gnu: shogun: Move package to machine-learning.scm.
* gnu/packages/bioinformatics.scm (shogun): Move from here... * gnu/packages/machine-learning.scm (shogun): ...to here.master
Ricardo Wurmus
parent
365481116c
commit
c1670a8196
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@ -46,7 +46,6 @@
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages tbb)
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#:use-module (gnu packages textutils)
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#:use-module (gnu packages vim)
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@ -2476,145 +2475,6 @@ features; exactSNP: a SNP caller that discovers SNPs by testing signals
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against local background noises.")
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(license license:gpl3+)))
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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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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"ftp://shogun-toolbox.org/shogun/releases/"
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(version-major+minor version)
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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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(modules '((guix build utils)
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(ice-9 rdelim)))
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(snippet
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'(begin
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;; Remove non-free sources and files referencing them
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(for-each delete-file
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(find-files "src/shogun/classifier/svm/"
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"SVMLight\\.(cpp|h)"))
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(for-each delete-file
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(find-files "examples/undocumented/libshogun/"
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(string-append
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"(classifier_.*svmlight.*|"
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"evaluation_cross_validation_locked_comparison).cpp")))
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;; Remove non-free functions.
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(define (delete-ifdefs file)
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(with-atomic-file-replacement file
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(lambda (in out)
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(let loop ((line (read-line in 'concat))
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(skipping? #f))
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(if (eof-object? line)
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#t
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(let ((skip-next?
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(or (and skipping?
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(not (string-prefix?
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"#endif //USE_SVMLIGHT" line)))
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(string-prefix?
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"#ifdef USE_SVMLIGHT" line))))
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(when (or (not skipping?)
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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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(build-system cmake-build-system)
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(arguments
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'(#:tests? #f ;no check target
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#:phases
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(alist-cons-after
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'unpack 'delete-broken-symlinks
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(lambda _
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(for-each delete-file '("applications/arts/data"
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"applications/asp/data"
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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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#t)
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(alist-cons-after
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'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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(("\\$\\{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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(alist-cons-after
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'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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(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
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"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
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;; change target directory
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(substitute* "src/interfaces/octave_modular/CMakeLists.txt"
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(("\\$\\{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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#t)
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(alist-cons-before
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'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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%standard-phases))))
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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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(inputs
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`(("python" ,python)
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("numpy" ,python-numpy)
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("r" ,r)
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("octave" ,octave)
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("swig" ,swig)
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("hdf5" ,hdf5)
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("atlas" ,atlas)
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("arpack" ,arpack-ng)
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("lapack" ,lapack)
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("glpk" ,glpk)
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("libxml2" ,libxml2)
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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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(home-page "http://shogun-toolbox.org/")
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(synopsis "Machine learning toolbox")
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(description
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"The Shogun Machine learning toolbox provides a wide range of unified and
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efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
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combine multiple data representations, algorithm classes, and general purpose
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tools. This enables both rapid prototyping of data pipelines and extensibility
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in terms of new algorithms.")
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(license license:gpl3+)))
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(define-public vcftools
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(package
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(name "vcftools")
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@ -21,13 +21,17 @@
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix download)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (gnu packages)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages xml))
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(define-public libsvm
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@ -144,3 +148,142 @@ learning method. Most interesting features are variable selection, missing
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value imputation, classifier creation, generalization error estimation and
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sample proximities between pairs of cases.")
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(license license:gpl3+)))
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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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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"ftp://shogun-toolbox.org/shogun/releases/"
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(version-major+minor version)
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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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(modules '((guix build utils)
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(ice-9 rdelim)))
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(snippet
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'(begin
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;; Remove non-free sources and files referencing them
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(for-each delete-file
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(find-files "src/shogun/classifier/svm/"
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"SVMLight\\.(cpp|h)"))
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(for-each delete-file
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(find-files "examples/undocumented/libshogun/"
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(string-append
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"(classifier_.*svmlight.*|"
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"evaluation_cross_validation_locked_comparison).cpp")))
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;; Remove non-free functions.
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(define (delete-ifdefs file)
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(with-atomic-file-replacement file
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(lambda (in out)
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(let loop ((line (read-line in 'concat))
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(skipping? #f))
|
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(if (eof-object? line)
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#t
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(let ((skip-next?
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(or (and skipping?
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(not (string-prefix?
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"#endif //USE_SVMLIGHT" line)))
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(string-prefix?
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"#ifdef USE_SVMLIGHT" line))))
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(when (or (not skipping?)
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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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(build-system cmake-build-system)
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(arguments
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'(#:tests? #f ;no check target
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#:phases
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(alist-cons-after
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'unpack 'delete-broken-symlinks
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(lambda _
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(for-each delete-file '("applications/arts/data"
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"applications/asp/data"
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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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#t)
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(alist-cons-after
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'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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(("\\$\\{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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(alist-cons-after
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'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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(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
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"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
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;; change target directory
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(substitute* "src/interfaces/octave_modular/CMakeLists.txt"
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(("\\$\\{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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#t)
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(alist-cons-before
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'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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%standard-phases))))
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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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(inputs
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`(("python" ,python)
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("numpy" ,python-numpy)
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("r" ,r)
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("octave" ,octave)
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("swig" ,swig)
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("hdf5" ,hdf5)
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("atlas" ,atlas)
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("arpack" ,arpack-ng)
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("lapack" ,lapack)
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("glpk" ,glpk)
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("libxml2" ,libxml2)
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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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(home-page "http://shogun-toolbox.org/")
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(synopsis "Machine learning toolbox")
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(description
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"The Shogun Machine learning toolbox provides a wide range of unified and
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efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
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combine multiple data representations, algorithm classes, and general purpose
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tools. This enables both rapid prototyping of data pipelines and extensibility
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in terms of new algorithms.")
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(license license:gpl3+)))
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