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.master
Kei Kebreau
parent
3771000f89
commit
5a14e81e41
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@ -37,6 +37,7 @@
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#:use-module (guix build-system r)
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#:use-module (guix git-download)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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@ -367,7 +368,7 @@ sample proximities between pairs of cases.")
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(define-public shogun
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(package
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(name "shogun")
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(version "4.0.0")
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(version "6.1.3")
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(source
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(origin
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(method url-fetch)
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@ -377,7 +378,7 @@ sample proximities between pairs of cases.")
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"/sources/shogun-" version ".tar.bz2"))
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(sha256
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(base32
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"159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
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"1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
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(modules '((guix build utils)
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(ice-9 rdelim)))
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(snippet
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@ -409,8 +410,20 @@ sample proximities between pairs of cases.")
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(and skipping? (not skip-next?)))
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(display line out))
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(loop (read-line in 'concat) skip-next?)))))))
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(for-each delete-ifdefs (find-files "src/shogun/kernel/"
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"^Kernel\\.(cpp|h)"))))))
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(for-each delete-ifdefs
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(append
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(find-files "src/shogun/classifier/mkl"
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"^MKLClassification\\.cpp")
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(find-files "src/shogun/classifier/svm"
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"^SVMLightOneClass\\.(cpp|h)")
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(find-files "src/shogun/multiclass"
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"^ScatterSVM\\.(cpp|h)")
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(find-files "src/shogun/kernel/"
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"^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
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(find-files "src/shogun/regression/svr"
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"^(MKLRegression|SVRLight)\\.(cpp|h)")
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(find-files "src/shogun/transfer/domain_adaptation"
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"^DomainAdaptationSVM\\.(cpp|h)")))))))
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(build-system cmake-build-system)
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(arguments
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'(#:tests? #f ;no check target
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@ -423,62 +436,59 @@ sample proximities between pairs of cases.")
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"applications/easysvm/data"
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"applications/msplicer/data"
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"applications/ocr/data"
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"examples/documented/data"
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"examples/documented/matlab_static"
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"examples/documented/octave_static"
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"examples/undocumented/data"
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"examples/undocumented/matlab_static"
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"examples/undocumented/octave_static"
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"tests/integration/data"
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"tests/integration/matlab_static"
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"tests/integration/octave_static"
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"tests/integration/python_modular/tests"))
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"examples/meta/data"
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"examples/undocumented/data"))
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#t))
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(add-after 'unpack 'change-R-target-path
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* '("src/interfaces/r_modular/CMakeLists.txt"
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"src/interfaces/r_static/CMakeLists.txt"
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"examples/undocumented/r_modular/CMakeLists.txt")
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(substitute* '("src/interfaces/r/CMakeLists.txt"
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"examples/meta/r/CMakeLists.txt")
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(("\\$\\{R_COMPONENT_LIB_PATH\\}")
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(string-append (assoc-ref outputs "out")
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"/lib/R/library/")))
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#t))
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(add-after 'unpack 'fix-octave-modules
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
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"src/interfaces/octave_static/CMakeLists.txt")
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(substitute* "src/interfaces/octave/CMakeLists.txt"
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(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
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"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
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;; change target directory
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(substitute* "src/interfaces/octave_modular/CMakeLists.txt"
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"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
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;; change target directory
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(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
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(string-append (assoc-ref outputs "out")
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"/share/octave/packages")))
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(substitute* '("src/interfaces/octave/swig_typemaps.i"
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"src/interfaces/octave/sg_print_functions.cpp")
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;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
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(("octave/config\\.h") "octave/octave-config.h")
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(("octave/oct-obj.h") "octave/ovl.h"))
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#t))
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(add-after 'unpack 'move-rxcpp
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((rxcpp-dir "shogun/third-party/rxcpp"))
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(mkdir-p rxcpp-dir)
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(install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
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#t)))
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(add-before 'build 'set-HOME
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;; $HOME needs to be set at some point during the build phase
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(lambda _ (setenv "HOME" "/tmp") #t)))
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#:configure-flags
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(list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
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"-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
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;;"-DJavaModular=ON" ;requires unpackaged jblas
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;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
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;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
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;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
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"-DOctaveModular=ON"
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"-DOctaveStatic=ON"
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"-DPythonModular=ON"
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"-DPythonStatic=ON"
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"-DRModular=ON"
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"-DRStatic=ON"
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"-DCmdLineStatic=ON")))
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"-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
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;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
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;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
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;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
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;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
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"-DINTERFACE_OCTAVE=ON"
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"-DINTERFACE_PYTHON=ON"
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"-DINTERFACE_R=ON")))
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(inputs
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`(("python" ,python)
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("numpy" ,python-numpy)
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("r-minimal" ,r-minimal)
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("octave" ,octave)
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("swig" ,swig)
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("eigen" ,eigen)
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("hdf5" ,hdf5)
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("atlas" ,atlas)
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("arpack" ,arpack-ng)
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@ -488,7 +498,8 @@ sample proximities between pairs of cases.")
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("lzo" ,lzo)
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("zlib" ,zlib)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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`(("pkg-config" ,pkg-config)
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("rxcpp" ,rxcpp)))
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;; Non-portable SSE instructions are used so building fails on platforms
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;; other than x86_64.
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(supported-systems '("x86_64-linux"))
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