma
@@ -65,8 +68,10 @@ LIBS_LNX_D_LAPACK = -llapack
 LIBS_LNX_D_BLAS = -lblas
 LIBS_LNX_D_OPENBLAS = -lopenblas
 LIBS_MAC_D_LAPACK = -framework Veclib
+# LIBS_LNX_S_LAPACK = /usr/lib/libgsl.a  /usr/lib/libgslcblas.a /usr/lib/lapack/liblapack.a -lz
 LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran  /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition
 
+
 SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp $(SRC_DIR)/ldr.cpp $(SRC_DIR)/bslmmdap.cpp $(SRC_DIR)/logistic.cpp $(SRC_DIR)/varcov.cpp
 HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
 
@@ -82,6 +87,8 @@ else
       LIBS += $(LIBS_LNX_D_BLAS)
     endif
     LIBS += $(LIBS_LNX_D_LAPACK)
+  else
+    LIBS += $(LIBS_LNX_S_LAPACK)
   endif
 endif
   SOURCES += $(SRC_DIR)/lapack.cpp
@@ -97,11 +104,6 @@ ifdef NO_INTEL_COMPAT
   endif
 endif
 
-ifdef FORCE_DYNAMIC
-else
-  CPPFLAGS += -static
-endif
-
 # all
 OBJS = $(SOURCES:.cpp=.o)
 
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