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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 2018-05-16 11:56:18 -04:00
parent 3771000f89
commit 5a14e81e41
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GPG Key ID: E6A5EE3C19467A0D
1 changed files with 46 additions and 35 deletions
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gnu/packages/machine-learning.scm
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@ -37,6 +37,7 @@
#:use-module (guix build-system r) #:use-module (guix build-system r)
#:use-module (guix git-download) #:use-module (guix git-download)
#:use-module (gnu packages) #:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools) #:use-module (gnu packages autotools)
#:use-module (gnu packages boost) #:use-module (gnu packages boost)
#:use-module (gnu packages check) #:use-module (gnu packages check)
@ -367,7 +368,7 @@ sample proximities between pairs of cases.")
(define-public shogun (define-public shogun
(package (package
(name "shogun") (name "shogun")
(version "4.0.0") (version "6.1.3")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
@ -377,7 +378,7 @@ sample proximities between pairs of cases.")
"/sources/shogun-" version ".tar.bz2")) "/sources/shogun-" version ".tar.bz2"))
(sha256 (sha256
(base32 (base32
"159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")) "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
(modules '((guix build utils) (modules '((guix build utils)
(ice-9 rdelim))) (ice-9 rdelim)))
(snippet (snippet
@ -409,8 +410,20 @@ sample proximities between pairs of cases.")
(and skipping? (not skip-next?))) (and skipping? (not skip-next?)))
(display line out)) (display line out))
(loop (read-line in 'concat) skip-next?))))))) (loop (read-line in 'concat) skip-next?)))))))
(for-each delete-ifdefs (find-files "src/shogun/kernel/" (for-each delete-ifdefs
"^Kernel\\.(cpp|h)")))))) (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) (build-system cmake-build-system)
(arguments (arguments
'(#:tests? #f ;no check target '(#:tests? #f ;no check target
@ -423,62 +436,59 @@ sample proximities between pairs of cases.")
"applications/easysvm/data" "applications/easysvm/data"
"applications/msplicer/data" "applications/msplicer/data"
"applications/ocr/data" "applications/ocr/data"
"examples/documented/data" "examples/meta/data"
"examples/documented/matlab_static" "examples/undocumented/data"))
"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"))
#t)) #t))
(add-after 'unpack 'change-R-target-path (add-after 'unpack 'change-R-target-path
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(substitute* '("src/interfaces/r_modular/CMakeLists.txt" (substitute* '("src/interfaces/r/CMakeLists.txt"
"src/interfaces/r_static/CMakeLists.txt" "examples/meta/r/CMakeLists.txt")
"examples/undocumented/r_modular/CMakeLists.txt")
(("\\$\\{R_COMPONENT_LIB_PATH\\}") (("\\$\\{R_COMPONENT_LIB_PATH\\}")
(string-append (assoc-ref outputs "out") (string-append (assoc-ref outputs "out")
"/lib/R/library/"))) "/lib/R/library/")))
#t)) #t))
(add-after 'unpack 'fix-octave-modules (add-after 'unpack 'fix-octave-modules
(lambda* (#:key outputs #:allow-other-keys) (lambda* (#:key outputs #:allow-other-keys)
(substitute* '("src/interfaces/octave_modular/CMakeLists.txt" (substitute* "src/interfaces/octave/CMakeLists.txt"
"src/interfaces/octave_static/CMakeLists.txt")
(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")) "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
;; change target directory
;; change target directory
(substitute* "src/interfaces/octave_modular/CMakeLists.txt"
(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
(string-append (assoc-ref outputs "out") (string-append (assoc-ref outputs "out")
"/share/octave/packages"))) "/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)) #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 (add-before 'build 'set-HOME
;; $HOME needs to be set at some point during the build phase ;; $HOME needs to be set at some point during the build phase
(lambda _ (setenv "HOME" "/tmp") #t))) (lambda _ (setenv "HOME" "/tmp") #t)))
#:configure-flags #:configure-flags
(list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE" (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
"-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
;;"-DJavaModular=ON" ;requires unpackaged jblas "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
;;"-DRubyModular=ON" ;requires unpackaged ruby-narray ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
"-DOctaveModular=ON" ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
"-DOctaveStatic=ON" "-DINTERFACE_OCTAVE=ON"
"-DPythonModular=ON" "-DINTERFACE_PYTHON=ON"
"-DPythonStatic=ON" "-DINTERFACE_R=ON")))
"-DRModular=ON"
"-DRStatic=ON"
"-DCmdLineStatic=ON")))
(inputs (inputs
`(("python" ,python) `(("python" ,python)
("numpy" ,python-numpy) ("numpy" ,python-numpy)
("r-minimal" ,r-minimal) ("r-minimal" ,r-minimal)
("octave" ,octave) ("octave" ,octave)
("swig" ,swig) ("swig" ,swig)
("eigen" ,eigen)
("hdf5" ,hdf5) ("hdf5" ,hdf5)
("atlas" ,atlas) ("atlas" ,atlas)
("arpack" ,arpack-ng) ("arpack" ,arpack-ng)
@ -488,7 +498,8 @@ sample proximities between pairs of cases.")
("lzo" ,lzo) ("lzo" ,lzo)
("zlib" ,zlib))) ("zlib" ,zlib)))
(native-inputs (native-inputs
`(("pkg-config" ,pkg-config))) `(("pkg-config" ,pkg-config)
("rxcpp" ,rxcpp)))
;; Non-portable SSE instructions are used so building fails on platforms ;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64. ;; other than x86_64.
(supported-systems '("x86_64-linux")) (supported-systems '("x86_64-linux"))