use libtool to create libraries; fixes to use embedded Torch3 lib

analyzer/Makefile.am

 include $(top_srcdir)/vars.mk
 
-noinst_LIBRARIES = libimmsanalyzer.a
+noinst_LTLIBRARIES = libimmsanalyzer.la
 bin_PROGRAMS = imms-analyzer
 
-libimmsanalyzer_a_SOURCES = \
+libimmsanalyzer_la_SOURCES = \
 	beatkeeper.cc \
 	beatkeeper.h \
 	fftprovider.cc \

analyzer/mfcckeeper.cc

@@ -18,16 +18,15 @@
 */
 #include <sstream>
 
-#include <torch/KMeans.h>
-#include <torch/Random.h>
-#include <torch/EMTrainer.h>
-#include <torch/NLLMeasurer.h>
-#include <torch/MemoryXFile.h>
-#include <torch/Sequence.h>
-#include <torch/MemoryDataSet.h>
-#include <torch/DiagonalGMM.h>
-
-//#include <sqlite++.h>
+// Torch3 headers.
+#include "KMeans.h"
+#include "Random.h"
+#include "EMTrainer.h"
+#include "NLLMeasurer.h"
+#include "MemoryXFile.h"
+#include "Sequence.h"
+#include "MemoryDataSet.h"
+#include "DiagonalGMM.h"
 
 #include "mfcckeeper.h"
 

configure.ac

@@ -21,6 +21,8 @@ AC_INIT([imms-analyzer],[svnversion],[mag@luminal.org])
 
 AM_INIT_AUTOMAKE([foreign])
 
+LT_INIT([disable-shared])
+
 AC_CONFIG_SRCDIR([immscore/immsutil.h])
 
 AC_PREFIX_DEFAULT("/usr")
@@ -221,7 +223,6 @@ AC_SUBST(OPTIONAL)
 
 AC_CONFIG_HEADERS(immsconf.h)
 AC_OUTPUT(
-vars.mk
 Makefile
 ext/Makefile
 ext/torch3/Makefile

ext/torch3/Makefile.am

 include $(top_srcdir)/vars.mk
 
-AM_CXXFLAGS += -ffast-math -malign-double
+AM_CXXFLAGS += -ffast-math
 
 PACKAGES = core distributions gradients matrix kernels
 
-nobase_noinst_LIBRARIES = libtorch.a
+nobase_noinst_LTLIBRARIES = libtorch.la
 
-libtorch_a_SOURCES = \
+libtorch_la_SOURCES = \
 	core/Allocator.cc \
 	core/Bagging.cc \
 	core/Boosting.cc \

immscore/Makefile.am

 include $(top_srcdir)/vars.mk
 
-noinst_LIBRARIES = libimmscore.a
+noinst_LTLIBRARIES = libimmscore.la
 
-libimmscore_a_SOURCES = \
+libimmscore_la_SOURCES = \
 	appname.h \
 	base64.cc \
 	base64.h \

model/Makefile.am

 include $(top_srcdir)/vars.mk
 
-lib_LIBRARIES = libimmsmodel.a
+AM_CPPFLAGS += -DWITH_TORCH
 
-libimmsmodel_a_SOURCES = \
+lib_LTLIBRARIES = libimmsmodel.la
+
+libimmsmodel_la_SOURCES = \
 	cint.cc \
 	cint.h \
 	distance.cc \
@@ -12,5 +14,5 @@ libimmsmodel_a_SOURCES = \
 	model.cc \
 	model.h
 
-libimmsmodel_a_LIBADD = $(ANALYZER_LIB) $(IMMSCORE_LIB) $(TORCH_LIB)
+libimmsmodel_la_LIBADD = $(ANALYZER_LIB) $(IMMSCORE_LIB) $(TORCH_LIB)
 

model/model.cc

@@ -19,17 +19,17 @@
 #include "immsconf.h"
 
 #ifdef WITH_TORCH
-#include "torch/ConnectedMachine.h"
-#include "torch/XFile.h"
-#include "torch/DiskXFile.h"
-#include "torch/MemoryXFile.h"
-#include "torch/Linear.h"
-#include "torch/LogSoftMax.h"
-#include "torch/MeanVarNorm.h"
-#include "torch/MemoryDataSet.h"
-#include "torch/OneHotClassFormat.h"
-#include "torch/SVMClassification.h"
-#include "torch/Tanh.h"
+#include "ConnectedMachine.h"
+#include "XFile.h"
+#include "DiskXFile.h"
+#include "MemoryXFile.h"
+#include "Linear.h"
+#include "LogSoftMax.h"
+#include "MeanVarNorm.h"
+#include "MemoryDataSet.h"
+#include "OneHotClassFormat.h"
+#include "SVMClassification.h"
+#include "Tanh.h"
 #endif  // WITH_TORCH
 
 #include <iostream>

vars.mk.in → vars.mk

 
-TORCH_LIB = $(top_builddir)/ext/torch3/libtorch.a
-IMMSCORE_LIB = $(top_builddir)/immscore/libimmscore.a
-ANALYZER_LIB = $(top_builddir)/analyzer/libimmsanalyzer.a
+TORCH_LIB = $(top_builddir)/ext/torch3/libtorch.la
+IMMSCORE_LIB = $(top_builddir)/immscore/libimmscore.la
+ANALYZER_LIB = $(top_builddir)/analyzer/libimmsanalyzer.la
 
 INCLUDES = \
 	-I$(top_srcdir)/ext/torch3/core \
 	-I$(top_srcdir)/ext/torch3/distributions \
 	-I$(top_srcdir)/ext/torch3/gradients \
-	-I$(top_srcdir)/ext/torch3/kernel \
+	-I$(top_srcdir)/ext/torch3/kernels \
 	-I$(top_srcdir)/immscore \
 	-I$(top_srcdir)/analyzer