Corrected a memory error at pymolfile C++ wrapper

pymolfile/molfile/external/CMakeLists.txt

@@ -4,7 +4,7 @@ include(ExternalProject)
 
 set(TNG_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/tng")
 set(TNG_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/tng")
-set(TNG_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${TNG_INSTALL_DIR})
+set(TNG_CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${TNG_INSTALL_DIR} -DBUILD_SHARED_LIBS=OFF)
 
 message("TNG_PREFIX='${TNG_PREFIX}'")
 message("TNG_INSTALL_DIR='${TNG_INSTALL_DIR}'")

pymolfile/molfile/molfile_plugins/compile/CMakeLists.txt

@@ -2,19 +2,23 @@ cmake_minimum_required(VERSION 2.8.12)
 
 project(molfileplugins)
 
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_BINARY_DIR})
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
 find_package(EXPAT)
 find_package(TCL)
-find_package(NetCDF)
-find_package(NETCDF)
+include (FindNetCDF.cmake)
+set (NETCDF_CXX "YES")
+find_package(NetCDF REQUIRED)
 
-if (EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.dylib"
-    OR EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.so"
-    OR EXISTS "${TNG_INSTALL_DIR}/include/tng/tng_io.h")
-   set(TNGIO_FOUND TRUE)
-   set(TNGIO_LIBRARIES "${TNG_INSTALL_DIR}/lib/")
-   set(TNGIO_INLCUDE_DIRS "${TNG_INSTALL_DIR}/include/")
-endif()
+set(TNG_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/../../external/tng")
+message(TNG_DIR= ${TNG_INSTALL_DIR})
+#if (EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.dylib"
+#    OR EXISTS "${TNG_INSTALL_DIR}/lib/libtng_io.so"
+#    OR EXISTS "${TNG_INSTALL_DIR}/include/tng/tng_io.h")
+set(TNGIO_FOUND TRUE)
+set(TNGIO_LIBRARIES "${TNG_INSTALL_DIR}/lib/libtng_io.a")
+set(TNGIO_LIBRARY_DIRS "${TNG_INSTALL_DIR}/lib/")
+set(TNGIO_INCLUDE_DIRS "${TNG_INSTALL_DIR}/include/")
+#endif()
 
 set(TARGET_ARCH_REGEX "^.*-march[= ]([^ ]+).*$")
 string(REGEX MATCH "${TARGET_ARCH_REGEX}" TARGET_ARCH_MATCH "${CMAKE_C_FLAGS}" "${CMAKE_CXX_FLAGS}")
@@ -50,21 +54,21 @@ endif()
 if(LINUX)
    if(CMAKE_CXX_COMPILER_ID MATCHES "^.*GNU.*$")
       if(ARCH64BIT)
-         set(TARGET_COPT " -fPIC -m64 -o ")
-         set(TARGET_LOPT " -fPIC -m64 -lstdc++ -o ")
-	 set(TARGET_CFLAGS " -m64 -O2 -fPIC -Wall ${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG " -m64 -O2 -fPIC -Wall ${CMAKE_CXX_FLAGS}")
+         set(TARGET_COPT -fPIC;-m64;-o)
+         set(TARGET_LOPT -fPIC;-m64;-lstdc++;-o)
+	 set(TARGET_CFLAGS -m64;-O2;-fPIC;-Wall;${CMAKE_C_FLAGS})
+	 set(TARGET_CXXFLG -m64;-O2;-fPIC;-Wall;${CMAKE_CXX_FLAGS})
       else()
-         set(TARGET_COPT " -fPIC -m32 -o ")
-         set(TARGET_LOPT " -fPIC -m32 -lstdc++ -o ")
-	 set(TARGET_CFLAGS " -m32 -O2 -fPIC -Wall ${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG " -m32 -O2 -fPIC -Wall ${CMAKE_CXX_FLAGS}")
+         set(TARGET_COPT -fPIC;-m32;-o)
+         set(TARGET_LOPT -fPIC;-m32;-lstdc++;-o)
+	 set(TARGET_CFLAGS -m32;-O2;-fPIC;-Wall;${CMAKE_C_FLAGS})
+	 set(TARGET_CXXFLG -m32;-O2;-fPIC;-Wall;${CMAKE_CXX_FLAGS})
       endif()
    else()
-         set(TARGET_COPT " -o ")
-         set(TARGET_LOPT " -o ")
-	 set(TARGET_CFLAGS " -O2 -Wall ${CMAKE_C_FLAGS}")
-	 set(TARGET_CXXFLG " -O2 -Wall ${CMAKE_CXX_FLAGS}")
+         set(TARGET_COPT -o)
+         set(TARGET_LOPT -o)
+	 set(TARGET_CFLAGS -O2;-Wall;${CMAKE_C_FLAGS})
+	 set(TARGET_CXXFLG -O2;-Wall;${CMAKE_CXX_FLAGS})
    endif()
 endif()
 
@@ -77,16 +81,16 @@ if(APPLE)
          set(TARGET_CFLAGS -m64;-Os;-Wall;-fPIC;-dynamic;${CMAKE_C_FLAGS})
          set(TARGET_CXXFLG -m64;-Os;-Wall;-fPIC;-dynamic;${CMAKE_CXX_FLAGS})
       else()
-         set(TARGET_COPT " -fPIC -m32 -o ")
-         set(TARGET_LOPT " -fPIC -m32 -o ")
-         set(TARGET_CFLAGS " -m32 -Os -Wall -fPIC -dynamic ${CMAKE_C_FLAGS}")
-         set(TARGET_CXXFLG " -m32 -Os -Wall -fPIC -dynamic ${CMAKE_CXX_FLAGS}")
+         set(TARGET_COPT -fPIC;-m32;-o)
+         set(TARGET_LOPT -fPIC;-m32;-o)
+         set(TARGET_CFLAGS -m32;-Os;-Wall;-fPIC;-dynamic;${CMAKE_C_FLAGS})
+         set(TARGET_CXXFLG -m32;-Os;-Wall;-fPIC;-dynamic;${CMAKE_CXX_FLAGS})
       endif()
    else()
-      set(TARGET_COPT " -o ")
-      set(TARGET_LOPT " -o ")
-      set(TARGET_CFLAGS " -O2 -Wall ${CMAKE_C_FLAGS}")
-      set(TARGET_CXXFLG " -O2 -Wall ${CMAKE_CXX_FLAGS}")
+      set(TARGET_COPT -o)
+      set(TARGET_LOPT -o)
+      set(TARGET_CFLAGS -O2;-Wall;${CMAKE_C_FLAGS})
+      set(TARGET_CXXFLG -O2;-Wall;${CMAKE_CXX_FLAGS})
    endif()
 endif()
 
@@ -103,25 +107,31 @@ if(UNIX)
       set(TCLINC "-I${TCL_INCLUDE_PATH}")
       set(TCLLIB "-L${TCL_LIBRARY}")
       set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"TCLLDFLAGS=${TCLLDFLAGS}\";\"TCLINC=${TCLINC}\";\"TCLLIB=${TCLLIB}\";)
+      message(TCL_FOUND= ${TCL_LIBRARY})
    endif()
    if(EXPAT_FOUND)
       set(EXPATLDFLAGS ${EXPAT_LIBRARIES})
       set(EXPATINC "-I${EXPAT_INCLUDE_DIRS}")
       set(EXPATLIB "-I${EXPAT_INCLUDE_DIRS}")
       set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"EXPATLDFLAGS=${EXPATLDFLAGS}\";\"EXPATINC=${EXPATINC}\";\"EXPATLIB=${EXPATLIB}\";)
+      message(EXPAT_FOUND= ${EXPAT_LIBRARIES})
    endif()
    if(NETCDF_FOUND)
-      set(NETCDFLDFLAGS ${NETCDF_LIBRARY})
-      set(NETCDFINC "-I${NETCDF_INCLUDE_DIRS}")
-      set(NETCDFLIB "-I${NETCDF_INCLUDE_DIRS}")
+      set(NETCDFLDFLAGS ${NETCDF_LIBRARIES})
+      set(NETCDFINC "-I${NETCDF_INCLUDES}")
+      set(NETCDFLIB "-L${NETCDF_INCLUDES}")
       set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"NETCDFLDFLAGS=${NETCDFLDFLAGS}\";\"NETCDFINC=${NETCDFINC}\";\"NETCDFLIB=${NETCDFLIB}\";)
+      message(NETCDF_FOUND= ${NETCDF_LIBRARIES})
+      message(NETCDF_FOUND= ${NETCDF_INCLUDES})
    endif()
    if(TNGIO_FOUND)
-      set(TNGIOLDFLAGS -ltng_io)
+      set(TNGIOLDFLAGS ${TNGIO_LIBRARIES})
       set(TNGIOINC "-I${TNGIO_INCLUDE_DIRS}")
-      set(TNGIOLIB "-L${TNGIO_LIBRARIES}")
+      set(TNGIOLIB "-L${TNGIO_LIBRARY_DIRS}")
       set(TARGET_MOL_LIBS ${TARGET_MOL_LIBS} \"TNGLDFLAGS=${TNGIOLDFLAGS}\";\"TNGINC=${TNGIOINC}\";\"TNGLIB=${TNGIOLIB}\";)
+      message(TNGIO_FOUND= ${TNGIO_LIBRARIES})
    endif()
+   #   message(MAKE_COMMAND= "make dynlibs staticlibs bins \"ARCH = ${TARGET_ARCH}\" \"COPTO = ${TARGET_COPT} \" \"LOPTO = ${TARGET_LOPT} \" \"CC = ${CMAKE_C_COMPILER} \" \"CXX =     ${CMAKE_CXX_COMPILER} \" \"DEF = ${TARGET_DEF}\" \"CCFLAGS = ${TARGET_CFLAGS} \" \"CXXFLAGS = ${TARGET_CXXFLG} \" \"AR = ${TARGET_AR}\" \"NM = ${TARGET_NM}\" \"RANLIB = ${TARGET_RANLIB}\" \"LIBTOOL = ${TARGET_LIBTOOL} \" ${TARGET_MOL_LIBS}")
    add_custom_command( 
       OUTPUT ${LIB_MOLFILE_FILES}
       COMMAND make dynlibs staticlibs bins \"ARCH = ${TARGET_ARCH}\" \"COPTO = ${TARGET_COPT} \" \"LOPTO = ${TARGET_LOPT} \" \"CC = ${CMAKE_C_COMPILER} \" \"CXX = ${CMAKE_CXX_COMPILER} \" \"DEF = ${TARGET_DEF}\" \"CCFLAGS = ${TARGET_CFLAGS} \" \"CXXFLAGS = ${TARGET_CXXFLG} \" \"AR = ${TARGET_AR}\" \"NM = ${TARGET_NM}\" \"RANLIB = ${TARGET_RANLIB}\" \"LIBTOOL = ${TARGET_LIBTOOL} \" ${TARGET_MOL_LIBS}

pymolfile/molfile/pymolfile.cxx

@@ -201,7 +201,7 @@ PyObject * molfile_plugin_info(PyObject* molcapsule, int plugin_no) {
 PyObject* read_fill_structure(PyObject* molpack, PyObject* prototype)
 {
     //Py_Initialize();
-    //import_array();
+    import_array();
     int options = 0;
     molfile_plugin_t* plugin;
     void* file_handle;