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

[Kei Kebreau <kkebreau@posteo.net>]

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Kei Kebreau <kkebreau@posteo.net> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> Hi Kei,
>>
>> please also note that Shogun contains references to proprietary
>> software.  It has support for SVMLight, which is non-free software.  It
>> includes a script to remove all references to and adapters for SVMLight,
>> but unfortunately we cannot run shell scripts in a snippet.  Changing
>> this requires changing the “package” syntax to delay evaluation more.
>>
>> Until then we need to remove the non-free bits in code, which is what
>> the current snippet does, but the code would need to be adjusted for
>> version 6.1.3.
>>
>> Thanks for taking this on!
>>
>> --
>> Ricardo
>
> Thank you for the tip!
>
> I've attached the four patches that make it possible to build Shogun
> 6.1.3 successfully, and I'm just looking through the source code to
> remove the proprietary bits.
>
> P.S. Ricardo, you'll notice the eigen patch is actually yours from
> another patchset! I verified that it works as expected.

The shogun patch below builds successfully for me! If no corrections
need to be made, I'll push this patch series to master!


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From 2c41c81ad77ee20c89c3056908c13635ee3f5e10 Mon Sep 17 00:00:00 2001
From: Kei Kebreau <kkebreau@posteo.net>
Date: Wed, 16 May 2018 11:56:18 -0400
Subject: [PATCH 5/5] gnu: Update shogun to 6.1.3.

* gnu/packages/machine-learning.scm (shogun): Update to 6.1.3.
[source]: Update snippet to remove proprietary software.
[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.  Adjust 'fix-octave-modules' for the update.
Add 'move-rxcpp' phase.  Rewrite configure-flags for the update.
[inputs]: Add eigen.
[native-inputs]: Add rxcpp.
---
 gnu/packages/machine-learning.scm | 81 ++++++++++++++++++-------------
 1 file changed, 46 insertions(+), 35 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 6536d861e..e135ee0ee 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
@@ -409,8 +410,20 @@ sample proximities between pairs of cases.")
                                    (and skipping? (not skip-next?)))
                            (display line out))
                          (loop (read-line in 'concat) skip-next?)))))))
-           (for-each delete-ifdefs (find-files "src/shogun/kernel/"
-                                               "^Kernel\\.(cpp|h)"))))))
+           (for-each delete-ifdefs
+                     (append
+                      (find-files "src/shogun/classifier/mkl"
+                                  "^MKLClassification\\.cpp")
+                      (find-files "src/shogun/classifier/svm"
+                                  "^SVMLightOneClass\\.(cpp|h)")
+                      (find-files "src/shogun/multiclass"
+                                  "^ScatterSVM\\.(cpp|h)")
+                      (find-files "src/shogun/kernel/"
+                                  "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
+                      (find-files "src/shogun/regression/svr"
+                                  "^(MKLRegression|SVRLight)\\.(cpp|h)")
+                      (find-files "src/shogun/transfer/domain_adaptation"
+                                  "^DomainAdaptationSVM\\.(cpp|h)")))))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ;no check target
@@ -423,62 +436,59 @@ 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")))
+             (substitute* '("src/interfaces/octave/swig_typemaps.i"
+                            "src/interfaces/octave/sg_print_functions.cpp")
+               ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
+               (("octave/config\\.h") "octave/octave-config.h")
+               (("octave/oct-obj.h") "octave/ovl.h"))
              #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 +498,8 @@ 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


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