Update to 6.1.3

3 files changed, 283 insertions, 30 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 187c3823789a..a850849dd7a3 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,20 +1,47 @@
-# Generated by mksrcinfo v8
-# Tue Dec  8 12:31:47 UTC 2015
 pkgbase = shogun
-	pkgdesc = Shogun - A Large Scale Machine Learning Toolbox with the python interface
-	pkgver = 4.0.0
-	pkgrel = 2
-	url = http://www.shogun-toolbox.org
-	arch = i686
+	pkgdesc = A Large Scale Machine Learning Toolbox
+	pkgver = 6.1.3
+	pkgrel = 1
+	url = http://shogun.ml/
 	arch = x86_64
-	license = GPLv3
+	license = GPL3
+	makedepends = ctags
+	makedepends = doxygen
+	makedepends = eigen3
+	makedepends = gdb
+	makedepends = opencv
+	makedepends = pandoc
+	makedepends = protobuf
+	makedepends = python-numpy
+	makedepends = python-ply
+	makedepends = python-sphinx
+	makedepends = swig
+	makedepends = rxcpp-git
+	makedepends = viennacl
+	depends = arpack
+	depends = arprec
 	depends = cblas
-	depends = lapack
-	depends = swig-git
-	depends = python-numpy
-	depends = libcl
-	source = http://shogun-toolbox.org/archives/shogun/releases/4.0/sources/shogun-4.0.0.tar.bz2
-	md5sums = 57370e869f3b24f74ce9c7b8741000b0
+	depends = glpk
+	depends = hdf5
+	depends = lapacke
+	depends = libxml2
+	depends = json-c
+	depends = lua
+	depends = nlopt
+	depends = openblas
+	depends = ocl-icd
+	depends = python
+	depends = r
+	depends = snappy
+	optdepends = opencv: OpenCV support
+	optdepends = python-numpy: Python bindings
+	optdepends = python-ply: Python bindings
+	source = https://github.com/shogun-toolbox/shogun/archive/shogun_6.1.3.tar.gz
+	source = https://github.com/shogun-toolbox/shogun-gpl/archive/v6.1.3.tar.gz
+	source = 0001-Removed-is_error-macro-dependency-4098.patch
+	sha256sums = 75f4d555efe06eaa7c4c12a1dc942f6e4d41a8ed495777a790b9bd9df936c19c
+	sha256sums = e8e2fea9804d3e0924a318b00a764bbf9d751c29d32adeeffbb83aec9fbca966
+	sha256sums = 571172d9f31554c1e41cf1e3467cec38c527f1ccf9a2866bf49acfa0c1a84ac4
 
 pkgname = shogun
 
diff --git a/0001-Removed-is_error-macro-dependency-4098.patch b/0001-Removed-is_error-macro-dependency-4098.patch
new file mode 100644
index 000000000000..89a7f9ffb448
--- /dev/null
+++ b/0001-Removed-is_error-macro-dependency-4098.patch
@@ -0,0 +1,169 @@
+From 365ce4c4c700736d2eec8ba6c975327a5ac2cd9b Mon Sep 17 00:00:00 2001
+From: Andrew Wildman <apw4@uw.edu>
+Date: Mon, 22 Jan 2018 22:56:29 -0800
+Subject: [PATCH] Removed is_error macro dependency (#4098)
+
+---
+ src/shogun/io/NeuralNetworkFileReader.cpp  |  4 ++--
+ src/shogun/io/SerializableJsonFile.cpp     | 27 +++++++++++-----------
+ src/shogun/io/SerializableJsonReader00.cpp |  6 +++--
+ 3 files changed, 19 insertions(+), 18 deletions(-)
+
+diff --git a/src/shogun/io/NeuralNetworkFileReader.cpp b/src/shogun/io/NeuralNetworkFileReader.cpp
+index be90fddf3..d4d5f5d4a 100644
+--- a/src/shogun/io/NeuralNetworkFileReader.cpp
++++ b/src/shogun/io/NeuralNetworkFileReader.cpp
+@@ -51,7 +51,7 @@ CNeuralNetwork* CNeuralNetworkFileReader::read_file(const char* file_path)
+ {
+ 	json_object* json_network = json_object_from_file(file_path);
+ 
+-	if (is_error(json_network))
++	if (json_network == nullptr)
+ 	{
+ 		SG_ERROR("Error while opening file: %s!\n", file_path);
+ 		return NULL;
+@@ -68,7 +68,7 @@ CNeuralNetwork* CNeuralNetworkFileReader::read_string(const char* str)
+ {
+ 	json_object* json_network = json_tokener_parse(str);
+ 
+-	if (is_error(json_network))
++	if (json_network == nullptr)
+ 	{
+ 		SG_ERROR("Error while parsing the given string\n");
+ 		return NULL;
+diff --git a/src/shogun/io/SerializableJsonFile.cpp b/src/shogun/io/SerializableJsonFile.cpp
+index 901c4bf44..af00971c0 100644
+--- a/src/shogun/io/SerializableJsonFile.cpp
++++ b/src/shogun/io/SerializableJsonFile.cpp
+@@ -42,7 +42,6 @@ CSerializableJsonFile::new_reader(char* dest_version, size_t n)
+                          m_stack_stream.back(), STR_KEY_FILETYPE, &buf);
+ 
+ 	if (!success || buf == NULL
+-		|| is_error(buf)
+ 		|| (ftype = json_object_get_string(buf)) == NULL)
+ 		return NULL;
+ 
+@@ -77,11 +76,10 @@ bool
+ CSerializableJsonFile::get_object(json_object** dest, json_object* src,
+ 								  const char* key, json_type t)
+ {
+-        bool success = true ;
+-        success = json_object_object_get_ex(src, key, & *dest);
++	bool success = true;
++	success = json_object_object_get_ex(src, key, &*dest);
+ 
+-	return success && *dest != NULL && !is_error(*dest)
+-		&& json_object_is_type(*dest, t);
++	return success && *dest != nullptr && json_object_is_type(*dest, t);
+ }
+ 
+ void
+@@ -97,7 +95,8 @@ CSerializableJsonFile::init(const char* fname)
+ 	switch (m_task) {
+ 	case 'r':
+ 		buf = json_object_from_file((char*) fname);
+-		if (is_error(buf)) {
++		if (buf == nullptr)
++		{
+ 			SG_ERROR("Could not open file `%s' for reading!\n",
+ 					   fname);
+ 			return;
+@@ -219,7 +218,7 @@ CSerializableJsonFile::write_scalar_wrapped(
+ 		break;
+ 	}
+ 
+-	if (is_error(m_stack_stream.back()))
++	if (m_stack_stream.back() == nullptr)
+ 		return false;
+ 
+ 	return true;
+@@ -289,7 +288,7 @@ CSerializableJsonFile::write_sparse_begin_wrapped(
+ 	push_object(json_object_new_object());
+ 
+ 	json_object* buf = json_object_new_array();
+-	if (is_error(buf))
++	if (buf == nullptr)
+ 		return false;
+ 
+ 	json_object_object_add(m_stack_stream.back(),
+@@ -319,7 +318,7 @@ CSerializableJsonFile::write_sparseentry_begin_wrapped(
+ 	push_object(buf);
+ 
+ 	buf = json_object_new_int(feat_index);
+-	if (is_error(buf))
++	if (buf == nullptr)
+ 		return false;
+ 
+ 	json_object_object_add(m_stack_stream.back(),
+@@ -380,7 +379,7 @@ CSerializableJsonFile::write_sgserializable_begin_wrapped(
+ 
+ 	json_object* buf;
+ 	buf = json_object_new_string(sgserializable_name);
+-	if (is_error(buf))
++	if (buf == nullptr)
+ 		return false;
+ 
+ 	json_object_object_add(m_stack_stream.back(),
+@@ -390,7 +389,7 @@ CSerializableJsonFile::write_sgserializable_begin_wrapped(
+ 		string_t buf_str;
+ 		TSGDataType::ptype_to_string(buf_str, generic, STRING_LEN);
+ 		buf = json_object_new_string(buf_str);
+-		if (is_error(buf))
++		if (buf == nullptr)
+ 			return false;
+ 
+ 		json_object_object_add(m_stack_stream.back(),
+@@ -398,7 +397,7 @@ CSerializableJsonFile::write_sgserializable_begin_wrapped(
+ 	}
+ 
+ 	buf = json_object_new_object();
+-	if (is_error(buf))
++	if (buf == nullptr)
+ 		return false;
+ 	json_object_object_add(m_stack_stream.back(), STR_KEY_INSTANCE,
+ 						   buf);
+@@ -423,7 +422,7 @@ CSerializableJsonFile::write_type_begin_wrapped(
+ 	const TSGDataType* type, const char* name, const char* prefix)
+ {
+ 	json_object* buf = json_object_new_object();
+-	if (is_error(buf))
++	if (buf == nullptr)
+ 		return false;
+ 
+ 	json_object_object_add(m_stack_stream.back(), name, buf);
+@@ -432,7 +431,7 @@ CSerializableJsonFile::write_type_begin_wrapped(
+ 	string_t str_buf;
+ 	type->to_string(str_buf, STRING_LEN);
+ 	buf = json_object_new_string(str_buf);
+-	if (is_error(buf))
++	if (buf == nullptr)
+ 		return false;
+ 
+ 	json_object_object_add(m_stack_stream.back(), STR_KEY_TYPE, buf);
+diff --git a/src/shogun/io/SerializableJsonReader00.cpp b/src/shogun/io/SerializableJsonReader00.cpp
+index 06a602b6e..a885c787e 100644
+--- a/src/shogun/io/SerializableJsonReader00.cpp
++++ b/src/shogun/io/SerializableJsonReader00.cpp
+@@ -151,7 +151,8 @@ SerializableJsonReader00::read_stringentry_begin_wrapped(
+ 	json_object* m = m_file->m_stack_stream.back();
+ 
+ 	json_object* buf = json_object_array_get_idx(m, y);
+-	if (is_error(buf)) return false;
++	if (buf == nullptr)
++		return false;
+ 
+ 	m_file->push_object(buf);
+ 	return true;
+@@ -199,7 +200,8 @@ SerializableJsonReader00::read_sparseentry_begin_wrapped(
+ 
+ 	json_object* buf_obj
+ 		= json_object_array_get_idx(m, y);
+-	if (is_error(buf_obj)) return false;
++	if (buf_obj == nullptr)
++		return false;
+ 	if (!json_object_is_type(buf_obj, json_type_object)) return false;
+ 
+ 	json_object* buf;
+-- 
+2.20.0
+
diff --git a/PKGBUILD b/PKGBUILD
index b0e1a25430db..e907896fd2a3 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,23 +1,80 @@
-# Maintainer: Zdeněk Janeček <jan.zdenek@gmail.com>
+# Maintainer: Christian Pfeiffer <xpipe at hotmail dot de>
 pkgname=shogun
-pkgver=4.0.0
-pkgrel=2
-pkgdesc="Shogun - A Large Scale Machine Learning Toolbox with the python interface"
-arch=('i686' 'x86_64')
-url="http://www.shogun-toolbox.org"
-license=('GPLv3')
-depends=('cblas' 'lapack' 'swig-git' 'python-numpy' 'libcl')
-source=(http://shogun-toolbox.org/archives/shogun/releases/4.0/sources/$pkgname-$pkgver.tar.bz2)
-md5sums=('57370e869f3b24f74ce9c7b8741000b0')
+pkgver=6.1.3
+pkgrel=1
+pkgdesc="A Large Scale Machine Learning Toolbox"
+arch=('x86_64')
+url="http://shogun.ml/"
+license=('GPL3')
+depends=('arpack' 'arprec' 'cblas' 'glpk' 'hdf5' 'lapacke' 'libxml2'
+         'json-c' 'lua' 'nlopt' 'openblas' 'ocl-icd' 'python' 'r' 'snappy')
+makedepends=('ctags' 'doxygen' 'eigen3' 'gdb' 'opencv' 'pandoc' 'protobuf'
+			 'python-numpy' 'python-ply' 'python-sphinx' 'swig' 'rxcpp-git' 'viennacl')
+optdepends=('opencv: OpenCV support'
+			'python-numpy: Python bindings'
+			'python-ply: Python bindings')
+source=(https://github.com/shogun-toolbox/shogun/archive/shogun_$pkgver.tar.gz
+        https://github.com/shogun-toolbox/shogun-gpl/archive/v$pkgver.tar.gz
+        0001-Removed-is_error-macro-dependency-4098.patch)
+sha256sums=('75f4d555efe06eaa7c4c12a1dc942f6e4d41a8ed495777a790b9bd9df936c19c'
+            'e8e2fea9804d3e0924a318b00a764bbf9d751c29d32adeeffbb83aec9fbca966'
+            '571172d9f31554c1e41cf1e3467cec38c527f1ccf9a2866bf49acfa0c1a84ac4')
+
+prepare() {
+  mkdir build
+  mv -T "${pkgname}-gpl-${pkgver}" "${srcdir}/${pkgname}-${pkgname}_${pkgver}/src/gpl"
+
+  cd "${srcdir}/${pkgname}-${pkgname}_${pkgver}"
+  patch -p1 -i ../0001-Removed-is_error-macro-dependency-4098.patch
+}
 
 build() {
-  cd "${srcdir}/${pkgname}-${pkgver}"
-  mkdir build && cd build
-  cmake -DCMAKE_INSTALL_PREFIX=/usr -DPythonModular=ON ..
+  cd build
+
+  # Enable all dependencies, except for:
+  #   Commercial ones (MOSEK, CPLEX)
+  #   Java - requires JBlas, which isn't packaged
+  #   Octave - doesn't work with Octave 4.4
+  #   Perl - apparently broken
+  #   Ruby - requires RubyNArray, which isn't packaged
+  # Requires OpenBLAS, because their CMake can't work with libblas.so, only
+  # ATLAS, OpenBLAS and Intel MKL.
+  cmake -DCMAKE_INSTALL_PREFIX=/usr -DENABLE_ARPREC=ON \
+    -DBUILD_EXAMPLES=OFF -DBUILD_META_EXAMPLES=OFF \
+    -DENABLE_ARPACK=ON -DENABLE_BZIP2=ON \
+    -DENABLE_COLPACK=OFF -DENABLE_VIENNACL=ON \
+    -DENABLE_EIGEN_LAPACK=ON \
+    -DENABLE_CPLEX=OFF -DENABLE_MOSEK=OFF \
+    -DENABLE_NLOPT=ON -DENABLE_GLPK=ON -DENABLE_LPSOLVE=ON \
+    -DENABLE_CURL=ON -DENABLE_HDF5=ON -DENABLE_JSON=ON \
+    -DENABLE_LDGOLD=ON -DENABLE_LTO=ON \
+    -DENABLE_PROTOBUF=ON -DENABLE_LIBXML2=ON \
+    -DENABLE_BZIP2=ON -DENABLE_LIBLZMA=ON -DENABLE_LZO=ON \
+    -DENABLE_SNAPPY=ON -DENABLE_ZLIB=ON \
+    -DLICENSE_GPL_SHOGUN=ON \
+    -DOpenCV=ON \
+    -DUSE_CPLEX=OFF -DUSE_MOSEK=OFF \
+    -DUSE_GLPK=ON -DUSE_LPSOLVE=ON -DUSE_BZIP2=ON \
+    -DUSE_GZIP=ON -DUSE_LZMA=ON -DUSE_LZO=ON -DUSE_SNAPPY=ON \
+    -DUSE_SVMLIGHT=ON -DUSE_SWIG_DIRECTORS=ON \
+    -DVIENNACL_WITH_OPENCL=ON \
+    -DINTERFACE_LUA=ON \
+    -DINTERFACE_PYTHON=ON -DINTERFACE_R=ON \
+    -DCMAKE_BUILD_TYPE=Release -DCMAKE_SKIP_RPATH=ON \
+    -DBUILD_SHARED_LIBS=ON \
+    -DLAPACK_lapack_LIBRARY="/usr/lib/liblapack.so\;/usr/lib/liblapacke.so\;/usr/lib/libcblas.so" \
+    "${srcdir}/${pkgname}-${pkgname}_${pkgver}"
+
+  make
 }
 
 package() {
-  cd "${srcdir}/${pkgname}-${pkgver}/build"
-  make DESTDIR="$pkgdir/" install
-}
+  cd build
+  make DESTDIR="${pkgdir}" install
+
+  # The minimal example is always being installed
+  rm -r "${pkgdir}/usr/share/shogun/examples"
 
+  # Shogun will install some empty directories
+  find "${pkgdir}" -type d -empty -delete
+}