diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 130 |
1 files changed, 92 insertions, 38 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index f0d35484ea..15e4d45749 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1,9 +1,10 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com> ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org> ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> @@ -36,6 +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) @@ -366,7 +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) @@ -376,7 +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 @@ -408,8 +410,21 @@ 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)"))) + #t)))) (build-system cmake-build-system) (arguments '(#:tests? #f ;no check target @@ -422,62 +437,59 @@ 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) @@ -487,7 +499,8 @@ 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")) @@ -501,6 +514,47 @@ tools. This enables both rapid prototyping of data pipelines and extensibility in terms of new algorithms.") (license license:gpl3+))) +(define-public rxcpp + (package + (name "rxcpp") + (version "4.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh")) + (file-name (string-append name "-" version ".tar.gz")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-werror + (lambda _ + (substitute* (find-files ".") + (("-Werror") "")) + #t)) + (replace 'check + (lambda _ + (invoke "ctest")))))) + (native-inputs + `(("catch" ,catch-framework))) + (home-page "http://reactivex.io/") + (synopsis "Reactive Extensions for C++") + (description + "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for +values-distributed-in-time. ReactiveX is a library for composing asynchronous +and event-based programs by using observable sequences. + +It extends the observer pattern to support sequences of data and/or events and +adds operators that allow you to compose sequences together declaratively while +abstracting away concerns about things like low-level threading, +synchronization, thread-safety, concurrent data structures, and non-blocking +I/O.") + (license license:asl2.0))) + (define-public r-adaptivesparsity (package (name "r-adaptivesparsity") @@ -538,14 +592,14 @@ geometric models.") (define-public r-kernlab (package (name "r-kernlab") - (version "0.9-25") + (version "0.9-26") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 - "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr")))) + "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") |