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05/05: gnu: Update shogun to 6.1.3.
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From: |
Kei Kebreau |
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Subject: |
05/05: gnu: Update shogun to 6.1.3. |
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Date: |
Tue, 29 May 2018 18:20:52 -0400 (EDT) |
kkebreau pushed a commit to branch master
in repository guix.
commit 5a14e81e41322c5ea90cdea704f45655711b0e20
Author: Kei Kebreau <address@hidden>
Date: Wed May 16 11:56:18 2018 -0400
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 6536d86..e135ee0 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"))