[Genabel-commits] r1036 - in pkg/ProbABEL: . src

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

Author: lckarssen
Date: 2012-11-29 11:40:25 +0100 (Thu, 29 Nov 2012)
New Revision: 1036

Modified:
   pkg/ProbABEL/configure.ac
   pkg/ProbABEL/src/Makefile.am
Log:
Fixed bug in ProbABEL: the --disable-eigen ./configure option didn't work. It turns out that in src/Makefile.am the eigen_mematrix.* files were put in as dependencies by default. Now these files are excluded if the --disable-eigen option is used. 

The copyright for this change is with the Erasmus MC, Rotterdam.


Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac	2012-11-29 09:27:29 UTC (rev 1035)
+++ pkg/ProbABEL/configure.ac	2012-11-29 10:40:25 UTC (rev 1036)
@@ -52,8 +52,8 @@
     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${withval} -DEIGEN"],
-	[CXXFLAGS+=' -I/usr/include/eigen3 -DEIGEN'
+	[CXXFLAGS+=" -I${withval}"],
+	[CXXFLAGS+=' -I/usr/include/eigen3'
 	CPPFLAGS+=' -I/usr/include/eigen3'])
     dnl AC_SUBST([EIGEN_CFLAGS])
 

Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am	2012-11-29 09:27:29 UTC (rev 1035)
+++ pkg/ProbABEL/src/Makefile.am	2012-11-29 10:40:25 UTC (rev 1036)
@@ -7,9 +7,10 @@
  command_line_settings.h command_line_settings.cpp reg1.h usage.h		\
  usage.cpp main.cpp utilities.h utilities.cpp phedata.h phedata.cpp	\
  cholesky.h cholesky.cpp regdata.h regdata.cpp 	\
- maskedmatrix.cpp maskedmatrix.h eigen_mematrix.h 	\
- eigen_mematrix.cpp reg1.cpp
+ maskedmatrix.cpp maskedmatrix.h reg1.cpp
 
+EIGENFILES = eigen_mematrix.h eigen_mematrix.cpp
+
 ## Filevector files:
 FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp			\
  fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp	\
@@ -41,16 +42,28 @@
 palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
 palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS)
 palinear_CPPFLAGS = $(AM_CPPFLAGS)
+if WITH_EIGEN
+palinear_SOURCES += $(EIGENFILES)
+palinear_CXXFLAGS += -DEIGEN
+endif
 
 palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
 palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS)
 palogist_CPPFLAGS = $(AM_CPPFLAGS)
+if WITH_EIGEN
+palogist_SOURCES += $(EIGENFILES)
+palogist_CXXFLAGS += -DEIGEN
+endif
 
 pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS)	\
  $(RHEADERS) survS.h survproto.h coxph_data.h coxph_data.cpp
 pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
 pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
 pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
+if WITH_EIGEN
+pacoxph_SOURCES += $(EIGENFILES)
+pacoxph_CXXFLAGS += -DEIGEN
+endif
 
 extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
 
@@ -63,6 +76,6 @@
 ## Insert the correct values of several variables in the installed probabel.pl
 install-exec-hook:
 	$(SED) -i "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
-		 $(DESTDIR)$(bindir)/probabel.pl
+		$(DESTDIR)$(bindir)/probabel.pl
 	$(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel.pl
 	$(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel.pl