gnu/packages/machine-learning.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
   4 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
   5 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
   6 ;;;
   7 ;;; This file is part of GNU Guix.
   8 ;;;
   9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  10 ;;; under the terms of the GNU General Public License as published by
  11 ;;; the Free Software Foundation; either version 3 of the License, or (at
  12 ;;; your option) any later version.
  13 ;;;
  14 ;;; GNU Guix is distributed in the hope that it will be useful, but
  15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  17 ;;; GNU General Public License for more details.
  18 ;;;
  19 ;;; You should have received a copy of the GNU General Public License
  20 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  21
  22 (define-module (gnu packages machine-learning)
  23   #:use-module ((guix licenses) #:prefix license:)
  24   #:use-module (guix packages)
  25   #:use-module (guix utils)
  26   #:use-module (guix download)
  27   #:use-module (guix svn-download)
  28   #:use-module (guix build-system cmake)
  29   #:use-module (guix build-system gnu)
  30   #:use-module (guix build-system ocaml)
  31   #:use-module (guix build-system python)
  32   #:use-module (guix build-system r)
  33   #:use-module (gnu packages)
  34   #:use-module (gnu packages autotools)
  35   #:use-module (gnu packages boost)
  36   #:use-module (gnu packages check)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages cran)
  39   #:use-module (gnu packages dejagnu)
  40   #:use-module (gnu packages gcc)
  41   #:use-module (gnu packages image)
  42   #:use-module (gnu packages maths)
  43   #:use-module (gnu packages ocaml)
  44   #:use-module (gnu packages perl)
  45   #:use-module (gnu packages pkg-config)
  46   #:use-module (gnu packages python)
  47   #:use-module (gnu packages statistics)
  48   #:use-module (gnu packages swig)
  49   #:use-module (gnu packages xml)
  50   #:use-module (gnu packages xorg))
  51
  52 (define-public libsvm
  53   (package
  54     (name "libsvm")
  55     (version "3.20")
  56     (source
  57      (origin
  58        (method url-fetch)
  59        (uri (string-append
  60              "https://github.com/cjlin1/libsvm/archive/v"
  61              (string-delete #\. version) ".tar.gz"))
  62        (file-name (string-append name "-" version ".tar.gz"))
  63        (sha256
  64         (base32
  65          "1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
  66     (build-system gnu-build-system)
  67     (arguments
  68      `(#:tests? #f ;no "check" target
  69        #:phases (modify-phases %standard-phases
  70                   (delete 'configure)
  71                   (replace
  72                    'install
  73                    (lambda* (#:key outputs #:allow-other-keys)
  74                      (let* ((out (assoc-ref outputs "out"))
  75                             (bin (string-append out "/bin/")))
  76                        (mkdir-p bin)
  77                        (for-each (lambda (file)
  78                                    (copy-file file (string-append bin file)))
  79                                  '("svm-train"
  80                                    "svm-predict"
  81                                    "svm-scale")))
  82                      #t)))))
  83     (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
  84     (synopsis "Library for Support Vector Machines")
  85     (description
  86      "LIBSVM is a machine learning library for support vector
  87 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
  88 distribution estimation (one-class SVM).  It supports multi-class
  89 classification.")
  90     (license license:bsd-3)))
  91
  92 (define-public python-libsvm
  93   (package (inherit libsvm)
  94     (name "python-libsvm")
  95     (build-system gnu-build-system)
  96     (arguments
  97      `(#:tests? #f ;no "check" target
  98        #:make-flags '("-C" "python")
  99        #:phases
 100        (modify-phases %standard-phases
 101          (delete 'configure)
 102          (replace
 103           'install
 104           (lambda* (#:key inputs outputs #:allow-other-keys)
 105             (let ((site (string-append (assoc-ref outputs "out")
 106                                        "/lib/python"
 107                                        (string-take
 108                                         (string-take-right
 109                                          (assoc-ref inputs "python") 5) 3)
 110                                        "/site-packages/")))
 111               (substitute* "python/svm.py"
 112                 (("../libsvm.so.2") "libsvm.so.2"))
 113               (mkdir-p site)
 114               (for-each (lambda (file)
 115                           (copy-file file (string-append site (basename file))))
 116                         (find-files "python" "\\.py"))
 117               (copy-file "libsvm.so.2"
 118                          (string-append site "libsvm.so.2")))
 119             #t)))))
 120     (inputs
 121      `(("python" ,python)))
 122     (synopsis "Python bindings of libSVM")))
 123
 124 (define-public ghmm
 125   ;; The latest release candidate is several years and a couple of fixes have
 126   ;; been published since.  This is why we download the sources from the SVN
 127   ;; repository.
 128   (let ((svn-revision 2341))
 129     (package
 130       (name "ghmm")
 131       (version (string-append "0.9-rc3-0." (number->string svn-revision)))
 132       (source (origin
 133                 (method svn-fetch)
 134                 (uri (svn-reference
 135                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
 136                       (revision svn-revision)))
 137                 (file-name (string-append name "-" version))
 138                 (sha256
 139                  (base32
 140                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
 141       (build-system gnu-build-system)
 142       (arguments
 143        `(#:imported-modules (,@%gnu-build-system-modules
 144                              (guix build python-build-system))
 145          #:phases
 146          (modify-phases %standard-phases
 147            (add-after 'unpack 'enter-dir
 148              (lambda _ (chdir "ghmm") #t))
 149            (delete 'check)
 150            (add-after 'install 'check
 151              (assoc-ref %standard-phases 'check))
 152            (add-before 'check 'fix-PYTHONPATH
 153              (lambda* (#:key inputs outputs #:allow-other-keys)
 154                (let ((python-version ((@@ (guix build python-build-system)
 155                                            get-python-version)
 156                                       (assoc-ref inputs "python"))))
 157                  (setenv "PYTHONPATH"
 158                          (string-append (getenv "PYTHONPATH")
 159                                         ":" (assoc-ref outputs "out")
 160                                         "/lib/python" python-version
 161                                         "/site-packages")))
 162                #t))
 163            (add-after 'enter-dir 'fix-runpath
 164              (lambda* (#:key outputs #:allow-other-keys)
 165                (substitute* "ghmmwrapper/setup.py"
 166                  (("^(.*)extra_compile_args = \\[" line indent)
 167                   (string-append indent
 168                                  "extra_link_args = [\"-Wl,-rpath="
 169                                  (assoc-ref outputs "out") "/lib\"],\n"
 170                                  line
 171                                  "\"-Wl,-rpath="
 172                                  (assoc-ref outputs "out")
 173                                  "/lib\", ")))
 174                #t))
 175            (add-after 'enter-dir 'disable-broken-tests
 176              (lambda _
 177                (substitute* "tests/Makefile.am"
 178                  ;; GHMM_SILENT_TESTS is assumed to be a command.
 179                  (("TESTS_ENVIRONMENT.*") "")
 180                  ;; Do not build broken tests.
 181                  (("chmm .*") "")
 182                  (("read_fa .*") "")
 183                  (("mcmc .*") "")
 184                  (("label_higher_order_test.*$")
 185                   "label_higher_order_test\n"))
 186
 187                ;; These Python unittests are broken as there is no gato.
 188                ;; See https://sourceforge.net/p/ghmm/support-requests/3/
 189                (substitute* "ghmmwrapper/ghmmunittests.py"
 190                  (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
 191                    line indent)
 192                   (string-append indent
 193                                  "@unittest.skip(\"Disabled by Guix\")\n"
 194                                  line)))
 195                #t))
 196            (add-after 'disable-broken-tests 'autogen
 197              (lambda _
 198                (zero? (system* "bash" "autogen.sh")))))))
 199       (inputs
 200        `(("python" ,python-2) ; only Python 2 is supported
 201          ("libxml2" ,libxml2)))
 202       (native-inputs
 203        `(("pkg-config" ,pkg-config)
 204          ("dejagnu" ,dejagnu)
 205          ("swig" ,swig)
 206          ("autoconf" ,autoconf)
 207          ("automake" ,automake)
 208          ("libtool" ,libtool)))
 209       (home-page "http://ghmm.org")
 210       (synopsis "Hidden Markov Model library")
 211       (description
 212        "The General Hidden Markov Model library (GHMM) is a C library with
 213 additional Python bindings implementing a wide range of types of @dfn{Hidden
 214 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
 215 training, HMM clustering, HMM mixtures.")
 216       (license license:lgpl2.0+))))
 217
 218 (define-public mcl
 219   (package
 220     (name "mcl")
 221     (version "14.137")
 222     (source (origin
 223               (method url-fetch)
 224               (uri (string-append
 225                     "http://micans.org/mcl/src/mcl-"
 226                     (string-replace-substring version "." "-")
 227                     ".tar.gz"))
 228               (sha256
 229                (base32
 230                 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
 231     (build-system gnu-build-system)
 232     (arguments
 233      `(#:configure-flags (list "--enable-blast")))
 234     (inputs
 235      `(("perl" ,perl)))
 236     (home-page "http://micans.org/mcl/")
 237     (synopsis "Clustering algorithm for graphs")
 238     (description
 239      "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
 240 fast and scalable unsupervised cluster algorithm for graphs (also known as
 241 networks) based on simulation of (stochastic) flow in graphs.")
 242     ;; In the LICENCE file and web page it says "The software is licensed
 243     ;; under the GNU General Public License, version 3.", but in several of
 244     ;; the source code files it suggests GPL3 or later.
 245     ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
 246     (license license:gpl3)))
 247
 248 (define-public ocaml-mcl
 249   (package
 250     (name "ocaml-mcl")
 251     (version "12-068oasis4")
 252     (source
 253      (origin
 254        (method url-fetch)
 255        (uri (string-append
 256              "https://github.com/fhcrc/mcl/archive/"
 257              version ".tar.gz"))
 258        (file-name (string-append name "-" version ".tar.gz"))
 259        (sha256
 260         (base32
 261          "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
 262     (build-system ocaml-build-system)
 263     (arguments
 264      `(#:phases
 265        (modify-phases %standard-phases
 266          (add-before 'configure 'patch-paths
 267            (lambda _
 268              (substitute* "configure"
 269                (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
 270              (substitute* "setup.ml"
 271                (("LDFLAGS=-fPIC")
 272                 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
 273              #t)))))
 274     (home-page "https://github.com/fhcrc/mcl")
 275     (synopsis "OCaml wrappers around MCL")
 276     (description
 277      "This package provides OCaml bindings for the MCL graph clustering
 278 algorithm.")
 279     (license license:gpl3)))
 280
 281 (define-public ocaml4.01-mcl
 282   (package-with-ocaml4.01 ocaml-mcl))
 283
 284 (define-public randomjungle
 285   (package
 286     (name "randomjungle")
 287     (version "2.1.0")
 288     (source
 289      (origin
 290        (method url-fetch)
 291        (uri (string-append
 292              "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
 293              "randomjungle-" version ".tar_.gz"))
 294        (sha256
 295         (base32
 296          "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
 297     (build-system gnu-build-system)
 298     (arguments
 299      `(#:configure-flags
 300        (list (string-append "--with-boost="
 301                             (assoc-ref %build-inputs "boost")))
 302        #:phases
 303        (modify-phases %standard-phases
 304          (add-before
 305           'configure 'set-CXXFLAGS
 306           (lambda _
 307             (setenv "CXXFLAGS" "-fpermissive ")
 308             #t)))))
 309     (inputs
 310      `(("boost" ,boost)
 311        ("gsl" ,gsl)
 312        ("libxml2" ,libxml2)
 313        ("zlib" ,zlib)))
 314     (native-inputs
 315      `(("gfortran" ,gfortran)
 316        ("gfortran:lib" ,gfortran "lib")))
 317     ;; Non-portable assembly instructions are used so building fails on
 318     ;; platforms other than x86_64 or i686.
 319     (supported-systems '("x86_64-linux" "i686-linux"))
 320     (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
 321     (synopsis "Implementation of the Random Forests machine learning method")
 322     (description
 323      "Random Jungle is an implementation of Random Forests.  It is supposed to
 324 analyse high dimensional data.  In genetics, it can be used for analysing big
 325 Genome Wide Association (GWA) data.  Random Forests is a powerful machine
 326 learning method.  Most interesting features are variable selection, missing
 327 value imputation, classifier creation, generalization error estimation and
 328 sample proximities between pairs of cases.")
 329     (license license:gpl3+)))
 330
 331 (define-public shogun
 332   (package
 333     (name "shogun")
 334     (version "4.0.0")
 335     (source
 336      (origin
 337        (method url-fetch)
 338        (uri (string-append
 339              "ftp://shogun-toolbox.org/shogun/releases/"
 340              (version-major+minor version)
 341              "/sources/shogun-" version ".tar.bz2"))
 342        (sha256
 343         (base32
 344          "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
 345        (modules '((guix build utils)
 346                   (ice-9 rdelim)))
 347        (snippet
 348         '(begin
 349            ;; Remove non-free sources and files referencing them
 350            (for-each delete-file
 351                      (find-files "src/shogun/classifier/svm/"
 352                                  "SVMLight\\.(cpp|h)"))
 353            (for-each delete-file
 354                      (find-files "examples/undocumented/libshogun/"
 355                                  (string-append
 356                                   "(classifier_.*svmlight.*|"
 357                                   "evaluation_cross_validation_locked_comparison).cpp")))
 358            ;; Remove non-free functions.
 359            (define (delete-ifdefs file)
 360              (with-atomic-file-replacement file
 361                (lambda (in out)
 362                  (let loop ((line (read-line in 'concat))
 363                             (skipping? #f))
 364                    (if (eof-object? line)
 365                        #t
 366                        (let ((skip-next?
 367                               (or (and skipping?
 368                                        (not (string-prefix?
 369                                              "#endif //USE_SVMLIGHT" line)))
 370                                   (string-prefix?
 371                                    "#ifdef USE_SVMLIGHT" line))))
 372                          (when (or (not skipping?)
 373                                    (and skipping? (not skip-next?)))
 374                            (display line out))
 375                          (loop (read-line in 'concat) skip-next?)))))))
 376            (for-each delete-ifdefs (find-files "src/shogun/kernel/"
 377                                                "^Kernel\\.(cpp|h)"))))))
 378     (build-system cmake-build-system)
 379     (arguments
 380      '(#:tests? #f ;no check target
 381        #:phases
 382        (modify-phases %standard-phases
 383          (add-after 'unpack 'delete-broken-symlinks
 384            (lambda _
 385              (for-each delete-file '("applications/arts/data"
 386                                      "applications/asp/data"
 387                                      "applications/easysvm/data"
 388                                      "applications/msplicer/data"
 389                                      "applications/ocr/data"
 390                                      "examples/documented/data"
 391                                      "examples/documented/matlab_static"
 392                                      "examples/documented/octave_static"
 393                                      "examples/undocumented/data"
 394                                      "examples/undocumented/matlab_static"
 395                                      "examples/undocumented/octave_static"
 396                                      "tests/integration/data"
 397                                      "tests/integration/matlab_static"
 398                                      "tests/integration/octave_static"
 399                                      "tests/integration/python_modular/tests"))
 400              #t))
 401          (add-after 'unpack 'change-R-target-path
 402            (lambda* (#:key outputs #:allow-other-keys)
 403              (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
 404                             "src/interfaces/r_static/CMakeLists.txt"
 405                             "examples/undocumented/r_modular/CMakeLists.txt")
 406                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
 407                 (string-append (assoc-ref outputs "out")
 408                                "/lib/R/library/")))
 409              #t))
 410          (add-after 'unpack 'fix-octave-modules
 411            (lambda* (#:key outputs #:allow-other-keys)
 412              (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
 413                             "src/interfaces/octave_static/CMakeLists.txt")
 414                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
 415                 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
 416
 417              ;; change target directory
 418              (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
 419                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
 420                 (string-append (assoc-ref outputs "out")
 421                                "/share/octave/packages")))
 422              #t))
 423          (add-before 'build 'set-HOME
 424            ;; $HOME needs to be set at some point during the build phase
 425            (lambda _ (setenv "HOME" "/tmp") #t)))
 426        #:configure-flags
 427        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
 428              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
 429              ;;"-DJavaModular=ON" ;requires unpackaged jblas
 430              ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
 431              ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
 432              ;;"-DLuaModular=ON"  ;fails because lua doesn't build pkgconfig file
 433              "-DOctaveModular=ON"
 434              "-DOctaveStatic=ON"
 435              "-DPythonModular=ON"
 436              "-DPythonStatic=ON"
 437              "-DRModular=ON"
 438              "-DRStatic=ON"
 439              "-DCmdLineStatic=ON")))
 440     (inputs
 441      `(("python" ,python)
 442        ("numpy" ,python-numpy)
 443        ("r-minimal" ,r-minimal)
 444        ("octave" ,octave)
 445        ("swig" ,swig)
 446        ("hdf5" ,hdf5)
 447        ("atlas" ,atlas)
 448        ("arpack" ,arpack-ng)
 449        ("lapack" ,lapack)
 450        ("glpk" ,glpk)
 451        ("libxml2" ,libxml2)
 452        ("lzo" ,lzo)
 453        ("zlib" ,zlib)))
 454     (native-inputs
 455      `(("pkg-config" ,pkg-config)))
 456     ;; Non-portable SSE instructions are used so building fails on platforms
 457     ;; other than x86_64.
 458     (supported-systems '("x86_64-linux"))
 459     (home-page "http://shogun-toolbox.org/")
 460     (synopsis "Machine learning toolbox")
 461     (description
 462      "The Shogun Machine learning toolbox provides a wide range of unified and
 463 efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
 464 combine multiple data representations, algorithm classes, and general purpose
 465 tools.  This enables both rapid prototyping of data pipelines and extensibility
 466 in terms of new algorithms.")
 467     (license license:gpl3+)))
 468
 469 (define-public r-adaptivesparsity
 470   (package
 471     (name "r-adaptivesparsity")
 472     (version "1.4")
 473     (source (origin
 474               (method url-fetch)
 475               (uri (cran-uri "AdaptiveSparsity" version))
 476               (sha256
 477                (base32
 478                 "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
 479     (properties
 480      `((upstream-name . "AdaptiveSparsity")))
 481     (build-system r-build-system)
 482     (arguments
 483      `(#:phases
 484        (modify-phases %standard-phases
 485          (add-after 'unpack 'link-against-armadillo
 486            (lambda _
 487              (substitute* "src/Makevars"
 488                (("PKG_LIBS=" prefix)
 489                 (string-append prefix "-larmadillo"))))))))
 490     (propagated-inputs
 491      `(("r-rcpp" ,r-rcpp)
 492        ("r-rcpparmadillo" ,r-rcpparmadillo)))
 493     (inputs
 494      `(("armadillo" ,armadillo)))
 495     (home-page "http://cran.r-project.org/web/packages/AdaptiveSparsity")
 496     (synopsis "Adaptive sparsity models")
 497     (description
 498      "This package implements the Figueiredo machine learning algorithm for
 499 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 500 geometric models.")
 501     (license license:lgpl3+)))
 502
 503 (define-public r-kernlab
 504   (package
 505     (name "r-kernlab")
 506     (version "0.9-25")
 507     (source
 508      (origin
 509        (method url-fetch)
 510        (uri (cran-uri "kernlab" version))
 511        (sha256
 512         (base32
 513          "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr"))))
 514     (build-system r-build-system)
 515     (home-page "http://cran.r-project.org/web/packages/kernlab")
 516     (synopsis "Kernel-based machine learning tools")
 517     (description
 518      "This package provides kernel-based machine learning methods for
 519 classification, regression, clustering, novelty detection, quantile regression
 520 and dimensionality reduction.  Among other methods @code{kernlab} includes
 521 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
 522 and a QP solver.")
 523     (license license:gpl2)))
 524
 525 (define-public dlib
 526   (package
 527     (name "dlib")
 528     (version "19.7")
 529     (source (origin
 530               (method url-fetch)
 531               (uri (string-append
 532                     "http://dlib.net/files/dlib-" version ".tar.bz2"))
 533               (sha256
 534                (base32
 535                 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
 536               (modules '((guix build utils)))
 537               (snippet
 538                '(begin
 539                   ;; Delete ~13MB of bundled dependencies.
 540                   (delete-file-recursively "dlib/external")
 541                   (delete-file-recursively "docs/dlib/external")
 542                   #t))))
 543     (build-system cmake-build-system)
 544     (arguments
 545      ;; Recent releases defaults to "lib64" on 64bit.
 546      `(#:configure-flags (list (string-append "-DCMAKE_INSTALL_LIBDIR="
 547                                               (assoc-ref %outputs "out")
 548                                               "/lib"))
 549        #:phases
 550        (modify-phases %standard-phases
 551          (add-after 'unpack 'disable-asserts
 552            (lambda _
 553              ;; config.h recommends explicitly enabling or disabling asserts
 554              ;; when building as a shared library. By default neither is set.
 555              (substitute* "dlib/config.h"
 556                (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
 557              #t))
 558          (add-after 'disable-asserts 'disable-failing-tests
 559            (lambda _
 560              ;; One test times out on MIPS, so we need to disable it.
 561              ;; Others are flaky on some platforms.
 562              (let* ((system ,(or (%current-target-system)
 563                                  (%current-system)))
 564                     (disabled-tests (cond
 565                                      ((string-prefix? "mips64" system)
 566                                       '("object_detector" ; timeout
 567                                         "data_io"))
 568                                      ((string-prefix? "armhf" system)
 569                                       '("learning_to_track"))
 570                                      ((string-prefix? "i686" system)
 571                                       '("optimization"))
 572                                      (else '()))))
 573                (for-each
 574                 (lambda (test)
 575                   (substitute* "dlib/test/makefile"
 576                     (((string-append "SRC \\+= " test "\\.cpp")) "")))
 577                 disabled-tests)
 578                #t)))
 579          (replace 'check
 580            (lambda _
 581              ;; No test target, so we build and run the unit tests here.
 582              (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
 583                (with-directory-excursion test-dir
 584                  (and (zero? (system* "make" "-j" (number->string (parallel-job-count))))
 585                       (zero? (system* "./dtest" "--runall")))))))
 586          (add-after 'install 'delete-static-library
 587            (lambda* (#:key outputs #:allow-other-keys)
 588              (delete-file (string-append (assoc-ref outputs "out")
 589                                          "/lib/libdlib.a"))
 590              #t)))))
 591     (native-inputs
 592      `(("pkg-config" ,pkg-config)))
 593     (inputs
 594      `(("giflib" ,giflib)
 595        ("lapack" ,lapack)
 596        ("libjpeg" ,libjpeg)
 597        ("libpng" ,libpng)
 598        ("libx11" ,libx11)
 599        ("openblas" ,openblas)
 600        ("zlib" ,zlib)))
 601     (synopsis
 602      "Toolkit for making machine learning and data analysis applications in C++")
 603     (description
 604      "Dlib is a modern C++ toolkit containing machine learning algorithms and
 605 tools.  It is used in both industry and academia in a wide range of domains
 606 including robotics, embedded devices, mobile phones, and large high performance
 607 computing environments.")
 608     (home-page "http://dlib.net")
 609     (license license:boost1.0)))
 610
 611 (define-public python-scikit-learn
 612   (package
 613     (name "python-scikit-learn")
 614     (version "0.19.1")
 615     (source
 616      (origin
 617        (method url-fetch)
 618        (uri (string-append
 619              "https://github.com/scikit-learn/scikit-learn/archive/"
 620              version ".tar.gz"))
 621        (file-name (string-append name "-" version ".tar.gz"))
 622        (sha256
 623         (base32
 624          "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))))
 625     (build-system python-build-system)
 626     (arguments
 627      `(#:phases
 628        (modify-phases %standard-phases
 629          (delete 'check)
 630          (add-after 'install 'check
 631            ;; Running tests from the source directory requires
 632            ;; an "inplace" build with paths relative to CWD.
 633            ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing
 634            ;; Use the installed version instead.
 635            (lambda* (#:key inputs outputs #:allow-other-keys)
 636              (add-installed-pythonpath inputs outputs)
 637              ;; some tests require access to "$HOME"
 638              (setenv "HOME" "/tmp")
 639              ;; Step out of the source directory just to be sure.
 640              (chdir "..")
 641              (zero? (system* "nosetests" "-v" "sklearn")))))))
 642     (inputs
 643      `(("openblas" ,openblas)))
 644     (native-inputs
 645      `(("python-nose" ,python-nose)
 646        ("python-cython" ,python-cython)))
 647     (propagated-inputs
 648      `(("python-numpy" ,python-numpy)
 649        ("python-scipy" ,python-scipy)))
 650     (home-page "http://scikit-learn.org/")
 651     (synopsis "Machine Learning in Python")
 652     (description
 653      "Scikit-learn provides simple and efficient tools for data
 654 mining and data analysis.")
 655     (license license:bsd-3)))
 656
 657 (define-public python2-scikit-learn
 658   (package-with-python2 python-scikit-learn))