mirror of
https://git.in.rschanz.org/ryan77627/guix.git
synced 2024-11-08 16:06:16 -05:00
9e37e537a2
This is a follow-up to commit a8cba9dd11.
Reported-by: Efraim Flashner <efraim@flashner.co.il>
605 lines
24 KiB
Scheme
605 lines
24 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
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;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages machine-learning)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix download)
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#:use-module (guix svn-download)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system ocaml)
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#:use-module (guix build-system r)
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#:use-module (gnu packages)
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#:use-module (gnu packages autotools)
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#:use-module (gnu packages boost)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages dejagnu)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages image)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages ocaml)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xorg))
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(define-public libsvm
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(package
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(name "libsvm")
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(version "3.20")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/cjlin1/libsvm/archive/v"
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(string-delete #\. version) ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"1jpjlql3frjza7zxzrqqr2firh44fjb8fqsdmvz6bjz7sb47zgp4"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no "check" target
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#:phases (modify-phases %standard-phases
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(delete 'configure)
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(replace
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'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin/")))
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(mkdir-p bin)
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(for-each (lambda (file)
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(copy-file file (string-append bin file)))
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'("svm-train"
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"svm-predict"
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"svm-scale")))
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#t)))))
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(home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
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(synopsis "Library for Support Vector Machines")
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(description
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"LIBSVM is a machine learning library for support vector
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classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
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distribution estimation (one-class SVM). It supports multi-class
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classification.")
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(license license:bsd-3)))
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(define-public python-libsvm
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(package (inherit libsvm)
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(name "python-libsvm")
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ;no "check" target
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#:make-flags '("-C" "python")
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#:phases
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(modify-phases %standard-phases
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(delete 'configure)
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(replace
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'install
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((site (string-append (assoc-ref outputs "out")
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"/lib/python"
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(string-take
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(string-take-right
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(assoc-ref inputs "python") 5) 3)
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"/site-packages/")))
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(substitute* "python/svm.py"
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(("../libsvm.so.2") "libsvm.so.2"))
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(mkdir-p site)
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(for-each (lambda (file)
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(copy-file file (string-append site (basename file))))
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(find-files "python" "\\.py"))
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(copy-file "libsvm.so.2"
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(string-append site "libsvm.so.2")))
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#t)))))
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(inputs
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`(("python" ,python)))
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(synopsis "Python bindings of libSVM")))
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(define-public ghmm
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;; The latest release candidate is several years and a couple of fixes have
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;; been published since. This is why we download the sources from the SVN
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;; repository.
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(let ((svn-revision 2341))
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(package
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(name "ghmm")
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(version (string-append "0.9-rc3-0." (number->string svn-revision)))
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(source (origin
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(method svn-fetch)
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(uri (svn-reference
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(url "http://svn.code.sf.net/p/ghmm/code/trunk")
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(revision svn-revision)))
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(file-name (string-append name "-" version))
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(sha256
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(base32
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"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
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(build-system gnu-build-system)
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(arguments
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`(#:imported-modules (,@%gnu-build-system-modules
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(guix build python-build-system))
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'enter-dir
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(lambda _ (chdir "ghmm") #t))
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(delete 'check)
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(add-after 'install 'check
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(assoc-ref %standard-phases 'check))
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(add-before 'check 'fix-PYTHONPATH
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((python-version ((@@ (guix build python-build-system)
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get-python-version)
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(assoc-ref inputs "python"))))
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(setenv "PYTHONPATH"
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(string-append (getenv "PYTHONPATH")
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":" (assoc-ref outputs "out")
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"/lib/python" python-version
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"/site-packages")))
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#t))
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(add-after 'enter-dir 'fix-runpath
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* "ghmmwrapper/setup.py"
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(("^(.*)extra_compile_args = \\[" line indent)
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(string-append indent
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"extra_link_args = [\"-Wl,-rpath="
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(assoc-ref outputs "out") "/lib\"],\n"
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line
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"\"-Wl,-rpath="
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(assoc-ref outputs "out")
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"/lib\", ")))
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#t))
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(add-after 'enter-dir 'disable-broken-tests
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(lambda _
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(substitute* "tests/Makefile.am"
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;; GHMM_SILENT_TESTS is assumed to be a command.
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(("TESTS_ENVIRONMENT.*") "")
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;; Do not build broken tests.
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(("chmm .*") "")
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(("read_fa .*") "")
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(("mcmc .*") "")
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(("label_higher_order_test.*$")
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"label_higher_order_test\n"))
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;; These Python unittests are broken as there is no gato.
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;; See https://sourceforge.net/p/ghmm/support-requests/3/
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(substitute* "ghmmwrapper/ghmmunittests.py"
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(("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
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line indent)
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(string-append indent
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"@unittest.skip(\"Disabled by Guix\")\n"
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line)))
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#t))
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(add-before 'configure 'autogen
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(lambda _
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(zero? (system* "bash" "./autogen.sh")))))))
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(inputs
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`(("python" ,python-2) ; only Python 2 is supported
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("libxml2" ,libxml2)))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("dejagnu" ,dejagnu)
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("swig" ,swig)
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("autoconf" ,autoconf)
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("automake" ,automake)
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("libtool" ,libtool)))
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(home-page "http://ghmm.org")
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(synopsis "Hidden Markov Model library")
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(description
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"The General Hidden Markov Model library (GHMM) is a C library with
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additional Python bindings implementing a wide range of types of @dfn{Hidden
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Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
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training, HMM clustering, HMM mixtures.")
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(license license:lgpl2.0+))))
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(define-public mcl
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(package
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(name "mcl")
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(version "14.137")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"http://micans.org/mcl/src/mcl-"
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(string-replace-substring version "." "-")
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".tar.gz"))
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(sha256
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(base32
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"15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
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(build-system gnu-build-system)
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(arguments
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`(#:configure-flags (list "--enable-blast")))
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(inputs
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`(("perl" ,perl)))
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(home-page "http://micans.org/mcl/")
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(synopsis "Clustering algorithm for graphs")
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(description
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"The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
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fast and scalable unsupervised cluster algorithm for graphs (also known as
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networks) based on simulation of (stochastic) flow in graphs.")
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;; In the LICENCE file and web page it says "The software is licensed
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;; under the GNU General Public License, version 3.", but in several of
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;; the source code files it suggests GPL3 or later.
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;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
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(license license:gpl3)))
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(define-public ocaml-mcl
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(package
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(name "ocaml-mcl")
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(version "12-068oasis4")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/fhcrc/mcl/archive/"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
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(build-system ocaml-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-before 'configure 'patch-paths
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(lambda _
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(substitute* "configure"
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(("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
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(substitute* "setup.ml"
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(("LDFLAGS=-fPIC")
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(string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
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#t)))))
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(home-page "https://github.com/fhcrc/mcl")
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(synopsis "OCaml wrappers around MCL")
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(description
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"This package provides OCaml bindings for the MCL graph clustering
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algorithm.")
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(license license:gpl3)))
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(define-public ocaml4.01-mcl
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(package-with-ocaml4.01 ocaml-mcl))
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(define-public randomjungle
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(package
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(name "randomjungle")
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(version "2.1.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
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"randomjungle-" version ".tar_.gz"))
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(sha256
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(base32
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"12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
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(build-system gnu-build-system)
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(arguments
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`(#:configure-flags
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(list (string-append "--with-boost="
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(assoc-ref %build-inputs "boost")))
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#:phases
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(modify-phases %standard-phases
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(add-before
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'configure 'set-CXXFLAGS
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(lambda _
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(setenv "CXXFLAGS" "-fpermissive ")
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#t)))))
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(inputs
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`(("boost" ,boost)
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("gsl" ,gsl)
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("libxml2" ,libxml2)
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("zlib" ,zlib)))
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(native-inputs
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`(("gfortran" ,gfortran)
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("gfortran:lib" ,gfortran "lib")))
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;; Non-portable assembly instructions are used so building fails on
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;; platforms other than x86_64 or i686.
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(supported-systems '("x86_64-linux" "i686-linux"))
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(home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
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(synopsis "Implementation of the Random Forests machine learning method")
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(description
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"Random Jungle is an implementation of Random Forests. It is supposed to
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analyse high dimensional data. In genetics, it can be used for analysing big
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Genome Wide Association (GWA) data. Random Forests is a powerful machine
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learning method. Most interesting features are variable selection, missing
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value imputation, classifier creation, generalization error estimation and
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sample proximities between pairs of cases.")
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(license license:gpl3+)))
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(define-public shogun
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(package
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(name "shogun")
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(version "4.0.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"ftp://shogun-toolbox.org/shogun/releases/"
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(version-major+minor version)
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"/sources/shogun-" version ".tar.bz2"))
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(sha256
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(base32
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"159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
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(modules '((guix build utils)
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(ice-9 rdelim)))
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(snippet
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'(begin
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;; Remove non-free sources and files referencing them
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(for-each delete-file
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(find-files "src/shogun/classifier/svm/"
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"SVMLight\\.(cpp|h)"))
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(for-each delete-file
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(find-files "examples/undocumented/libshogun/"
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(string-append
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"(classifier_.*svmlight.*|"
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"evaluation_cross_validation_locked_comparison).cpp")))
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;; Remove non-free functions.
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(define (delete-ifdefs file)
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(with-atomic-file-replacement file
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(lambda (in out)
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(let loop ((line (read-line in 'concat))
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(skipping? #f))
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(if (eof-object? line)
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#t
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(let ((skip-next?
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(or (and skipping?
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(not (string-prefix?
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"#endif //USE_SVMLIGHT" line)))
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(string-prefix?
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"#ifdef USE_SVMLIGHT" line))))
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(when (or (not skipping?)
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(and skipping? (not skip-next?)))
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(display line out))
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(loop (read-line in 'concat) skip-next?)))))))
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(for-each delete-ifdefs (find-files "src/shogun/kernel/"
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"^Kernel\\.(cpp|h)"))))))
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(build-system cmake-build-system)
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(arguments
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'(#:tests? #f ;no check target
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#:phases
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(alist-cons-after
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'unpack 'delete-broken-symlinks
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|
(lambda _
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|
(for-each delete-file '("applications/arts/data"
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|
"applications/asp/data"
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|
"applications/easysvm/data"
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"applications/msplicer/data"
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"applications/ocr/data"
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"examples/documented/data"
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"examples/documented/matlab_static"
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|
"examples/documented/octave_static"
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"examples/undocumented/data"
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|
"examples/undocumented/matlab_static"
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"examples/undocumented/octave_static"
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"tests/integration/data"
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"tests/integration/matlab_static"
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"tests/integration/octave_static"
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|
"tests/integration/python_modular/tests"))
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#t)
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|
(alist-cons-after
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'unpack 'change-R-target-path
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|
(lambda* (#:key outputs #:allow-other-keys)
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|
(substitute* '("src/interfaces/r_modular/CMakeLists.txt"
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|
"src/interfaces/r_static/CMakeLists.txt"
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|
"examples/undocumented/r_modular/CMakeLists.txt")
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|
(("\\$\\{R_COMPONENT_LIB_PATH\\}")
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|
(string-append (assoc-ref outputs "out")
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"/lib/R/library/")))
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|
#t)
|
|
(alist-cons-after
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|
'unpack 'fix-octave-modules
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|
(lambda* (#:key outputs #:allow-other-keys)
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|
(substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
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|
"src/interfaces/octave_static/CMakeLists.txt")
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(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
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"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
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|
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;; change target directory
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(substitute* "src/interfaces/octave_modular/CMakeLists.txt"
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(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
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|
(string-append (assoc-ref outputs "out")
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"/share/octave/packages")))
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|
#t)
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|
(alist-cons-before
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'build 'set-HOME
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|
;; $HOME needs to be set at some point during the build phase
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(lambda _ (setenv "HOME" "/tmp") #t)
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%standard-phases))))
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#:configure-flags
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(list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
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"-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
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;;"-DJavaModular=ON" ;requires unpackaged jblas
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;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
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;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
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;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
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"-DOctaveModular=ON"
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"-DOctaveStatic=ON"
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"-DPythonModular=ON"
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"-DPythonStatic=ON"
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"-DRModular=ON"
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"-DRStatic=ON"
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"-DCmdLineStatic=ON")))
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(inputs
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`(("python" ,python)
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("numpy" ,python-numpy)
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("r-minimal" ,r-minimal)
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("octave" ,octave)
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|
("swig" ,swig)
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|
("hdf5" ,hdf5)
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|
("atlas" ,atlas)
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("arpack" ,arpack-ng)
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("lapack" ,lapack)
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("glpk" ,glpk)
|
|
("libxml2" ,libxml2)
|
|
("lzo" ,lzo)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
;; Non-portable SSE instructions are used so building fails on platforms
|
|
;; other than x86_64.
|
|
(supported-systems '("x86_64-linux"))
|
|
(home-page "http://shogun-toolbox.org/")
|
|
(synopsis "Machine learning toolbox")
|
|
(description
|
|
"The Shogun Machine learning toolbox provides a wide range of unified and
|
|
efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
|
|
combine multiple data representations, algorithm classes, and general purpose
|
|
tools. This enables both rapid prototyping of data pipelines and extensibility
|
|
in terms of new algorithms.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-adaptivesparsity
|
|
(package
|
|
(name "r-adaptivesparsity")
|
|
(version "1.4")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "AdaptiveSparsity" version))
|
|
(sha256
|
|
(base32
|
|
"1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
|
|
(properties
|
|
`((upstream-name . "AdaptiveSparsity")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'link-against-armadillo
|
|
(lambda _
|
|
(substitute* "src/Makevars"
|
|
(("PKG_LIBS=" prefix)
|
|
(string-append prefix "-larmadillo"))))))))
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
|
(home-page "http://cran.r-project.org/web/packages/AdaptiveSparsity")
|
|
(synopsis "Adaptive sparsity models")
|
|
(description
|
|
"This package implements the Figueiredo machine learning algorithm for
|
|
adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
|
|
geometric models.")
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public r-kernlab
|
|
(package
|
|
(name "r-kernlab")
|
|
(version "0.9-25")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "kernlab" version))
|
|
(sha256
|
|
(base32
|
|
"0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/kernlab")
|
|
(synopsis "Kernel-based machine learning tools")
|
|
(description
|
|
"This package provides kernel-based machine learning methods for
|
|
classification, regression, clustering, novelty detection, quantile regression
|
|
and dimensionality reduction. Among other methods @code{kernlab} includes
|
|
Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
|
|
and a QP solver.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public dlib
|
|
(package
|
|
(name "dlib")
|
|
(version "19.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append
|
|
"http://dlib.net/files/dlib-" version ".tar.bz2"))
|
|
(sha256
|
|
(base32
|
|
"0gfy83av717qymv53yv7ki6mgh6mdw4xcxxbjk8lrs72f8qvnrcw"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; Delete ~13MB of bundled dependencies.
|
|
(delete-file-recursively "dlib/external")
|
|
(delete-file-recursively "docs/dlib/external")
|
|
#t))))
|
|
(build-system cmake-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'disable-asserts
|
|
(lambda _
|
|
;; config.h recommends explicitly enabling or disabling asserts
|
|
;; when building as a shared library. By default neither is set.
|
|
(substitute* "dlib/config.h"
|
|
(("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
|
|
#t))
|
|
(add-after 'disable-asserts 'disable-failing-tests
|
|
(lambda _
|
|
;; One test times out on MIPS, so we need to disable it.
|
|
;; Others are flaky on some platforms.
|
|
(let* ((system ,(or (%current-target-system)
|
|
(%current-system)))
|
|
(disabled-tests (cond
|
|
((string-prefix? "mips64" system)
|
|
'("object_detector" ; timeout
|
|
"data_io"))
|
|
((string-prefix? "armhf" system)
|
|
'("learning_to_track"))
|
|
((string-prefix? "i686" system)
|
|
'("optimization"))
|
|
(else '()))))
|
|
(for-each
|
|
(lambda (test)
|
|
(substitute* "dlib/test/makefile"
|
|
(((string-append "SRC \\+= " test "\\.cpp")) "")))
|
|
disabled-tests)
|
|
#t)))
|
|
(replace 'check
|
|
(lambda _
|
|
;; No test target, so we build and run the unit tests here.
|
|
(let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
|
|
(with-directory-excursion test-dir
|
|
(setenv "CXXFLAGS" "-std=gnu++11")
|
|
(and (zero? (system* "make" "-j" (number->string (parallel-job-count))))
|
|
(zero? (system* "./dtest" "--runall")))))))
|
|
(add-after 'install 'delete-static-library
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(delete-file (string-append (assoc-ref outputs "out")
|
|
"/lib/libdlib.a"))
|
|
#t)))))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("giflib" ,giflib)
|
|
("lapack" ,lapack)
|
|
("libjpeg" ,libjpeg)
|
|
("libpng" ,libpng)
|
|
("libx11" ,libx11)
|
|
("openblas" ,openblas)
|
|
("zlib" ,zlib)))
|
|
(synopsis
|
|
"Toolkit for making machine learning and data analysis applications in C++")
|
|
(description
|
|
"Dlib is a modern C++ toolkit containing machine learning algorithms and
|
|
tools. It is used in both industry and academia in a wide range of domains
|
|
including robotics, embedded devices, mobile phones, and large high performance
|
|
computing environments.")
|
|
(home-page "http://dlib.net")
|
|
(license license:boost1.0)))
|