[Genabel-commits] r1886 - in branches/ProbABEL-v0.4.3-coxfix/ProbABEL: . src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2014-11-07 15:54:30 +0100 (Fri, 07 Nov 2014)
New Revision: 1886

Modified:
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/Makefile.am
Log:
Backported the CPPFLAGS changes in configure.ac from ProbABEL trunk to the 0.4.3 coxfix branch.
Also includes a fix of a CXXFLAGS/CPPFLAGS bug introduced in Makefile.am in r1885.


Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac	2014-11-07 13:46:44 UTC (rev 1885)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac	2014-11-07 14:54:30 UTC (rev 1886)
@@ -25,7 +25,7 @@
 fi
 if test -z "$CPPFLAGS"; then
    # User did not set CPPFLAGS, so we can put in our own defaults
-    CPPFLAGS="-Wall"
+    CPPFLAGS="-Wall -DNDEBUG"
 fi
 # If CXXFLAGS/CPPFLAGS are already set AC_PROG_CXX will not overwrite them
 # with its own defaults
@@ -33,7 +33,7 @@
 
 
 #Tell compiler to build not R version of filevector
-CXXFLAGS+=" -D_NOT_R_FILEVECTOR"
+AC_SUBST(CPPFLAGS, "$CPPFLAGS -D_NOT_R_FILEVECTOR")
 
 
 # Since most of our code is in C++, set that language as the default
@@ -65,10 +65,8 @@
     AC_ARG_WITH([eigen-include-path],
         [AS_HELP_STRING([--with-eigen-include-path],
           [location of the Eigen headers, defaults to /usr/include/eigen3])],
-        [CXXFLAGS+=" -I${withval}"
-        CPPFLAGS+=" -I${withval}"],
-        [CXXFLAGS+=' -I/usr/include/eigen3'
-        CPPFLAGS+=' -I/usr/include/eigen3'])
+        [CPPFLAGS+=" -I${withval}"],
+        [CPPFLAGS+=' -I/usr/include/eigen3'])
 
     # Check for the EIGEN header files
     AC_CHECK_HEADERS([Eigen/Dense Eigen/LU])

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/Makefile.am
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/Makefile.am	2014-11-07 13:46:44 UTC (rev 1885)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/Makefile.am	2014-11-07 14:54:30 UTC (rev 1886)
@@ -55,14 +55,14 @@
 palinear_CPPFLAGS = -DLINEAR $(AM_CPPFLAGS)
 if WITH_EIGEN
 palinear_SOURCES += $(EIGENFILES)
-palinear_CXXFLAGS += -DEIGEN
+palinear_CPPFLAGS += -DEIGEN
 endif
 
 palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
 palogist_CPPFLAGS = -DLOGISTIC $(AM_CPPFLAGS)
 if WITH_EIGEN
 palogist_SOURCES += $(EIGENFILES)
-palogist_CXXFLAGS += -DEIGEN
+palogist_CPPFLAGS += -DEIGEN
 endif
 
 pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS)	\
@@ -72,7 +72,7 @@
 pacoxph_CFLAGS = -I $(top_srcdir)/src/include $(AM_CFLAGS)
 if WITH_EIGEN
 pacoxph_SOURCES += $(EIGENFILES)
-pacoxph_CXXFLAGS += -DEIGEN
+pacoxph_CPPFLAGS += -DEIGEN
 endif
 
 extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)