[bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3.

[Kei Kebreau]

* gnu/packages/machine-learning.scm (shogun): Update to 6.1.3.
[arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase.
Rewrite file lists given to substitute* in 'change-R-target-path' and
'fix-octave-modules' phases.  Add 'move-rxcpp' phase.  Rewrite configure-flags
for the update.
[inputs]: Add eigen.
[native-inputs]: Add rxcpp.
---
 gnu/packages/machine-learning.scm | 60 ++++++++++++++-----------------
 1 file changed, 27 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/machine-learning.scm 
b/gnu/packages/machine-learning.scm
index 6536d861e..e79aa6692 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -37,6 +37,7 @@
   #:use-module (guix build-system r)
   #:use-module (guix git-download)
   #:use-module (gnu packages)
+  #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -367,7 +368,7 @@ sample proximities between pairs of cases.")
 (define-public shogun
   (package
     (name "shogun")
-    (version "4.0.0")
+    (version "6.1.3")
     (source
      (origin
        (method url-fetch)
@@ -377,7 +378,7 @@ sample proximities between pairs of cases.")
              "/sources/shogun-" version ".tar.bz2"))
        (sha256
         (base32
-         "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
+         "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
        (modules '((guix build utils)
                   (ice-9 rdelim)))
        (snippet
@@ -423,62 +424,54 @@ sample proximities between pairs of cases.")
                                      "applications/easysvm/data"
                                      "applications/msplicer/data"
                                      "applications/ocr/data"
-                                     "examples/documented/data"
-                                     "examples/documented/matlab_static"
-                                     "examples/documented/octave_static"
-                                     "examples/undocumented/data"
-                                     "examples/undocumented/matlab_static"
-                                     "examples/undocumented/octave_static"
-                                     "tests/integration/data"
-                                     "tests/integration/matlab_static"
-                                     "tests/integration/octave_static"
-                                     "tests/integration/python_modular/tests"))
+                                     "examples/meta/data"
+                                     "examples/undocumented/data"))
              #t))
          (add-after 'unpack 'change-R-target-path
            (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
-                            "src/interfaces/r_static/CMakeLists.txt"
-                            "examples/undocumented/r_modular/CMakeLists.txt")
+             (substitute* '("src/interfaces/r/CMakeLists.txt"
+                            "examples/meta/r/CMakeLists.txt")
                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
                 (string-append (assoc-ref outputs "out")
                                "/lib/R/library/")))
              #t))
          (add-after 'unpack 'fix-octave-modules
            (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
-                            "src/interfaces/octave_static/CMakeLists.txt")
+             (substitute* "src/interfaces/octave/CMakeLists.txt"
                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
-                "include_directories(${OCTAVE_INCLUDE_DIRS} 
${OCTAVE_INCLUDE_DIRS}/octave"))
-
-             ;; change target directory
-             (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
+                "include_directories(${OCTAVE_INCLUDE_DIRS} 
${OCTAVE_INCLUDE_DIRS}/octave")
+               ;; change target directory
                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
                 (string-append (assoc-ref outputs "out")
                                "/share/octave/packages")))
              #t))
+         (add-after 'unpack 'move-rxcpp
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((rxcpp-dir "shogun/third-party/rxcpp"))
+               (mkdir-p rxcpp-dir)
+               (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
+               #t)))
          (add-before 'build 'set-HOME
            ;; $HOME needs to be set at some point during the build phase
            (lambda _ (setenv "HOME" "/tmp") #t)))
        #:configure-flags
        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
-             ;;"-DJavaModular=ON" ;requires unpackaged jblas
-             ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
-             ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
-             ;;"-DLuaModular=ON"  ;fails because lua doesn't build pkgconfig 
file
-             "-DOctaveModular=ON"
-             "-DOctaveStatic=ON"
-             "-DPythonModular=ON"
-             "-DPythonStatic=ON"
-             "-DRModular=ON"
-             "-DRStatic=ON"
-             "-DCmdLineStatic=ON")))
+             "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
+             ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
+             ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
+             ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
+             ;;"-DINTERFACE_LUA=ON"  ;fails because lua doesn't build 
pkgconfig file
+             "-DINTERFACE_OCTAVE=ON"
+             "-DINTERFACE_PYTHON=ON"
+             "-DINTERFACE_R=ON")))
     (inputs
      `(("python" ,python)
        ("numpy" ,python-numpy)
        ("r-minimal" ,r-minimal)
        ("octave" ,octave)
        ("swig" ,swig)
+       ("eigen" ,eigen)
        ("hdf5" ,hdf5)
        ("atlas" ,atlas)
        ("arpack" ,arpack-ng)
@@ -488,7 +481,8 @@ sample proximities between pairs of cases.")
        ("lzo" ,lzo)
        ("zlib" ,zlib)))
     (native-inputs
-     `(("pkg-config" ,pkg-config)))
+     `(("pkg-config" ,pkg-config)
+       ("rxcpp" ,rxcpp)))
     ;; Non-portable SSE instructions are used so building fails on platforms
     ;; other than x86_64.
     (supported-systems '("x86_64-linux"))
-- 
2.17.0