gnu/packages/machine-learning.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 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 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
   7 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
   8 ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
   9 ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
  10 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
  11 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
  12 ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
  13 ;;;
  14 ;;; This file is part of GNU Guix.
  15 ;;;
  16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  17 ;;; under the terms of the GNU General Public License as published by
  18 ;;; the Free Software Foundation; either version 3 of the License, or (at
  19 ;;; your option) any later version.
  20 ;;;
  21 ;;; GNU Guix is distributed in the hope that it will be useful, but
  22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  24 ;;; GNU General Public License for more details.
  25 ;;;
  26 ;;; You should have received a copy of the GNU General Public License
  27 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  28
  29 (define-module (gnu packages machine-learning)
  30   #:use-module ((guix licenses) #:prefix license:)
  31   #:use-module (guix packages)
  32   #:use-module (guix utils)
  33   #:use-module (guix download)
  34   #:use-module (guix svn-download)
  35   #:use-module (guix build-system cmake)
  36   #:use-module (guix build-system gnu)
  37   #:use-module (guix build-system ocaml)
  38   #:use-module (guix build-system python)
  39   #:use-module (guix build-system r)
  40   #:use-module (guix git-download)
  41   #:use-module (gnu packages)
  42   #:use-module (gnu packages adns)
  43   #:use-module (gnu packages algebra)
  44   #:use-module (gnu packages audio)
  45   #:use-module (gnu packages autotools)
  46   #:use-module (gnu packages base)
  47   #:use-module (gnu packages bash)
  48   #:use-module (gnu packages boost)
  49   #:use-module (gnu packages check)
  50   #:use-module (gnu packages compression)
  51   #:use-module (gnu packages cran)
  52   #:use-module (gnu packages databases)
  53   #:use-module (gnu packages dejagnu)
  54   #:use-module (gnu packages gcc)
  55   #:use-module (gnu packages glib)
  56   #:use-module (gnu packages gstreamer)
  57   #:use-module (gnu packages image)
  58   #:use-module (gnu packages linux)
  59   #:use-module (gnu packages maths)
  60   #:use-module (gnu packages mpi)
  61   #:use-module (gnu packages ocaml)
  62   #:use-module (gnu packages onc-rpc)
  63   #:use-module (gnu packages perl)
  64   #:use-module (gnu packages pkg-config)
  65   #:use-module (gnu packages protobuf)
  66   #:use-module (gnu packages python)
  67   #:use-module (gnu packages python-web)
  68   #:use-module (gnu packages python-xyz)
  69   #:use-module (gnu packages serialization)
  70   #:use-module (gnu packages statistics)
  71   #:use-module (gnu packages sqlite)
  72   #:use-module (gnu packages swig)
  73   #:use-module (gnu packages tls)
  74   #:use-module (gnu packages web)
  75   #:use-module (gnu packages xml)
  76   #:use-module (gnu packages xorg)
  77   #:use-module (ice-9 match))
  78
  79 (define-public fann
  80   ;; The last release is >100 commits behind, so we package from git.
  81   (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
  82     (package
  83       (name "fann")
  84       (version (string-append "2.2.0-1." (string-take commit 8)))
  85       (source (origin
  86                 (method git-fetch)
  87                 (uri (git-reference
  88                       (url "https://github.com/libfann/fann.git")
  89                       (commit commit)))
  90                 (file-name (string-append name "-" version "-checkout"))
  91                 (sha256
  92                  (base32
  93                   "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
  94       (build-system cmake-build-system)
  95       (arguments
  96        `(#:phases
  97          (modify-phases %standard-phases
  98            (replace 'check
  99              (lambda* (#:key outputs #:allow-other-keys)
 100                (let* ((out (assoc-ref outputs "out")))
 101                  (with-directory-excursion (string-append (getcwd) "/tests")
 102                    (invoke "./fann_tests"))))))))
 103       (home-page "http://leenissen.dk/fann/wp/")
 104       (synopsis "Fast Artificial Neural Network")
 105       (description
 106        "FANN is a free open source neural network library, which implements
 107 multilayer artificial neural networks in C with support for both fully
 108 connected and sparsely connected networks.")
 109       (license license:lgpl2.1))))
 110
 111 (define-public libsvm
 112   (package
 113     (name "libsvm")
 114     (version "3.22")
 115     (source
 116      (origin
 117        (method url-fetch)
 118        (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
 119                            name "-" version ".tar.gz"))
 120        (sha256
 121         (base32
 122          "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
 123     (build-system gnu-build-system)
 124     (arguments
 125      `(#:tests? #f ;no "check" target
 126        #:phases (modify-phases %standard-phases
 127                   (delete 'configure)
 128                   (replace
 129                    'install             ; no ‘install’ target
 130                    (lambda* (#:key outputs #:allow-other-keys)
 131                      (let* ((out (assoc-ref outputs "out"))
 132                             (bin (string-append out "/bin/")))
 133                        (mkdir-p bin)
 134                        (for-each (lambda (file)
 135                                    (copy-file file (string-append bin file)))
 136                                  '("svm-train"
 137                                    "svm-predict"
 138                                    "svm-scale")))
 139                      #t)))))
 140     (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
 141     (synopsis "Library for Support Vector Machines")
 142     (description
 143      "LIBSVM is a machine learning library for support vector
 144 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
 145 distribution estimation (one-class SVM).  It supports multi-class
 146 classification.")
 147     (license license:bsd-3)))
 148
 149 (define-public python-libsvm
 150   (package (inherit libsvm)
 151     (name "python-libsvm")
 152     (build-system gnu-build-system)
 153     (arguments
 154      `(#:tests? #f ;no "check" target
 155        #:make-flags '("-C" "python")
 156        #:phases
 157        (modify-phases %standard-phases
 158          (delete 'configure)
 159          (replace
 160           'install                      ; no ‘install’ target
 161           (lambda* (#:key inputs outputs #:allow-other-keys)
 162             (let ((site (string-append (assoc-ref outputs "out")
 163                                        "/lib/python"
 164                                        (string-take
 165                                         (string-take-right
 166                                          (assoc-ref inputs "python") 5) 3)
 167                                        "/site-packages/")))
 168               (substitute* "python/svm.py"
 169                 (("../libsvm.so.2") "libsvm.so.2"))
 170               (mkdir-p site)
 171               (for-each (lambda (file)
 172                           (copy-file file (string-append site (basename file))))
 173                         (find-files "python" "\\.py"))
 174               (copy-file "libsvm.so.2"
 175                          (string-append site "libsvm.so.2")))
 176             #t)))))
 177     (inputs
 178      `(("python" ,python)))
 179     (synopsis "Python bindings of libSVM")))
 180
 181 (define-public ghmm
 182   ;; The latest release candidate is several years and a couple of fixes have
 183   ;; been published since.  This is why we download the sources from the SVN
 184   ;; repository.
 185   (let ((svn-revision 2341))
 186     (package
 187       (name "ghmm")
 188       (version (string-append "0.9-rc3-0." (number->string svn-revision)))
 189       (source (origin
 190                 (method svn-fetch)
 191                 (uri (svn-reference
 192                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
 193                       (revision svn-revision)))
 194                 (file-name (string-append name "-" version))
 195                 (sha256
 196                  (base32
 197                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
 198       (build-system gnu-build-system)
 199       (arguments
 200        `(#:imported-modules (,@%gnu-build-system-modules
 201                              (guix build python-build-system))
 202          #:phases
 203          (modify-phases %standard-phases
 204            (add-after 'unpack 'enter-dir
 205              (lambda _ (chdir "ghmm") #t))
 206            (delete 'check)
 207            (add-after 'install 'check
 208              (assoc-ref %standard-phases 'check))
 209            (add-before 'check 'fix-PYTHONPATH
 210              (lambda* (#:key inputs outputs #:allow-other-keys)
 211                (let ((python-version ((@@ (guix build python-build-system)
 212                                            get-python-version)
 213                                       (assoc-ref inputs "python"))))
 214                  (setenv "PYTHONPATH"
 215                          (string-append (getenv "PYTHONPATH")
 216                                         ":" (assoc-ref outputs "out")
 217                                         "/lib/python" python-version
 218                                         "/site-packages")))
 219                #t))
 220            (add-after 'enter-dir 'fix-runpath
 221              (lambda* (#:key outputs #:allow-other-keys)
 222                (substitute* "ghmmwrapper/setup.py"
 223                  (("^(.*)extra_compile_args = \\[" line indent)
 224                   (string-append indent
 225                                  "extra_link_args = [\"-Wl,-rpath="
 226                                  (assoc-ref outputs "out") "/lib\"],\n"
 227                                  line
 228                                  "\"-Wl,-rpath="
 229                                  (assoc-ref outputs "out")
 230                                  "/lib\", ")))
 231                #t))
 232            (add-after 'enter-dir 'disable-broken-tests
 233              (lambda _
 234                (substitute* "tests/Makefile.am"
 235                  ;; GHMM_SILENT_TESTS is assumed to be a command.
 236                  (("TESTS_ENVIRONMENT.*") "")
 237                  ;; Do not build broken tests.
 238                  (("chmm .*") "")
 239                  (("read_fa .*") "")
 240                  (("mcmc .*") "")
 241                  (("label_higher_order_test.*$")
 242                   "label_higher_order_test\n"))
 243
 244                ;; These Python unittests are broken as there is no gato.
 245                ;; See https://sourceforge.net/p/ghmm/support-requests/3/
 246                (substitute* "ghmmwrapper/ghmmunittests.py"
 247                  (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
 248                    line indent)
 249                   (string-append indent
 250                                  "@unittest.skip(\"Disabled by Guix\")\n"
 251                                  line)))
 252                #t))
 253            (add-after 'disable-broken-tests 'autogen
 254              (lambda _
 255                (invoke "bash" "autogen.sh"))))))
 256       (inputs
 257        `(("python" ,python-2) ; only Python 2 is supported
 258          ("libxml2" ,libxml2)))
 259       (native-inputs
 260        `(("pkg-config" ,pkg-config)
 261          ("dejagnu" ,dejagnu)
 262          ("swig" ,swig)
 263          ("autoconf" ,autoconf)
 264          ("automake" ,automake)
 265          ("libtool" ,libtool)))
 266       (home-page "http://ghmm.org")
 267       (synopsis "Hidden Markov Model library")
 268       (description
 269        "The General Hidden Markov Model library (GHMM) is a C library with
 270 additional Python bindings implementing a wide range of types of @dfn{Hidden
 271 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
 272 training, HMM clustering, HMM mixtures.")
 273       (license license:lgpl2.0+))))
 274
 275 (define-public mcl
 276   (package
 277     (name "mcl")
 278     (version "14.137")
 279     (source (origin
 280               (method url-fetch)
 281               (uri (string-append
 282                     "http://micans.org/mcl/src/mcl-"
 283                     (string-replace-substring version "." "-")
 284                     ".tar.gz"))
 285               (sha256
 286                (base32
 287                 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
 288     (build-system gnu-build-system)
 289     (arguments
 290      `(#:configure-flags (list "--enable-blast")))
 291     (inputs
 292      `(("perl" ,perl)))
 293     (home-page "http://micans.org/mcl/")
 294     (synopsis "Clustering algorithm for graphs")
 295     (description
 296      "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
 297 fast and scalable unsupervised cluster algorithm for graphs (also known as
 298 networks) based on simulation of (stochastic) flow in graphs.")
 299     ;; In the LICENCE file and web page it says "The software is licensed
 300     ;; under the GNU General Public License, version 3.", but in several of
 301     ;; the source code files it suggests GPL3 or later.
 302     ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
 303     (license license:gpl3)))
 304
 305 (define-public ocaml-mcl
 306   (package
 307     (name "ocaml-mcl")
 308     (version "12-068oasis4")
 309     (source
 310      (origin
 311        (method git-fetch)
 312        (uri (git-reference
 313              (url "https://github.com/fhcrc/mcl.git")
 314              (commit version)))
 315        (file-name (git-file-name name version))
 316        (sha256
 317         (base32
 318          "0009dc3h2jp3qg5val452wngpqnbfyhbcxylghq0mrjqxx0jdq5p"))))
 319     (build-system ocaml-build-system)
 320     (arguments
 321      `(#:phases
 322        (modify-phases %standard-phases
 323          (add-before 'configure 'patch-paths
 324            (lambda _
 325              (substitute* "configure"
 326                (("/bin/sh") (which "sh")))
 327              (substitute* "setup.ml"
 328                (("LDFLAGS=-fPIC")
 329                 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh")))
 330                (("-std=c89") "-std=gnu99")
 331
 332                ;; This is a mutable string, which is no longer supported.  Use
 333                ;; a byte buffer instead.
 334                (("String.make \\(String.length s\\)")
 335                 "Bytes.make (String.length s)")
 336
 337                ;; These two belong together.
 338                (("OASISString.replace_chars")
 339                 "Bytes.to_string (OASISString.replace_chars")
 340                ((" s;")
 341                 " s);"))
 342              (substitute* "myocamlbuild.ml"
 343                (("std=c89") "std=gnu99"))
 344              ;; Since we build with a more recent OCaml, we have to use C99 or
 345              ;; later.  This causes problems with the old C code.
 346              (substitute* "src/impala/matrix.c"
 347                (("restrict") "restrict_"))
 348              #t)))))
 349     (native-inputs
 350      `(("ocamlbuild" ,ocamlbuild)))
 351     (home-page "https://github.com/fhcrc/mcl")
 352     (synopsis "OCaml wrappers around MCL")
 353     (description
 354      "This package provides OCaml bindings for the MCL graph clustering
 355 algorithm.")
 356     (license license:gpl3)))
 357
 358 (define-public randomjungle
 359   (package
 360     (name "randomjungle")
 361     (version "2.1.0")
 362     (source
 363      (origin
 364        (method url-fetch)
 365        (uri (string-append
 366              "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
 367              "/randomjungle/randomjungle-" version ".tar_.gz"))
 368        (patches (search-patches "randomjungle-disable-static-build.patch"))
 369        (sha256
 370         (base32
 371          "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
 372     (build-system gnu-build-system)
 373     (arguments
 374      `(#:configure-flags
 375        (list "--disable-static"
 376              (string-append "--with-boost="
 377                             (assoc-ref %build-inputs "boost")))
 378        #:phases
 379        (modify-phases %standard-phases
 380          (add-before
 381           'configure 'set-CXXFLAGS
 382           (lambda _
 383             (setenv "CXXFLAGS" "-fpermissive ")
 384             #t)))))
 385     (inputs
 386      `(("boost" ,boost)
 387        ("gsl" ,gsl)
 388        ("libxml2" ,libxml2)
 389        ("zlib" ,zlib)))
 390     (native-inputs
 391      `(("gfortran" ,gfortran)
 392        ("gfortran:lib" ,gfortran "lib")))
 393     ;; Non-portable assembly instructions are used so building fails on
 394     ;; platforms other than x86_64 or i686.
 395     (supported-systems '("x86_64-linux" "i686-linux"))
 396     (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
 397     (synopsis "Implementation of the Random Forests machine learning method")
 398     (description
 399      "Random Jungle is an implementation of Random Forests.  It is supposed to
 400 analyse high dimensional data.  In genetics, it can be used for analysing big
 401 Genome Wide Association (GWA) data.  Random Forests is a powerful machine
 402 learning method.  Most interesting features are variable selection, missing
 403 value imputation, classifier creation, generalization error estimation and
 404 sample proximities between pairs of cases.")
 405     (license license:gpl3+)))
 406
 407 (define-public openfst
 408   (package
 409     (name "openfst")
 410     (version "1.7.1")
 411     (source (origin
 412               (method url-fetch)
 413               (uri (string-append "http://www.openfst.org/twiki/pub/FST/"
 414                                   "FstDownload/openfst-" version ".tar.gz"))
 415               (sha256
 416                (base32
 417                 "0x9wfcqd8hq4h349s7j77sr60h8xjdfshqw1m3a2n6z5bdr9qkm1"))))
 418     (build-system gnu-build-system)
 419     (home-page "http://www.openfst.org")
 420     (synopsis "Library for weighted finite-state transducers")
 421     (description "OpenFst is a library for constructing, combining,
 422 optimizing, and searching weighted finite-state transducers (FSTs).")
 423     (license license:asl2.0)))
 424
 425 (define-public shogun
 426   (package
 427     (name "shogun")
 428     (version "6.1.3")
 429     (source
 430      (origin
 431        (method url-fetch)
 432        (uri (string-append
 433              "ftp://shogun-toolbox.org/shogun/releases/"
 434              (version-major+minor version)
 435              "/sources/shogun-" version ".tar.bz2"))
 436        (sha256
 437         (base32
 438          "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
 439        (modules '((guix build utils)
 440                   (ice-9 rdelim)))
 441        (snippet
 442         '(begin
 443            ;; Remove non-free sources and files referencing them
 444            (for-each delete-file
 445                      (find-files "src/shogun/classifier/svm/"
 446                                  "SVMLight\\.(cpp|h)"))
 447            (for-each delete-file
 448                      (find-files "examples/undocumented/libshogun/"
 449                                  (string-append
 450                                   "(classifier_.*svmlight.*|"
 451                                   "evaluation_cross_validation_locked_comparison).cpp")))
 452            ;; Remove non-free functions.
 453            (define (delete-ifdefs file)
 454              (with-atomic-file-replacement file
 455                (lambda (in out)
 456                  (let loop ((line (read-line in 'concat))
 457                             (skipping? #f))
 458                    (if (eof-object? line)
 459                        #t
 460                        (let ((skip-next?
 461                               (or (and skipping?
 462                                        (not (string-prefix?
 463                                              "#endif //USE_SVMLIGHT" line)))
 464                                   (string-prefix?
 465                                    "#ifdef USE_SVMLIGHT" line))))
 466                          (when (or (not skipping?)
 467                                    (and skipping? (not skip-next?)))
 468                            (display line out))
 469                          (loop (read-line in 'concat) skip-next?)))))))
 470            (for-each delete-ifdefs
 471                      (append
 472                       (find-files "src/shogun/classifier/mkl"
 473                                   "^MKLClassification\\.cpp")
 474                       (find-files "src/shogun/classifier/svm"
 475                                   "^SVMLightOneClass\\.(cpp|h)")
 476                       (find-files "src/shogun/multiclass"
 477                                   "^ScatterSVM\\.(cpp|h)")
 478                       (find-files "src/shogun/kernel/"
 479                                   "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
 480                       (find-files "src/shogun/regression/svr"
 481                                   "^(MKLRegression|SVRLight)\\.(cpp|h)")
 482                       (find-files "src/shogun/transfer/domain_adaptation"
 483                                   "^DomainAdaptationSVM\\.(cpp|h)")))
 484            #t))))
 485     (build-system cmake-build-system)
 486     (arguments
 487      '(#:tests? #f ;no check target
 488        #:phases
 489        (modify-phases %standard-phases
 490          (add-after 'unpack 'delete-broken-symlinks
 491            (lambda _
 492              (for-each delete-file '("applications/arts/data"
 493                                      "applications/asp/data"
 494                                      "applications/easysvm/data"
 495                                      "applications/msplicer/data"
 496                                      "applications/ocr/data"
 497                                      "examples/meta/data"
 498                                      "examples/undocumented/data"))
 499              #t))
 500          (add-after 'unpack 'change-R-target-path
 501            (lambda* (#:key outputs #:allow-other-keys)
 502              (substitute* '("src/interfaces/r/CMakeLists.txt"
 503                             "examples/meta/r/CMakeLists.txt")
 504                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
 505                 (string-append (assoc-ref outputs "out")
 506                                "/lib/R/library/")))
 507              #t))
 508          (add-after 'unpack 'fix-octave-modules
 509            (lambda* (#:key outputs #:allow-other-keys)
 510              (substitute* "src/interfaces/octave/CMakeLists.txt"
 511                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
 512                 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
 513                ;; change target directory
 514                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
 515                 (string-append (assoc-ref outputs "out")
 516                                "/share/octave/packages")))
 517              (substitute* '("src/interfaces/octave/swig_typemaps.i"
 518                             "src/interfaces/octave/sg_print_functions.cpp")
 519                ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
 520                (("octave/config\\.h") "octave/octave-config.h")
 521                (("octave/oct-obj.h") "octave/ovl.h"))
 522              #t))
 523          (add-after 'unpack 'move-rxcpp
 524            (lambda* (#:key inputs #:allow-other-keys)
 525              (let ((rxcpp-dir "shogun/third-party/rxcpp"))
 526                (mkdir-p rxcpp-dir)
 527                (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
 528                #t)))
 529          (add-before 'build 'set-HOME
 530            ;; $HOME needs to be set at some point during the build phase
 531            (lambda _ (setenv "HOME" "/tmp") #t)))
 532        #:configure-flags
 533        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
 534              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
 535              "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
 536              ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
 537              ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
 538              ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
 539              ;;"-DINTERFACE_LUA=ON"  ;fails because lua doesn't build pkgconfig file
 540              "-DINTERFACE_OCTAVE=ON"
 541              "-DINTERFACE_PYTHON=ON"
 542              "-DINTERFACE_R=ON")))
 543     (inputs
 544      `(("python" ,python)
 545        ("numpy" ,python-numpy)
 546        ("r-minimal" ,r-minimal)
 547        ("octave" ,octave-cli)
 548        ("swig" ,swig)
 549        ("eigen" ,eigen)
 550        ("hdf5" ,hdf5)
 551        ("atlas" ,atlas)
 552        ("arpack" ,arpack-ng)
 553        ("lapack" ,lapack)
 554        ("glpk" ,glpk)
 555        ("libxml2" ,libxml2)
 556        ("lzo" ,lzo)
 557        ("zlib" ,zlib)))
 558     (native-inputs
 559      `(("pkg-config" ,pkg-config)
 560        ("rxcpp" ,rxcpp)))
 561     ;; Non-portable SSE instructions are used so building fails on platforms
 562     ;; other than x86_64.
 563     (supported-systems '("x86_64-linux"))
 564     (home-page "http://shogun-toolbox.org/")
 565     (synopsis "Machine learning toolbox")
 566     (description
 567      "The Shogun Machine learning toolbox provides a wide range of unified and
 568 efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
 569 combine multiple data representations, algorithm classes, and general purpose
 570 tools.  This enables both rapid prototyping of data pipelines and extensibility
 571 in terms of new algorithms.")
 572     (license license:gpl3+)))
 573
 574 (define-public rxcpp
 575   (package
 576     (name "rxcpp")
 577     (version "4.0.0")
 578     (source
 579      (origin
 580        (method url-fetch)
 581        (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
 582                            version ".tar.gz"))
 583        (sha256
 584         (base32
 585          "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
 586        (file-name (string-append name "-" version ".tar.gz"))))
 587     (build-system cmake-build-system)
 588     (arguments
 589      `(#:phases
 590        (modify-phases %standard-phases
 591          (add-after 'unpack 'remove-werror
 592            (lambda _
 593              (substitute* (find-files ".")
 594                (("-Werror") ""))
 595              #t))
 596          (replace 'check
 597            (lambda _
 598              (invoke "ctest"))))))
 599     (native-inputs
 600      `(("catch" ,catch-framework)))
 601     (home-page "http://reactivex.io/")
 602     (synopsis "Reactive Extensions for C++")
 603     (description
 604      "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
 605 values-distributed-in-time.  ReactiveX is a library for composing asynchronous
 606 and event-based programs by using observable sequences.
 607
 608 It extends the observer pattern to support sequences of data and/or events and
 609 adds operators that allow you to compose sequences together declaratively while
 610 abstracting away concerns about things like low-level threading,
 611 synchronization, thread-safety, concurrent data structures, and non-blocking
 612 I/O.")
 613     (license license:asl2.0)))
 614
 615 (define-public r-adaptivesparsity
 616   (package
 617     (name "r-adaptivesparsity")
 618     (version "1.6")
 619     (source (origin
 620               (method url-fetch)
 621               (uri (cran-uri "AdaptiveSparsity" version))
 622               (sha256
 623                (base32
 624                 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
 625     (properties
 626      `((upstream-name . "AdaptiveSparsity")))
 627     (build-system r-build-system)
 628     (arguments
 629      `(#:phases
 630        (modify-phases %standard-phases
 631          (add-after 'unpack 'link-against-armadillo
 632            (lambda _
 633              (substitute* "src/Makevars"
 634                (("PKG_LIBS=" prefix)
 635                 (string-append prefix "-larmadillo"))))))))
 636     (propagated-inputs
 637      `(("r-mass" ,r-mass)
 638        ("r-matrix" ,r-matrix)
 639        ("r-rcpp" ,r-rcpp)
 640        ("r-rcpparmadillo" ,r-rcpparmadillo)))
 641     (inputs
 642      `(("armadillo" ,armadillo)))
 643     (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
 644     (synopsis "Adaptive sparsity models")
 645     (description
 646      "This package implements the Figueiredo machine learning algorithm for
 647 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 648 geometric models.")
 649     (license license:lgpl3+)))
 650
 651 (define-public gemmlowp-for-tensorflow
 652   ;; The commit hash is taken from "tensorflow/workspace.bzl".
 653   (let ((commit "38ebac7b059e84692f53e5938f97a9943c120d98")
 654         (revision "2"))
 655     (package
 656       (name "gemmlowp")
 657       (version (git-version "0" revision commit))
 658       (source (origin
 659                 (method url-fetch)
 660                 (uri (string-append "https://mirror.bazel.build/"
 661                                     "github.com/google/gemmlowp/archive/"
 662                                     commit ".zip"))
 663                 (file-name (string-append "gemmlowp-" version ".zip"))
 664                 (sha256
 665                  (base32
 666                   "0n56s2g8hrssm4w8qj1v58gfm56a04n9v992ixkmvk6zjiralzxq"))))
 667       (build-system cmake-build-system)
 668       (arguments
 669        `(#:configure-flags
 670          (list ,@(match (%current-system)
 671                    ((or "x86_64-linux" "i686-linux")
 672                     '("-DCMAKE_CXX_FLAGS=-msse4.1"))
 673                    (_ '())))
 674          #:phases
 675          (modify-phases %standard-phases
 676            ;; This directory contains the CMakeLists.txt.
 677            (add-after 'unpack 'chdir
 678              (lambda _ (chdir "contrib") #t))
 679            ;; There is no install target
 680            (replace 'install
 681              (lambda* (#:key outputs #:allow-other-keys)
 682                (let* ((out (assoc-ref outputs "out"))
 683                       (lib (string-append out "/lib/"))
 684                       (inc (string-append out "/include/")))
 685                  (install-file "../build/libeight_bit_int_gemm.so" lib)
 686                  (for-each (lambda (dir)
 687                              (let ((target (string-append inc "/" dir)))
 688                                (mkdir-p target)
 689                                (for-each (lambda (h)
 690                                            (install-file h target))
 691                                          (find-files (string-append "../" dir)
 692                                                      "\\.h$"))))
 693                            '("meta" "profiling" "public" "fixedpoint"
 694                              "eight_bit_int_gemm" "internal"))
 695                  #t))))))
 696       (native-inputs
 697        `(("unzip" ,unzip)))
 698       (home-page "https://github.com/google/gemmlowp")
 699       (synopsis "Small self-contained low-precision GEMM library")
 700       (description
 701        "This is a small self-contained low-precision @dfn{general matrix
 702 multiplication} (GEMM) library.  It is not a full linear algebra library.
 703 Low-precision means that the input and output matrix entries are integers on
 704 at most 8 bits.  To avoid overflow, results are internally accumulated on more
 705 than 8 bits, and at the end only some significant 8 bits are kept.")
 706       (license license:asl2.0))))
 707
 708 (define-public dlib
 709   (package
 710     (name "dlib")
 711     (version "19.7")
 712     (source (origin
 713               (method url-fetch)
 714               (uri (string-append
 715                     "http://dlib.net/files/dlib-" version ".tar.bz2"))
 716               (sha256
 717                (base32
 718                 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
 719               (modules '((guix build utils)))
 720               (snippet
 721                '(begin
 722                   ;; Delete ~13MB of bundled dependencies.
 723                   (delete-file-recursively "dlib/external")
 724                   (delete-file-recursively "docs/dlib/external")
 725                   #t))))
 726     (build-system cmake-build-system)
 727     (arguments
 728      `(#:phases
 729        (modify-phases %standard-phases
 730          (add-after 'unpack 'disable-asserts
 731            (lambda _
 732              ;; config.h recommends explicitly enabling or disabling asserts
 733              ;; when building as a shared library. By default neither is set.
 734              (substitute* "dlib/config.h"
 735                (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
 736              #t))
 737          (add-after 'disable-asserts 'disable-failing-tests
 738            (lambda _
 739              ;; One test times out on MIPS, so we need to disable it.
 740              ;; Others are flaky on some platforms.
 741              (let* ((system ,(or (%current-target-system)
 742                                  (%current-system)))
 743                     (disabled-tests (cond
 744                                      ((string-prefix? "mips64" system)
 745                                       '("object_detector" ; timeout
 746                                         "data_io"))
 747                                      ((string-prefix? "armhf" system)
 748                                       '("learning_to_track"))
 749                                      ((string-prefix? "i686" system)
 750                                       '("optimization"))
 751                                      (else '()))))
 752                (for-each
 753                 (lambda (test)
 754                   (substitute* "dlib/test/makefile"
 755                     (((string-append "SRC \\+= " test "\\.cpp")) "")))
 756                 disabled-tests)
 757                #t)))
 758          (replace 'check
 759            (lambda _
 760              ;; No test target, so we build and run the unit tests here.
 761              (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
 762                (with-directory-excursion test-dir
 763                  (invoke "make" "-j" (number->string (parallel-job-count)))
 764                  (invoke "./dtest" "--runall"))
 765                #t)))
 766          (add-after 'install 'delete-static-library
 767            (lambda* (#:key outputs #:allow-other-keys)
 768              (delete-file (string-append (assoc-ref outputs "out")
 769                                          "/lib/libdlib.a"))
 770              #t)))))
 771     (native-inputs
 772      `(("pkg-config" ,pkg-config)
 773        ;; For tests.
 774        ("libnsl" ,libnsl)))
 775     (inputs
 776      `(("giflib" ,giflib)
 777        ("lapack" ,lapack)
 778        ("libjpeg" ,libjpeg)
 779        ("libpng" ,libpng)
 780        ("libx11" ,libx11)
 781        ("openblas" ,openblas)
 782        ("zlib" ,zlib)))
 783     (synopsis
 784      "Toolkit for making machine learning and data analysis applications in C++")
 785     (description
 786      "Dlib is a modern C++ toolkit containing machine learning algorithms and
 787 tools.  It is used in both industry and academia in a wide range of domains
 788 including robotics, embedded devices, mobile phones, and large high performance
 789 computing environments.")
 790     (home-page "http://dlib.net")
 791     (license license:boost1.0)))
 792
 793 (define-public python-scikit-learn
 794   (package
 795     (name "python-scikit-learn")
 796     (version "0.20.1")
 797     (source
 798      (origin
 799        (method git-fetch)
 800        (uri (git-reference
 801              (url "https://github.com/scikit-learn/scikit-learn.git")
 802              (commit version)))
 803        (file-name (git-file-name name version))
 804        (sha256
 805         (base32
 806          "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d"))))
 807     (build-system python-build-system)
 808     (arguments
 809      `(#:phases
 810        (modify-phases %standard-phases
 811          (add-after 'build 'build-ext
 812            (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
 813          (replace 'check
 814            (lambda _
 815              ;; Restrict OpenBLAS threads to prevent segfaults while testing!
 816              (setenv "OPENBLAS_NUM_THREADS" "1")
 817
 818              ;; Some tests require write access to $HOME.
 819              (setenv "HOME" "/tmp")
 820
 821              (invoke "pytest" "sklearn" "-m" "not network")))
 822          ;; FIXME: This fails with permission denied
 823          (delete 'reset-gzip-timestamps))))
 824     (inputs
 825      `(("openblas" ,openblas)))
 826     (native-inputs
 827      `(("python-pytest" ,python-pytest)
 828        ("python-pandas" ,python-pandas) ;for tests
 829        ("python-cython" ,python-cython)))
 830     (propagated-inputs
 831      `(("python-numpy" ,python-numpy)
 832        ("python-scipy" ,python-scipy)))
 833     (home-page "http://scikit-learn.org/")
 834     (synopsis "Machine Learning in Python")
 835     (description
 836      "Scikit-learn provides simple and efficient tools for data mining and
 837 data analysis.")
 838     (license license:bsd-3)))
 839
 840 (define-public python2-scikit-learn
 841   (package-with-python2 python-scikit-learn))
 842
 843 (define-public python-autograd
 844   (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
 845          (revision "0")
 846          (version (git-version "0.0.0" revision commit)))
 847     (package
 848       (name "python-autograd")
 849       (home-page "https://github.com/HIPS/autograd")
 850       (source (origin
 851                 (method git-fetch)
 852                 (uri (git-reference
 853                       (url home-page)
 854                       (commit commit)))
 855                 (sha256
 856                  (base32
 857                   "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
 858                 (file-name (git-file-name name version))))
 859       (version version)
 860       (build-system python-build-system)
 861       (native-inputs
 862        `(("python-nose" ,python-nose)
 863          ("python-pytest" ,python-pytest)))
 864       (propagated-inputs
 865        `(("python-future" ,python-future)
 866          ("python-numpy" ,python-numpy)))
 867       (arguments
 868        `(#:phases (modify-phases %standard-phases
 869                     (replace 'check
 870                       (lambda _
 871                         (invoke "py.test" "-v"))))))
 872       (synopsis "Efficiently computes derivatives of NumPy code")
 873       (description "Autograd can automatically differentiate native Python and
 874 NumPy code.  It can handle a large subset of Python's features, including loops,
 875 ifs, recursion and closures, and it can even take derivatives of derivatives
 876 of derivatives.  It supports reverse-mode differentiation
 877 (a.k.a. backpropagation), which means it can efficiently take gradients of
 878 scalar-valued functions with respect to array-valued arguments, as well as
 879 forward-mode differentiation, and the two can be composed arbitrarily.  The
 880 main intended application of Autograd is gradient-based optimization.")
 881       (license license:expat))))
 882
 883 (define-public python2-autograd
 884   (package-with-python2 python-autograd))
 885
 886 (define-public lightgbm
 887   (package
 888     (name "lightgbm")
 889     (version "2.0.12")
 890     (source (origin
 891               (method url-fetch)
 892               (uri (string-append
 893                     "https://github.com/Microsoft/LightGBM/archive/v"
 894                     version ".tar.gz"))
 895               (sha256
 896                (base32
 897                 "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
 898               (file-name (string-append name "-" version ".tar.gz"))))
 899     (native-inputs
 900      `(("python-pytest" ,python-pytest)
 901        ("python-nose" ,python-nose)))
 902     (inputs
 903      `(("openmpi" ,openmpi)))
 904     (propagated-inputs
 905      `(("python-numpy" ,python-numpy)
 906        ("python-scipy" ,python-scipy)))
 907     (arguments
 908      `(#:configure-flags
 909        '("-DUSE_MPI=ON")
 910        #:phases
 911        (modify-phases %standard-phases
 912          (replace 'check
 913            (lambda* (#:key outputs #:allow-other-keys)
 914              (with-directory-excursion ,(string-append "../LightGBM-" version)
 915                (invoke "pytest" "tests/c_api_test/test_.py")))))))
 916     (build-system cmake-build-system)
 917     (home-page "https://github.com/Microsoft/LightGBM")
 918     (synopsis "Gradient boosting framework based on decision tree algorithms")
 919     (description "LightGBM is a gradient boosting framework that uses tree
 920 based learning algorithms.  It is designed to be distributed and efficient with
 921 the following advantages:
 922
 923 @itemize
 924 @item Faster training speed and higher efficiency
 925 @item Lower memory usage
 926 @item Better accuracy
 927 @item Parallel and GPU learning supported (not enabled in this package)
 928 @item Capable of handling large-scale data
 929 @end itemize\n")
 930     (license license:expat)))
 931
 932 (define-public vowpal-wabbit
 933   ;; Language bindings not included.
 934   (package
 935     (name "vowpal-wabbit")
 936     (version "8.5.0")
 937     (source (origin
 938               (method url-fetch)
 939               (uri (string-append
 940                     "https://github.com/JohnLangford/vowpal_wabbit/archive/"
 941                     version ".tar.gz"))
 942               (sha256
 943                (base32
 944                 "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
 945               (file-name (string-append name "-" version ".tar.gz"))))
 946     (inputs
 947      `(("boost" ,boost)
 948        ("zlib" ,zlib)))
 949     (arguments
 950      `(#:configure-flags
 951        (list (string-append "--with-boost="
 952                             (assoc-ref %build-inputs "boost")))))
 953     (build-system gnu-build-system)
 954     (home-page "https://github.com/JohnLangford/vowpal_wabbit")
 955     (synopsis "Fast machine learning library for online learning")
 956     (description "Vowpal Wabbit is a machine learning system with techniques
 957 such as online, hashing, allreduce, reductions, learning2search, active, and
 958 interactive learning.")
 959     (license license:bsd-3)))
 960
 961 (define-public python2-fastlmm
 962   (package
 963     (name "python2-fastlmm")
 964     (version "0.2.21")
 965     (source
 966      (origin
 967        (method url-fetch)
 968        (uri (pypi-uri "fastlmm" version ".zip"))
 969        (sha256
 970         (base32
 971          "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
 972     (build-system python-build-system)
 973     (arguments
 974      `(#:tests? #f ; some test files are missing
 975        #:python ,python-2)) ; only Python 2.7 is supported
 976     (propagated-inputs
 977      `(("python2-numpy" ,python2-numpy)
 978        ("python2-scipy" ,python2-scipy)
 979        ("python2-matplotlib" ,python2-matplotlib)
 980        ("python2-pandas" ,python2-pandas)
 981        ("python2-scikit-learn" ,python2-scikit-learn)
 982        ("python2-pysnptools" ,python2-pysnptools)))
 983     (native-inputs
 984      `(("unzip" ,unzip)
 985        ("python2-cython" ,python2-cython)
 986        ("python2-mock" ,python2-mock)
 987        ("python2-nose" ,python2-nose)))
 988     (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
 989     (synopsis "Perform genome-wide association studies on large data sets")
 990     (description
 991      "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
 992 Models, is a program for performing both single-SNP and SNP-set genome-wide
 993 association studies (GWAS) on extremely large data sets.")
 994     (license license:asl2.0)))
 995
 996 ;; There have been no proper releases yet.
 997 (define-public kaldi
 998   (let ((commit "2f95609f0bb085bd3a1dc5eb0a39f3edea59e606")
 999         (revision "1"))
1000     (package
1001       (name "kaldi")
1002       (version (git-version "0" revision commit))
1003       (source (origin
1004                 (method git-fetch)
1005                 (uri (git-reference
1006                       (url "https://github.com/kaldi-asr/kaldi.git")
1007                       (commit commit)))
1008                 (file-name (git-file-name name version))
1009                 (sha256
1010                  (base32
1011                   "082qh3pfi7hvncylp4xsmkfahbd7gb0whdfa4rwrx7fxk9rdh3kz"))))
1012       (build-system gnu-build-system)
1013       (arguments
1014        `(#:test-target "test"
1015          #:phases
1016          (modify-phases %standard-phases
1017            (add-after 'unpack 'chdir
1018              (lambda _ (chdir "src") #t))
1019            (replace 'configure
1020              (lambda* (#:key build system inputs outputs #:allow-other-keys)
1021                (when (not (or (string-prefix? "x86_64" system)
1022                               (string-prefix? "i686" system)))
1023                  (substitute* "makefiles/linux_openblas.mk"
1024                    (("-msse -msse2") "")))
1025                (substitute* "makefiles/default_rules.mk"
1026                  (("/bin/bash") (which "bash")))
1027                (substitute* "Makefile"
1028                  (("ext_depend: check_portaudio")
1029                   "ext_depend:"))
1030                (substitute* '("online/Makefile"
1031                               "onlinebin/Makefile"
1032                               "gst-plugin/Makefile")
1033                  (("../../tools/portaudio/install")
1034                   (assoc-ref inputs "portaudio")))
1035
1036                ;; This `configure' script doesn't support variables passed as
1037                ;; arguments, nor does it support "prefix".
1038                (let ((out (assoc-ref outputs "out"))
1039                      (openblas (assoc-ref inputs "openblas"))
1040                      (openfst (assoc-ref inputs "openfst")))
1041                  (substitute* "configure"
1042                    (("check_for_slow_expf;") "")
1043                    ;; This affects the RPATH and also serves as the installation
1044                    ;; directory.
1045                    (("KALDILIBDIR=`pwd`/lib")
1046                     (string-append "KALDILIBDIR=" out "/lib")))
1047                  (mkdir-p out) ; must exist
1048                  (setenv "CONFIG_SHELL" (which "bash"))
1049                  (setenv "OPENFST_VER" ,(package-version openfst))
1050                  (invoke "./configure"
1051                          "--use-cuda=no"
1052                          "--shared"
1053                          (string-append "--openblas-root=" openblas)
1054                          (string-append "--fst-root=" openfst)))))
1055            (add-after 'build 'build-ext-and-gstreamer-plugin
1056              (lambda _
1057                (invoke "make" "-C" "online" "depend")
1058                (invoke "make" "-C" "online")
1059                (invoke "make" "-C" "onlinebin" "depend")
1060                (invoke "make" "-C" "onlinebin")
1061                (invoke "make" "-C" "gst-plugin" "depend")
1062                (invoke "make" "-C" "gst-plugin")
1063                #t))
1064            ;; TODO: also install the executables.
1065            (replace 'install
1066              (lambda* (#:key outputs #:allow-other-keys)
1067                (let* ((out (assoc-ref outputs "out"))
1068                       (inc (string-append out "/include"))
1069                       (lib (string-append out "/lib")))
1070                  (mkdir-p lib)
1071                  ;; The build phase installed symlinks to the actual
1072                  ;; libraries.  Install the actual targets.
1073                  (for-each (lambda (file)
1074                              (let ((target (readlink file)))
1075                                (delete-file file)
1076                                (install-file target lib)))
1077                            (find-files lib "\\.so"))
1078                  ;; Install headers
1079                  (for-each (lambda (file)
1080                              (let ((target-dir (string-append inc "/" (dirname file))))
1081                                (install-file file target-dir)))
1082                            (find-files "." "\\.h"))
1083                  (install-file "gst-plugin/libgstonlinegmmdecodefaster.so"
1084                                (string-append lib "/gstreamer-1.0"))
1085                  #t))))))
1086       (inputs
1087        `(("alsa-lib" ,alsa-lib)
1088          ("gfortran" ,gfortran "lib")
1089          ("glib" ,glib)
1090          ("gstreamer" ,gstreamer)
1091          ("jack" ,jack-1)
1092          ("openblas" ,openblas)
1093          ("openfst" ,openfst)
1094          ("portaudio" ,portaudio)
1095          ("python" ,python)))
1096       (native-inputs
1097        `(("glib" ,glib "bin")             ; glib-genmarshal
1098          ("grep" ,grep)
1099          ("sed" ,sed)
1100          ("pkg-config" ,pkg-config)
1101          ("which" ,which)))
1102       (home-page "https://kaldi-asr.org/")
1103       (synopsis "Speech recognition toolkit")
1104       (description "Kaldi is an extensible toolkit for speech recognition
1105 written in C++.")
1106       (license license:asl2.0))))
1107
1108 (define-public gst-kaldi-nnet2-online
1109   (let ((commit "617e43e73c7cc45eb9119028c02bd4178f738c4a")
1110         (revision "1"))
1111     (package
1112       (name "gst-kaldi-nnet2-online")
1113       (version (git-version "0" revision commit))
1114       (source (origin
1115                 (method git-fetch)
1116                 (uri (git-reference
1117                       (url "https://github.com/alumae/gst-kaldi-nnet2-online.git")
1118                       (commit commit)))
1119                 (file-name (git-file-name name version))
1120                 (sha256
1121                  (base32
1122                   "0xh3w67b69818s6ib02ara4lw7wamjdmh4jznvkpzrs4skbs9jx9"))))
1123       (build-system gnu-build-system)
1124       (arguments
1125        `(#:tests? #f                    ; there are none
1126          #:make-flags
1127          (list (string-append "SHELL="
1128                               (assoc-ref %build-inputs "bash") "/bin/bash")
1129                (string-append "KALDI_ROOT="
1130                               (assoc-ref %build-inputs "kaldi-src"))
1131                (string-append "KALDILIBDIR="
1132                               (assoc-ref %build-inputs "kaldi") "/lib")
1133                "KALDI_FLAVOR=dynamic")
1134          #:phases
1135          (modify-phases %standard-phases
1136            (add-after 'unpack 'chdir
1137              (lambda _ (chdir "src") #t))
1138            (replace 'configure
1139              (lambda* (#:key inputs #:allow-other-keys)
1140                (let ((glib (assoc-ref inputs "glib")))
1141                  (setenv "CXXFLAGS" "-std=c++11 -fPIC")
1142                  (setenv "CPLUS_INCLUDE_PATH"
1143                          (string-append glib "/include/glib-2.0:"
1144                                         glib "/lib/glib-2.0/include:"
1145                                         (assoc-ref inputs "gstreamer")
1146                                         "/include/gstreamer-1.0:"
1147                                         (getenv "CPLUS_INCLUDE_PATH"))))
1148                (substitute* "Makefile"
1149                  (("include \\$\\(KALDI_ROOT\\)/src/kaldi.mk") "")
1150                  (("\\$\\(error Cannot find") "#"))))
1151            (add-before 'build 'build-depend
1152              (lambda* (#:key make-flags #:allow-other-keys)
1153                (apply invoke "make" "depend" make-flags)))
1154            (replace 'install
1155              (lambda* (#:key outputs #:allow-other-keys)
1156                (let* ((out (assoc-ref outputs "out"))
1157                       (lib (string-append out "/lib/gstreamer-1.0")))
1158                  (install-file "libgstkaldinnet2onlinedecoder.so" lib)
1159                  #t))))))
1160       (inputs
1161        `(("glib" ,glib)
1162          ("gstreamer" ,gstreamer)
1163          ("jansson" ,jansson)
1164          ("openfst" ,openfst)
1165          ("kaldi" ,kaldi)))
1166       (native-inputs
1167        `(("bash" ,bash)
1168          ("glib:bin" ,glib "bin")       ; glib-genmarshal
1169          ("kaldi-src" ,(package-source kaldi))
1170          ("pkg-config" ,pkg-config)))
1171       (home-page "https://kaldi-asr.org/")
1172       (synopsis "Gstreamer plugin for decoding speech")
1173       (description "This package provides a GStreamer plugin that wraps
1174 Kaldi's @code{SingleUtteranceNnet2Decoder}.  It requires iVector-adapted DNN
1175 acoustic models.  The iVectors are adapted to the current audio stream
1176 automatically.")
1177       (license license:asl2.0))))
1178
1179 (define-public kaldi-gstreamer-server
1180   (let ((commit "1735ba49c5dc0ebfc184e45105fc600cd9f1f508")
1181         (revision "1"))
1182     (package
1183       (name "kaldi-gstreamer-server")
1184       (version (git-version "0" revision commit))
1185       (source (origin
1186                 (method git-fetch)
1187                 (uri (git-reference
1188                       (url "https://github.com/alumae/kaldi-gstreamer-server.git")
1189                       (commit commit)))
1190                 (file-name (git-file-name name version))
1191                 (sha256
1192                  (base32
1193                   "0j701m7lbwmzqxsfanj882v7881hrbmpqybbczbxqpcbg8q34w0k"))))
1194       (build-system gnu-build-system)
1195       (arguments
1196        `(#:tests? #f ; there are no tests that can be run automatically
1197          #:modules ((guix build utils)
1198                     (guix build gnu-build-system)
1199                     (srfi srfi-26))
1200          #:phases
1201          (modify-phases %standard-phases
1202            (delete 'configure)
1203            (replace 'build
1204              (lambda* (#:key outputs #:allow-other-keys)
1205                ;; Disable hash randomization to ensure the generated .pycs
1206                ;; are reproducible.
1207                (setenv "PYTHONHASHSEED" "0")
1208                (with-directory-excursion "kaldigstserver"
1209                  (for-each (lambda (file)
1210                              (apply invoke
1211                                     `("python"
1212                                       "-m" "compileall"
1213                                       "-f" ; force rebuild
1214                                       ,file)))
1215                            (find-files "." "\\.py$")))
1216                #t))
1217            (replace 'install
1218              (lambda* (#:key inputs outputs #:allow-other-keys)
1219                (let* ((out (assoc-ref outputs "out"))
1220                       (bin (string-append out "/bin"))
1221                       (share (string-append out "/share/kaldi-gstreamer-server/")))
1222                  ;; Install Python files
1223                  (with-directory-excursion "kaldigstserver"
1224                    (for-each (cut install-file <> share)
1225                              (find-files "." ".*")))
1226
1227                  ;; Install sample configuration files
1228                  (for-each (cut install-file <> share)
1229                            (find-files "." "\\.yaml"))
1230
1231                  ;; Install executables
1232                  (mkdir-p bin)
1233                  (let* ((server (string-append bin "/kaldi-gst-server"))
1234                         (client (string-append bin "/kaldi-gst-client"))
1235                         (worker (string-append bin "/kaldi-gst-worker"))
1236                         (PYTHONPATH (getenv "PYTHONPATH"))
1237                         (GST_PLUGIN_PATH (string-append
1238                                           (assoc-ref inputs "gst-kaldi-nnet2-online")
1239                                           "/lib/gstreamer-1.0:${GST_PLUGIN_PATH}"))
1240                         (wrap (lambda (wrapper what)
1241                                 (with-output-to-file wrapper
1242                                   (lambda _
1243                                     (format #t
1244                                             "#!~a
1245 export PYTHONPATH=~a
1246 export GST_PLUGIN_PATH=~a
1247 exec ~a ~a/~a \"$@\"~%"
1248                                             (which "bash") PYTHONPATH GST_PLUGIN_PATH
1249                                             (which "python") share what)))
1250                                 (chmod wrapper #o555))))
1251                    (for-each wrap
1252                              (list server client worker)
1253                              (list "master_server.py"
1254                                    "client.py"
1255                                    "worker.py")))
1256                  #t))))))
1257       (inputs
1258        `(("gst-kaldi-nnet2-online" ,gst-kaldi-nnet2-online)
1259          ("python2" ,python-2)
1260          ("python2-futures" ,python2-futures)
1261          ("python2-pygobject" ,python2-pygobject)
1262          ("python2-pyyaml" ,python2-pyyaml)
1263          ("python2-tornado" ,python2-tornado)
1264          ("python2-ws4py" ,python2-ws4py-for-kaldi-gstreamer-server)))
1265       (home-page "https://github.com/alumae/kaldi-gstreamer-server")
1266       (synopsis "Real-time full-duplex speech recognition server")
1267       (description "This is a real-time full-duplex speech recognition server,
1268 based on the Kaldi toolkit and the GStreamer framework and implemented in
1269 Python.")
1270       (license license:bsd-2))))
1271
1272 (define-public grpc
1273   (package
1274     (name "grpc")
1275     (version "1.16.1")
1276     (source (origin
1277               (method git-fetch)
1278               (uri (git-reference
1279                     (url "https://github.com/grpc/grpc.git")
1280                     (commit (string-append "v" version))))
1281               (file-name (git-file-name name version))
1282               (sha256
1283                (base32
1284                 "1jimqz3115f9pli5w6ik9wi7mjc7ix6y7yrq4a1ab9fc3dalj7p2"))))
1285     (build-system cmake-build-system)
1286     (arguments
1287      `(#:tests? #f ; no test target
1288        #:configure-flags
1289        (list "-DgRPC_ZLIB_PROVIDER=package"
1290              "-DgRPC_CARES_PROVIDER=package"
1291              "-DgRPC_SSL_PROVIDER=package"
1292              "-DgRPC_PROTOBUF_PROVIDER=package")))
1293     (inputs
1294      `(("c-ares" ,c-ares-next)
1295        ("openssl" ,openssl)
1296        ("zlib" ,zlib)))
1297     (native-inputs
1298      `(("protobuf" ,protobuf-next)
1299        ("python" ,python-wrapper)))
1300     (home-page "https://grpc.io")
1301     (synopsis "High performance universal RPC framework")
1302     (description "gRPC is a modern open source high performance @dfn{Remote
1303 Procedure Call} (RPC) framework that can run in any environment.  It can
1304 efficiently connect services in and across data centers with pluggable support
1305 for load balancing, tracing, health checking and authentication.  It is also
1306 applicable in last mile of distributed computing to connect devices, mobile
1307 applications and browsers to backend services.")
1308     (license license:asl2.0)))
1309
1310 ;; Note that Tensorflow includes a "third_party" directory, which seems to not
1311 ;; only contain modified subsets of upstream library source code, but also
1312 ;; adapter headers provided by Google (such as the fft.h header, which is not
1313 ;; part of the upstream project code).  The Tensorflow code includes headers
1314 ;; from the "third_party" directory.  It does not look like we can replace
1315 ;; these headers with unmodified upstream files, so we keep them.
1316 (define-public tensorflow
1317   (package
1318     (name "tensorflow")
1319     (version "1.9.0")
1320     (source
1321      (origin
1322        (method git-fetch)
1323        (uri (git-reference
1324              (url "https://github.com/tensorflow/tensorflow.git")
1325              (commit (string-append "v" version))))
1326        (file-name (string-append "tensorflow-" version "-checkout"))
1327        (sha256
1328         (base32
1329          "0a9kwha395g3wgxfwln5j8vn9nkspmd75xldrlqdq540w996g8xa"))))
1330     (build-system cmake-build-system)
1331     (arguments
1332      `(#:tests? #f                      ; no "check" target
1333        #:build-type "Release"
1334        #:configure-flags
1335        (let ((protobuf (assoc-ref %build-inputs "protobuf"))
1336              (protobuf:native (assoc-ref %build-inputs "protobuf:native"))
1337              (jsoncpp (assoc-ref %build-inputs "jsoncpp"))
1338              (snappy (assoc-ref %build-inputs "snappy"))
1339              (sqlite (assoc-ref %build-inputs "sqlite")))
1340          (list
1341           ;; Use protobuf from Guix
1342           (string-append "-Dprotobuf_STATIC_LIBRARIES="
1343                          protobuf "/lib/libprotobuf.so")
1344           (string-append "-DPROTOBUF_PROTOC_EXECUTABLE="
1345                          protobuf:native "/bin/protoc")
1346
1347           ;; Use snappy from Guix
1348           (string-append "-Dsnappy_STATIC_LIBRARIES="
1349                          snappy "/lib/libsnappy.so")
1350           ;; Yes, this is not actually the include directory but a prefix...
1351           (string-append "-Dsnappy_INCLUDE_DIR=" snappy)
1352
1353           ;; Use jsoncpp from Guix
1354           (string-append "-Djsoncpp_STATIC_LIBRARIES="
1355                          jsoncpp "/lib/libjsoncpp.so")
1356           ;; Yes, this is not actually the include directory but a prefix...
1357           (string-append "-Djsoncpp_INCLUDE_DIR=" jsoncpp)
1358
1359           ;; Use sqlite from Guix
1360           (string-append "-Dsqlite_STATIC_LIBRARIES="
1361                          sqlite "/lib/libsqlite.a")
1362
1363           ;; Use system libraries wherever possible.  Currently, this
1364           ;; only affects zlib.
1365           "-Dsystemlib_ALL=ON"
1366           "-Dtensorflow_ENABLE_POSITION_INDEPENDENT_CODE=ON"
1367           "-Dtensorflow_BUILD_SHARED_LIB=ON"
1368           "-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=OFF"
1369           "-Dtensorflow_ENABLE_SSL_SUPPORT=OFF"
1370           "-Dtensorflow_BUILD_CONTRIB_KERNELS=OFF"))
1371        #:make-flags
1372        (list "CC=gcc")
1373        #:modules ((ice-9 ftw)
1374                   (guix build utils)
1375                   (guix build cmake-build-system))
1376        #:phases
1377        (modify-phases %standard-phases
1378          (add-after 'unpack 'set-source-file-times-to-1980
1379            ;; At the end of the tf_python_build_pip_package target, a ZIP
1380            ;; archive should be generated via bdist_wheel, but it fails with
1381            ;; "ZIP does not support timestamps before 1980".  Luckily,
1382            ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
1383            ;; 1980.
1384            (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800") #t))
1385          ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
1386          (add-after 'unpack 'python3.7-compatibility
1387            (lambda _
1388              (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
1389                             "tensorflow/python/lib/core/ndarray_tensor.cc"
1390                             "tensorflow/python/lib/core/py_func.cc")
1391                (("PyUnicode_AsUTF8") "(char *)PyUnicode_AsUTF8"))
1392              (substitute* "tensorflow/c/eager/c_api.h"
1393                (("unsigned char async")
1394                 "unsigned char is_async"))
1395
1396              ;; Remove dependency on tensorboard, a complicated but probably
1397              ;; optional package.
1398              (substitute* "tensorflow/tools/pip_package/setup.py"
1399                ((".*'tensorboard >.*") ""))
1400              #t))
1401          (add-after 'python3.7-compatibility 'chdir
1402            (lambda _ (chdir "tensorflow/contrib/cmake") #t))
1403          (add-after 'chdir 'disable-downloads
1404            (lambda* (#:key inputs #:allow-other-keys)
1405              (substitute* (find-files "external" "\\.cmake$")
1406                (("GIT_REPOSITORY.*") "")
1407                (("GIT_TAG.*") "")
1408                (("PREFIX ")
1409                 "DOWNLOAD_COMMAND \"\"\nPREFIX "))
1410
1411              ;; Use packages from Guix
1412              (let ((grpc (assoc-ref inputs "grpc")))
1413                (substitute* "CMakeLists.txt"
1414                  ;; Sqlite
1415                  (("include\\(sqlite\\)") "")
1416                  (("\\$\\{sqlite_STATIC_LIBRARIES\\}")
1417                   (string-append (assoc-ref inputs "sqlite")
1418                                  "/lib/libsqlite3.so"))
1419                  (("sqlite_copy_headers_to_destination") "")
1420
1421                  ;; PNG
1422                  (("include\\(png\\)") "")
1423                  (("\\$\\{png_STATIC_LIBRARIES\\}")
1424                   (string-append (assoc-ref inputs "libpng")
1425                                  "/lib/libpng16.so"))
1426                  (("png_copy_headers_to_destination") "")
1427
1428                  ;; JPEG
1429                  (("include\\(jpeg\\)") "")
1430                  (("\\$\\{jpeg_STATIC_LIBRARIES\\}")
1431                   (string-append (assoc-ref inputs "libjpeg")
1432                                  "/lib/libjpeg.so"))
1433                  (("jpeg_copy_headers_to_destination") "")
1434
1435                  ;; GIF
1436                  (("include\\(gif\\)") "")
1437                  (("\\$\\{gif_STATIC_LIBRARIES\\}")
1438                   (string-append (assoc-ref inputs "giflib")
1439                                  "/lib/libgif.so"))
1440                  (("gif_copy_headers_to_destination") "")
1441
1442                  ;; lmdb
1443                  (("include\\(lmdb\\)") "")
1444                  (("\\$\\{lmdb_STATIC_LIBRARIES\\}")
1445                   (string-append (assoc-ref inputs "lmdb")
1446                                  "/lib/liblmdb.so"))
1447                  (("lmdb_copy_headers_to_destination") "")
1448
1449                  ;; Protobuf
1450                  (("include\\(protobuf\\)") "")
1451                  (("protobuf_copy_headers_to_destination") "")
1452                  (("^ +protobuf") "")
1453
1454                  ;; gRPC
1455                  (("include\\(grpc\\)")
1456                   "find_package(grpc REQUIRED NAMES gRPC)")
1457                  (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES grpc\\)") "")
1458
1459                  ;; Eigen
1460                  (("include\\(eigen\\)")
1461                   (string-append "find_package(eigen REQUIRED NAMES Eigen3)
1462 set(eigen_INCLUDE_DIRS ${CMAKE_CURRENT_BINARY_DIR}/external/eigen_archive "
1463                                  (assoc-ref inputs "eigen") "/include/eigen3)"))
1464                  (("^ +eigen") "")
1465
1466                  ;; snappy
1467                  (("include\\(snappy\\)")
1468                   "add_definitions(-DTF_USE_SNAPPY)")
1469                  (("list\\(APPEND tensorflow_EXTERNAL_DEPENDENCIES snappy\\)") "")
1470
1471                  ;; jsoncpp
1472                  (("include\\(jsoncpp\\)") "")
1473                  (("^ +jsoncpp") ""))
1474
1475                (substitute* "tf_core_framework.cmake"
1476                  ((" grpc") "")
1477                  (("\\$\\{GRPC_BUILD\\}/grpc_cpp_plugin")
1478                   (which "grpc_cpp_plugin"))
1479                  ;; Link with gRPC libraries
1480                  (("add_library\\(tf_protos_cc.*" m)
1481                   (string-append m
1482                                  (format #f "\ntarget_link_libraries(tf_protos_cc PRIVATE \
1483 ~a/lib/libgrpc++_unsecure.a \
1484 ~a/lib/libgrpc_unsecure.a \
1485 ~a/lib/libaddress_sorting.a \
1486 ~a/lib/libgpr.a \
1487 ~a//lib/libcares.so
1488 )\n"
1489                                          grpc grpc grpc grpc
1490                                          (assoc-ref inputs "c-ares"))))))
1491              (substitute* "tf_tools.cmake"
1492                (("add_dependencies\\(\\$\\{proto_text.*") ""))
1493              ;; Remove dependency on bundled grpc
1494              (substitute* "tf_core_distributed_runtime.cmake"
1495                (("tf_core_cpu grpc") "tf_core_cpu"))
1496
1497              ;; This directory is a dependency of many targets.
1498              (mkdir-p "protobuf")
1499              #t))
1500          (add-after 'configure 'unpack-third-party-sources
1501            (lambda* (#:key inputs #:allow-other-keys)
1502              ;; This is needed to configure bundled packages properly.
1503              (setenv "CONFIG_SHELL" (which "bash"))
1504              (for-each
1505               (lambda (name)
1506                 (let* ((what  (assoc-ref inputs (string-append name "-src")))
1507                        (name* (string-map (lambda (c)
1508                                             (if (char=? c #\-)
1509                                                 #\_ c)) name))
1510                        (where (string-append "../build/" name* "/src/" name*)))
1511                   (cond
1512                    ((string-suffix? ".zip" what)
1513                     (mkdir-p where)
1514                     (with-directory-excursion where
1515                       (invoke "unzip" what)))
1516                    ((string-suffix? ".tar.gz" what)
1517                     (mkdir-p where)
1518                     (invoke "tar" "xf" what
1519                             "-C" where "--strip-components=1"))
1520                    (else
1521                     (let ((parent (dirname where)))
1522                       (mkdir-p parent)
1523                       (with-directory-excursion parent
1524                         (when (file-exists? name*)
1525                           (delete-file-recursively name*))
1526                         (copy-recursively what name*)
1527                         (map make-file-writable
1528                              (find-files name* ".*"))))))))
1529               (list "boringssl"
1530                     "cub"
1531                     "double-conversion"
1532                     "farmhash"
1533                     "fft2d"
1534                     "highwayhash"
1535                     "nsync"
1536                     "re2"))
1537
1538              (rename-file "../build/cub/src/cub/cub-1.8.0/"
1539                           "../build/cub/src/cub/cub/")
1540              #t))
1541          (add-after 'unpack 'fix-python-build
1542            (lambda* (#:key inputs outputs #:allow-other-keys)
1543              (mkdir-p "protobuf-src")
1544              (invoke "tar" "xf" (assoc-ref inputs "protobuf:src")
1545                      "-C" "protobuf-src" "--strip-components=1")
1546              (mkdir-p "eigen-src")
1547              (invoke "tar" "xf" (assoc-ref inputs "eigen:src")
1548                      "-C" "eigen-src" "--strip-components=1")
1549
1550              (substitute* "tensorflow/contrib/cmake/tf_python.cmake"
1551                ;; Ensure that all Python dependencies can be found at build time.
1552                (("PYTHONPATH=\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/tf_python" m)
1553                 (string-append m ":" (getenv "PYTHONPATH")))
1554                ;; Take protobuf source files from our source package.
1555                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/protobuf/src/protobuf/src/google")
1556                 (string-append (getcwd) "/protobuf-src/src/google")))
1557
1558              (substitute* '("tensorflow/contrib/cmake/tf_shared_lib.cmake"
1559                             "tensorflow/contrib/cmake/tf_python.cmake")
1560                ;; Take Eigen source files from our source package.
1561                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/eigen/src/eigen/")
1562                 (string-append (getcwd) "/eigen-src/"))
1563                ;; Take Eigen headers from our own package.
1564                (("\\$\\{CMAKE_CURRENT_BINARY_DIR\\}/external/eigen_archive")
1565                 (string-append (assoc-ref inputs "eigen") "/include/eigen3")))
1566
1567              ;; Correct the RUNPATH of ops libraries generated for Python.
1568              ;; TODO: this doesn't work :(
1569              ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1570              ;; warning: RUNPATH contains bogus entries: ("/tmp/guix-build-tensorflow-1.9.0.drv-0/source/tensorflow/contrib/build")
1571              ;; /gnu/store/...-tensorflow-1.9.0/lib/python3.7/site-packages/tensorflow/contrib/seq2seq/python/ops/lib_beam_search_ops.so:
1572              ;; error: depends on 'libpywrap_tensorflow_internal.so', which
1573              ;; cannot be found in RUNPATH ...
1574              (substitute* "tensorflow/contrib/cmake/tf_cc_ops.cmake"
1575                (("set_target_properties.*")
1576                 (string-append "set_target_properties(${_AT_TARGET} PROPERTIES \
1577 COMPILE_FLAGS ${target_compile_flags} \
1578 INSTALL_RPATH_USE_LINK_PATH TRUE \
1579 INSTALL_RPATH " (assoc-ref outputs "out") "/lib)\n")))
1580              #t))
1581          (add-after 'build 'build-pip-package
1582            (lambda* (#:key outputs #:allow-other-keys)
1583              (setenv "LDFLAGS"
1584                      (string-append "-Wl,-rpath="
1585                                     (assoc-ref outputs "out") "/lib"))
1586              (invoke "make" "tf_python_build_pip_package")
1587              #t))
1588          (add-after 'build-pip-package 'install-python
1589            (lambda* (#:key outputs #:allow-other-keys)
1590              (let ((out (assoc-ref outputs "out"))
1591                    (wheel (car (find-files "../build/tf_python/dist/" "\\.whl$"))))
1592                (invoke "python" "-m" "pip" "install" wheel
1593                        (string-append "--prefix=" out))
1594
1595                ;; XXX: broken RUNPATH, see fix-python-build phase.
1596                (delete-file
1597                 (string-append
1598                  out "/lib/python3.7/site-packages/tensorflow/contrib/"
1599                  "seq2seq/python/ops/lib_beam_search_ops.so"))
1600                #t))))))
1601     (native-inputs
1602      `(("pkg-config" ,pkg-config)
1603        ("protobuf:native" ,protobuf-next) ; protoc
1604        ("protobuf:src" ,(package-source protobuf-next))
1605        ("eigen:src" ,(package-source eigen-for-tensorflow))
1606        ;; The commit hashes and URLs for third-party source code are taken
1607        ;; from "tensorflow/workspace.bzl".
1608        ("boringssl-src"
1609         ,(let ((commit "ee7aa02")
1610                (revision "1"))
1611            (origin
1612              (method git-fetch)
1613              (uri (git-reference
1614                    (url "https://boringssl.googlesource.com/boringssl")
1615                    (commit commit)))
1616              (file-name (string-append "boringssl-0-" revision
1617                                        (string-take commit 7)
1618                                        "-checkout"))
1619              (sha256
1620               (base32
1621                "1jf693q0nw0adsic6cgmbdx6g7wr4rj4vxa8j1hpn792fqhd8wgw")))))
1622        ("cub-src"
1623         ,(let ((version "1.8.0"))
1624            (origin
1625              (method url-fetch)
1626              (uri (string-append "https://mirror.bazel.build/github.com/NVlabs/"
1627                                  "cub/archive/" version ".zip"))
1628              (file-name (string-append "cub-" version ".zip"))
1629              (sha256
1630               (base32
1631                "1hsqikqridb90dkxkjr2918dcry6pfh46ccnwrzawl56aamhdykb")))))
1632        ("double-conversion-src"
1633         ,(let ((commit "5664746")
1634                (revision "1"))
1635            (origin
1636              (method git-fetch)
1637              (uri (git-reference
1638                    (url "https://github.com/google/double-conversion.git")
1639                    (commit commit)))
1640              (file-name
1641               (git-file-name "double-conversion"
1642                              (string-append "0-" revision "."
1643                                             (string-take commit 7))))
1644              (sha256
1645               (base32
1646                "1h5lppqqxcvdg5jq42i5msgwx20ryij3apvmndflngrgdpc04gn1")))))
1647        ("farmhash-src"
1648         ,(let ((commit "816a4ae622e964763ca0862d9dbd19324a1eaf45"))
1649            (origin
1650              (method url-fetch)
1651              (uri (string-append
1652                    "https://mirror.bazel.build/github.com/google/farmhash/archive/"
1653                    commit ".tar.gz"))
1654              (file-name (string-append "farmhash-0-" (string-take commit 7)
1655                                        ".tar.gz"))
1656              (sha256
1657               (base32
1658                "185b2xdxl4d4cnsnv6abg8s22gxvx8673jq2yaq85bz4cdy58q35")))))
1659        ;; The license notice on the home page at
1660        ;; http://www.kurims.kyoto-u.ac.jp/~ooura/fft.html says:
1661        ;;   Copyright Takuya OOURA, 1996-2001
1662        ;;
1663        ;;   You may use, copy, modify and distribute this code for any purpose
1664        ;;   (include commercial use) and without fee. Please refer to this
1665        ;;   package when you modify this code.
1666        ;;
1667        ;; We take the identical tarball from the Bazel mirror, because the URL
1668        ;; at the home page is not versioned and might change.
1669        ("fft2d-src"
1670         ,(origin
1671            (method url-fetch)
1672            (uri "https://mirror.bazel.build/www.kurims.kyoto-u.ac.jp/~ooura/fft.tgz")
1673            (file-name "fft2d.tar.gz")
1674            (sha256
1675             (base32
1676              "15jjkfvhqvl2c0753d2di8hz0pyzn598g74wqy79awdrf1y67fsj"))))
1677        ("highwayhash-src"
1678         ,(let ((commit "be5edafc2e1a455768e260ccd68ae7317b6690ee")
1679                (revision "1"))
1680            (origin
1681              (method git-fetch)
1682              (uri (git-reference
1683                    (url "https://github.com/google/highwayhash.git")
1684                    (commit commit)))
1685              (file-name (string-append "highwayhash-0-" revision
1686                                        (string-take commit 7)
1687                                        "-checkout"))
1688              (sha256
1689               (base32
1690                "154jwf98cyy54hldr94pgjn85zynly3abpnc1avmb8a18lzwjyb6")))))
1691        ("nsync-src"
1692         ,(let ((version "0559ce013feac8db639ee1bf776aca0325d28777")
1693                (revision "1"))
1694            (origin
1695              (method url-fetch)
1696              (uri (string-append "https://mirror.bazel.build/"
1697                                  "github.com/google/nsync/archive/"
1698                                  version ".tar.gz"))
1699              (file-name (string-append "nsync-0." revision
1700                                        "-" (string-take version 7)
1701                                        ".tar.gz"))
1702              (sha256
1703               (base32
1704                "0qdkyqym34x739mmzv97ah5r7ph462v5xkxqxvidmcfqbi64b132")))))
1705        ("re2-src"
1706         ,(let ((commit "e7efc48")
1707                (revision "1"))
1708            (origin
1709              (method git-fetch)
1710              (uri (git-reference
1711                    (url "https://github.com/google/re2")
1712                    (commit commit)))
1713              (file-name (string-append "re2-0-" revision
1714                                        (string-take commit 7)
1715                                        "-checkout"))
1716              (sha256
1717               (base32
1718                "161g9841rjfsy5pn52fcis0s9hdr7rxvb06pad38j5rppfihvign")))))
1719        ("googletest" ,googletest)
1720        ("swig" ,swig)
1721        ("unzip" ,unzip)))
1722     (propagated-inputs
1723      `(("python-absl-py" ,python-absl-py)
1724        ("python-astor" ,python-astor)
1725        ("python-gast" ,python-gast)
1726        ("python-grpcio" ,python-grpcio)
1727        ("python-numpy" ,python-numpy)
1728        ("python-protobuf" ,python-protobuf-next)
1729        ("python-six" ,python-six)
1730        ("python-termcolo" ,python-termcolor)
1731        ("python-wheel" ,python-wheel)))
1732     (inputs
1733      `(("c-ares" ,c-ares-next)
1734        ("eigen" ,eigen-for-tensorflow)
1735        ("gemmlowp" ,gemmlowp-for-tensorflow)
1736        ("lmdb" ,lmdb)
1737        ("libjpeg" ,libjpeg)
1738        ("libpng" ,libpng)
1739        ("giflib" ,giflib)
1740        ("grpc" ,grpc)
1741        ("jsoncpp" ,jsoncpp-for-tensorflow)
1742        ("snappy" ,snappy)
1743        ("sqlite" ,sqlite)
1744        ("protobuf" ,protobuf-next)
1745        ("python" ,python-wrapper)
1746        ("zlib" ,zlib)))
1747     (home-page "https://tensorflow.org")
1748     (synopsis "Machine learning framework")
1749     (description
1750      "TensorFlow is a flexible platform for building and training machine
1751 learning models.  It provides a library for high performance numerical
1752 computation and includes high level Python APIs, including both a sequential
1753 API for beginners that allows users to build models quickly by plugging
1754 together building blocks and a subclassing API with an imperative style for
1755 advanced research.")
1756     (license license:asl2.0)))