[Genabel-commits] r1694 - in pkg/ProbABEL: . checks/R-tests src

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

Author: lckarssen
Date: 2014-04-23 11:52:41 +0200 (Wed, 23 Apr 2014)
New Revision: 1694

Modified:
   pkg/ProbABEL/checks/R-tests/Makefile.am
   pkg/ProbABEL/configure.ac
   pkg/ProbABEL/src/Makefile.am
Log:
Removed the option to compile ProbABEL without EIGEN from the configure.ac and the Makefile.am files.

Checked that ./configure --with-eigen-include-path= still works.


Modified: pkg/ProbABEL/checks/R-tests/Makefile.am
===================================================================
--- pkg/ProbABEL/checks/R-tests/Makefile.am	2014-04-22 18:06:05 UTC (rev 1693)
+++ pkg/ProbABEL/checks/R-tests/Makefile.am	2014-04-23 09:52:41 UTC (rev 1694)
@@ -30,11 +30,6 @@
 ## The palogist R test still doesn't run correctly.
 XFAIL_TESTS = run_R_test_palogist.sh
 
-## The pacoxph R test fails on SNP 6 when EIGEN is not enabled.
-if !WITH_EIGEN
-XFAIL_TESTS += run_R_test_pacox.sh
-endif
-
 EXTRA_DIST = $(check_SCRIPTS) $(R_test_files)
 
 

Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac	2014-04-22 18:06:05 UTC (rev 1693)
+++ pkg/ProbABEL/configure.ac	2014-04-23 09:52:41 UTC (rev 1694)
@@ -73,40 +73,22 @@
                           stdint.h stdlib.h string.h sys/param.h \
                           wchar.h wctype.h])
 
+# Option that lets the user specify a path to the EIGEN include files.
+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'])
 
-# See if we want use of the Eigen library enabled (yes by default) and if so,
-# whether we can find the library files.
-AC_ARG_WITH([eigen],
- AS_HELP_STRING([--with-eigen], [Use the Eigen template library for fast \
-                                    linear algebra (Eigen can be downloaded \
-                                    from eigen.tuxfamily.org); this is enabled \
-                                    by default]
-               )
-)
+# Check for the EIGEN header files
+AC_CHECK_HEADERS([Eigen/Dense Eigen/LU])
 
-if test "x$with_eigen" != "xno"; then
-    AC_MSG_NOTICE([building using the Eigen headers enabled])
-
-    AC_ARG_WITH([eigen-include-path],
-        [AS_HELP_STRING([--with-eigen-include-path],
-          [location of the Eigen headers, defaults to /usr/include/eigen3])],
-        [CXXFLAGS+=" -I${withval}"
-        CPPFLAGS+=" -I${withval}"],
-        [CXXFLAGS+=' -I/usr/include/eigen3'
-        CPPFLAGS+=' -I/usr/include/eigen3'])
-
-    # Check for the EIGEN header files
-    AC_CHECK_HEADERS([Eigen/Dense Eigen/LU])
-
-    if test x$ac_cv_header_Eigen_Dense = xno; then
-      AC_MSG_ERROR([Could not find the Eigen header files. Did you specify \
---with-eigen-include-path correctly? Or use --without-eigen \
-to disable use of fast linear algebra.])
-    fi
-else
-   AC_MSG_NOTICE([not using Eigen for linear algebra])
+if test x$ac_cv_header_Eigen_Dense = xno; then
+  AC_MSG_ERROR([Could not find the Eigen header files. Did you specify \
+--with-eigen-include-path correctly?])
 fi
-AM_CONDITIONAL([WITH_EIGEN], test "x$with_eigen" != "xno")
 
 
 # Checks for typedefs, structures, and compiler characteristics.

Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am	2014-04-22 18:06:05 UTC (rev 1693)
+++ pkg/ProbABEL/src/Makefile.am	2014-04-23 09:52:41 UTC (rev 1694)
@@ -54,28 +54,22 @@
 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)