Rename stadenio module - now it links against Ruby

doc/wikitex/MAPPING_TRICKS.tex

@@ -21,6 +21,18 @@
 
 rm CMakeCache.txt ; cmake .
 
+=== Naming modules ===
+
+The way BioLib uses CMake and SWIG depends on a strict naming
+convention of modules. There is no freedom. The location of C sources
+for a C library with name 'module' and version 1.0 is in:
+
+  ./src/clibs/module-1.0
+
+The Ruby mapping module is in:
+
+  ./src/bindings/swig/ruby/module
+
 === Debugging CMake ===
 
 CMake can be run at any level in the tree. Start from the
@@ -60,6 +72,17 @@
 	cmake .
 	make
 
+It may also be necessary to remove the shared libraries installed in
+your Ruby/Perl/Python etc. tree. Unfortunately, because of naming
+conventions, it is hard to version those, so make sure they don't link
+in by accident. Typically:
+
+  rm /usr/lib/ruby/1.8/i486-linux/biolib/example.so
+
+or
+
+	rm /usr/lib/ruby/1.8/i486-linux/biolib/*
+
 As a convention the shared libraries are built in
 ./src/clibs/module-1.0/build, so the mapper can find them easily. E.g.
 
@@ -100,3 +123,16 @@
 there will be a mismatch between the names in
 ./src/clibs/module-version and the build/libmodule-version.so names.
 
+=== undefined symbol Init_module ===
+
+A message like:
+
+  ../stadenio/staden_io_lib.so: ../stadenio/staden_io_lib.so: undefined symbol: Init_staden_io_lib - ../stadenio/staden_io_lib.so (LoadError)
+
+indicates another naming problem. A grep in the module gives:
+
+  ruby_staden_io_libRUBY_wrap.cxx:#define SWIG_init    Init_stadenio
+
+which shows the Init function naming does not match the module
+(stadenio rather than staden_io_lib).
+

src/bindings/swig/ruby/CMakeLists.txt

@@ -1,3 +1,3 @@
 add_subdirectory (example)
 add_subdirectory (affyio)
-add_subdirectory (stadenio)
+add_subdirectory (staden_io_lib)

src/bindings/swig/ruby/stadenio/CMakeLists.txt → src/bindings/swig/ruby/staden_io_lib/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Make biolib_ruby_staden-io_lib module
+# Make biolib_ruby_staden_io_lib module
 
 cmake_minimum_required(VERSION 2.6)
 ENABLE_TESTING()
@@ -18,7 +18,7 @@ INCLUDE(CMakeBackwardCompatibilityC)
 
 FIND_PACKAGE(BioLibRuby)
 
-# ADD_TEST(TestRubyAffyio ${RUBY_EXECUTABLE} -I../${M_NAME} ./../test/test_${M_NAME}.rb)
+ADD_TEST(TestRubyAffyio ${RUBY_EXECUTABLE} -I../${M_NAME} ./../test/test_${M_NAME}.rb)
 
 INSTALL(TARGETS ${M_MODULE}
   LIBRARY DESTINATION ${RUBY_LIB_PATH}/biolib

src/bindings/swig/ruby/staden_io_lib/ruby_staden_io_lib.i

@@ -0,0 +1,3 @@
+%module staden_io_lib
+
+%include ../../staden_io_lib.i

src/bindings/swig/ruby/test/test_staden_io_lib.rb

@@ -0,0 +1,6 @@
+
+require 'staden_io_lib'
+
+# result = Biolib::Example.my_mod(7,3)
+# print "Biolib::Example.my_mod(7,3) renders #{result}\n"
+exit 0