;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (gnu packages compression)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages gcc)
+ #:use-module (gnu packages image)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
- #:use-module (gnu packages xml))
+ #:use-module (gnu packages xml)
+ #:use-module (gnu packages xorg))
(define-public libsvm
(package
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
(build-system gnu-build-system)
(arguments
- `(#:phases
+ `(#:imported-modules (,@%gnu-build-system-modules
+ (guix build python-build-system))
+ #:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
(lambda _ (chdir "ghmm") #t))
- (add-after 'enter-dir 'fix-PYTHONPATH
- (lambda* (#:key outputs #:allow-other-keys)
- ;; The Python tests fail as the library is assumed to be stored
- ;; in ./build/lib.linux-i686-*. To fix this we detect the CPU
- ;; and use it in the path.
- (substitute* "configure.in"
- (("AM_INIT_AUTOMAKE" line)
- (string-append line "\nAC_CANONICAL_HOST\n")))
- (substitute* "ghmmwrapper/Makefile.am"
- (("i686") "@host_cpu@"))
+ (delete 'check)
+ (add-after 'install 'check
+ (assoc-ref %standard-phases 'check))
+ (add-before 'check 'fix-PYTHONPATH
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((python-version ((@@ (guix build python-build-system)
+ get-python-version)
+ (assoc-ref inputs "python"))))
+ (setenv "PYTHONPATH"
+ (string-append (getenv "PYTHONPATH")
+ ":" (assoc-ref outputs "out")
+ "/lib/python" python-version
+ "/site-packages")))
#t))
(add-after 'enter-dir 'fix-runpath
(lambda* (#:key outputs #:allow-other-keys)
training, HMM clustering, HMM mixtures.")
(license license:lgpl2.0+))))
+(define-public mcl
+ (package
+ (name "mcl")
+ (version "14.137")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://micans.org/mcl/src/mcl-"
+ (string-replace-substring version "." "-")
+ ".tar.gz"))
+ (sha256
+ (base32
+ "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:configure-flags (list "--enable-blast")))
+ (inputs
+ `(("perl" ,perl)))
+ (home-page "http://micans.org/mcl/")
+ (synopsis "Clustering algorithm for graphs")
+ (description
+ "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
+fast and scalable unsupervised cluster algorithm for graphs (also known as
+networks) based on simulation of (stochastic) flow in graphs.")
+ ;; In the LICENCE file and web page it says "The software is licensed
+ ;; under the GNU General Public License, version 3.", but in several of
+ ;; the source code files it suggests GPL3 or later.
+ ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
+ (license license:gpl3)))
+
(define-public randomjungle
(package
(name "randomjungle")
(native-inputs
`(("gfortran" ,gfortran)
("gfortran:lib" ,gfortran "lib")))
+ ;; Non-portable assembly instructions are used so building fails on
+ ;; platforms other than x86_64 or i686.
+ (supported-systems '("x86_64-linux" "i686-linux"))
(home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
(synopsis "Implementation of the Random Forests machine learning method")
(description
"This package provides functions for feed-forward neural networks with a
single hidden layer, and for multinomial log-linear models.")
(license (list license:gpl2+ license:gpl3+))))
+
+(define-public dlib
+ (package
+ (name "dlib")
+ (version "19.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://dlib.net/files/dlib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "0p2pvcdalc6jhb6r99ybvjd9x74sclr0ngswdg9j2xl5pj7knbr4"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete ~13MB of bundled dependencies.
+ (delete-file-recursively "dlib/external")
+ (delete-file-recursively "docs/dlib/external")))))
+ (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.
+ ;; The rest is known to fail on non-x86_64 platforms in the current release.
+ ;; Some have been fixed in git; this list should be readjusted next update.
+ (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" "max_cost_assignment"))
+ ((string-prefix? "i686" system)
+ '("optimization" "matrix2" "mpc"))
+ (else '()))))
+ ;; The following test fails due a bug in openblas < 0.2.18.
+ (append! disabled-tests '("empirical_map"))
+ (for-each
+ (lambda (test)
+ (substitute* "dlib/test/makefile"
+ (((string-append "SRC \\+= " test "\\.cpp")) "")) #t)
+ disabled-tests))))
+ (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")))))))
+ (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)))
HCoop / jackhill / guix / guix.git / blobdiff