RNAblueprint 1.2.2

ViennaRNA · Jan 18, 2019 · 3412c82 · 3412c82
1 parent ad94317
commit 3412c82
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Showing 7 changed files with 21 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -31,7 +31,6 @@ Please cite the software as specified at the bottom of the page!
  * Doxygen for documentation
  * LaTeX for PDF documentation
  * libGMP for multiprecision integers
- * openmp for parallel computation
  * Boost Unit Test Framework
 
 ## Installation
@@ -55,7 +54,6 @@ In case of a local installation, please do not forget to adopt your path variabl
     --disable-program  Disable RNAblueprint program compilation
     --disable-swig Disable all SWIG scripting interfaces
     --enable-libGMP Enable the calculation of big numbers with multiprecision
-    --disable-openmp Disable the usage of parallel computation
 
 TIP: You might want call `./configure --help` for all install options!
 

diff --git a/configure.ac b/configure.ac
@@ -1,7 +1,11 @@
 # RNAblueprint: configure.ac
 
 # initial information about the project
+<<<<<<< HEAD
 AC_INIT([RNAblueprint],[1.2.1],[s.hammer@univie.ac.at],[RNAblueprint],[http://www.tbi.univie.ac.at/~jango/])
+=======
+AC_INIT([RNAblueprint],[1.2.2],[s.hammer@univie.ac.at],[RNAblueprint],[https://github.com/ViennaRNA/RNAblueprint])
+>>>>>>> develop
 
 # automake initialisation (mandatory)
 AC_PREREQ([2.59])
@@ -107,8 +111,8 @@ fi
 
 # Check for OpenMP enabled and prepare flags
 ##########################################################################
-AC_OPENMP
-AC_SUBST(OPENMP_CXXFLAGS)
+#AC_OPENMP
+#AC_SUBST(OPENMP_CXXFLAGS)
 
 # Checks for libraries: gmp enabled?
 ##########################################################################
@@ -249,6 +253,13 @@ AM_COND_IF([ENABLE_SWIG], [
 AM_CONDITIONAL([ENABLE_PYTHON],[test "x$enable_python_status" = x"yes"])
 AM_CONDITIONAL([ENABLE_PERL5],[test "x$enable_perl_status" = x"yes"])
 
+# Configure supported platforms
+##########################################################################
+case $host in
+  *-apple-darwin*)
+    AC_DEFINE([OSX], [], [Define if building on Apple OSX.]) ;;
+esac
+
 # distribute additional compiler and linker flags
 # set these variables instead of CXXFLAGS or LDFLAGS
 ##########################################################################

diff --git a/lib/Makefile.am b/lib/Makefile.am
@@ -7,10 +7,10 @@ lib_LTLIBRARIES = libRNAblueprint.la
 libRNAblueprint_ladir = $(includedir)/RNAblueprint
 
 # ldflags to avoid version information
-libRNAblueprint_la_LDFLAGS = -avoid-version $(OPENMP_CXXFLAGS)
+libRNAblueprint_la_LDFLAGS = -avoid-version
 
 # additional include pathes necessary to compile the C++ library
-AM_CPPFLAGS = $(BOOST_CPPFLAGS) $(OPENMP_CXXFLAGS) @AM_CXXFLAGS@
+AM_CPPFLAGS = $(BOOST_CPPFLAGS) @AM_CXXFLAGS@
 
 # the list of header files that belong to the library
 libRNAblueprint_la_HEADERS = \

diff --git a/lib/RNAblueprint.h b/lib/RNAblueprint.h
@@ -40,7 +40,6 @@
  * - Doxygen for documentation
  * - LaTeX for PDF documentation
  * - libGMP for multiprecision integers
- * - openmp for parallel computation
  * - Boost Unit Test Framework
  *
  * \section install_sec Installation
@@ -61,7 +60,6 @@
  * - \-\-disable-program  Disable RNAblueprint program compilation
  * - \-\-disable-swig     Disable all SWIG scripting interfaces
  * - \-\-enable-libGMP    Enable the calculation of big numbers with multiprecision
- * - \-\-disable-openmp   Disable the usage of parallel computation
  * 
  * TIP: You might want call `./configure --help` for all install options!
  * 

diff --git a/src/Makefile.am b/src/Makefile.am
@@ -6,7 +6,11 @@ bin_PROGRAMS = RNAblueprint
 
 # additional include pathes necessary to compile the C++ programs
 RNAblueprint_CPPFLAGS = -I$(top_srcdir)/lib $(BOOST_CPPFLAGS) @AM_CXXFLAGS@
+<<<<<<< HEAD
 RNAblueprint_LDFLAGS =$(LDFLAGS) $(BOOST_GRAPH_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS)
+=======
+RNAblueprint_LDFLAGS = $(LDFLAGS) $(BOOST_GRAPH_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS)
+>>>>>>> develop
 RNAblueprint_LDADD = $(LDADD) $(top_builddir)/lib/libRNAblueprint.la $(BOOST_GRAPH_LIBS) $(BOOST_PROGRAM_OPTIONS_LIBS) $(AM_LDFLAGS)
 
 # list of sources for the 'RNAblueprint' binary

diff --git a/tests/Makefile.am b/tests/Makefile.am
@@ -6,7 +6,7 @@ check_PROGRAMS = testRNAblueprint
 
 # additional include pathes necessary to compile the C++ programs
 testRNAblueprint_CPPFLAGS = -I$(top_srcdir)/lib $(BOOST_CPPFLAGS) @AM_CXXFLAGS@
-testRNAblueprint_LDFLAGS = $(BOOST_GRAPH_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS)
+testRNAblueprint_LDFLAGS = $(LDFLAGS) $(BOOST_GRAPH_LDFLAGS) $(BOOST_UNIT_TEST_FRAMEWORK_LDFLAGS)
 testRNAblueprint_LDADD = $(LDADD) $(top_builddir)/lib/libRNAblueprint.la $(BOOST_GRAPH_LIBS) $(BOOST_UNIT_TEST_FRAMEWORK_LIBS) $(AM_LDFLAGS)
 
 # list of sources for the 'testRNAblueprint' binary

diff --git a/tests/test_decompose.cc b/tests/test_decompose.cc
@@ -13,7 +13,7 @@
 #include "test_common.h"
 
 // include headers containing functions to test
-#include "decompose.h"
+#include "decompose.cc"
 #include "printgraph.h"
 
 // include boost components