diff options
Diffstat (limited to 'gnu/packages/machine-learning.scm')
| -rw-r--r-- | gnu/packages/machine-learning.scm | 75 |
1 files changed, 41 insertions, 34 deletions
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index a86bdcb5ed..3f525e39a5 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -8,6 +8,8 @@ ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org> ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com> +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> +;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -300,7 +302,9 @@ networks) based on simulation of (stochastic) flow in graphs.") "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110")))) (build-system ocaml-build-system) (arguments - `(#:phases + `(#:ocaml ,ocaml-4.02 + #:findlib ,ocaml4.02-findlib + #:phases (modify-phases %standard-phases (add-before 'configure 'patch-paths (lambda _ @@ -328,15 +332,17 @@ algorithm.") (origin (method url-fetch) (uri (string-append - "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/" - "randomjungle-" version ".tar_.gz")) + "https://www.imbs.uni-luebeck.de/fileadmin/files/Software" + "/randomjungle/randomjungle-" version ".tar_.gz")) + (patches (search-patches "randomjungle-disable-static-build.patch")) (sha256 (base32 "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w")))) (build-system gnu-build-system) (arguments `(#:configure-flags - (list (string-append "--with-boost=" + (list "--disable-static" + (string-append "--with-boost=" (assoc-ref %build-inputs "boost"))) #:phases (modify-phases %standard-phases @@ -356,7 +362,7 @@ algorithm.") ;; 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/") + (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224") (synopsis "Implementation of the Random Forests machine learning method") (description "Random Jungle is an implementation of Random Forests. It is supposed to @@ -560,13 +566,13 @@ I/O.") (define-public r-adaptivesparsity (package (name "r-adaptivesparsity") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "AdaptiveSparsity" version)) (sha256 (base32 - "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z")))) + "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91")))) (properties `((upstream-name . "AdaptiveSparsity"))) (build-system r-build-system) @@ -579,7 +585,9 @@ I/O.") (("PKG_LIBS=" prefix) (string-append prefix "-larmadillo")))))))) (propagated-inputs - `(("r-rcpp" ,r-rcpp) + `(("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) ("r-rcpparmadillo" ,r-rcpparmadillo))) (inputs `(("armadillo" ,armadillo))) @@ -594,14 +602,14 @@ geometric models.") (define-public r-kernlab (package (name "r-kernlab") - (version "0.9-26") + (version "0.9-27") (source (origin (method url-fetch) (uri (cran-uri "kernlab" version)) (sha256 (base32 - "0xv0slf3ggw3sswsi34416lb1g3h1pqkrr2h7r1n1kvgii3l0jcm")))) + "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn")))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/kernlab") (synopsis "Kernel-based machine learning tools") @@ -701,40 +709,39 @@ computing environments.") (define-public python-scikit-learn (package (name "python-scikit-learn") - (version "0.19.1") + (version "0.20.1") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/scikit-learn/scikit-learn/archive/" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/scikit-learn/scikit-learn.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9")) - (patches (search-patches - "python-scikit-learn-fix-test-non-determinism.patch")))) + "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (delete 'check) - (add-after 'install 'check - ;; Running tests from the source directory requires - ;; an "inplace" build with paths relative to CWD. - ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing - ;; Use the installed version instead. - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - ;; some tests require access to "$HOME" + (add-after 'build 'build-ext + (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t)) + (replace 'check + (lambda _ + ;; Restrict OpenBLAS threads to prevent segfaults while testing! + (setenv "OPENBLAS_NUM_THREADS" "1") + + ;; Some tests require write access to $HOME. (setenv "HOME" "/tmp") - ;; Step out of the source directory just to be sure. - (chdir "..") - (invoke "nosetests" "-v" "sklearn")))))) + + (invoke "pytest" "sklearn" "-m" "not network"))) + ;; FIXME: This fails with permission denied + (delete 'reset-gzip-timestamps)))) (inputs `(("openblas" ,openblas))) (native-inputs - `(("python-nose" ,python-nose) + `(("python-pytest" ,python-pytest) + ("python-pandas" ,python-pandas) ;for tests ("python-cython" ,python-cython))) (propagated-inputs `(("python-numpy" ,python-numpy) @@ -742,8 +749,8 @@ computing environments.") (home-page "http://scikit-learn.org/") (synopsis "Machine Learning in Python") (description - "Scikit-learn provides simple and efficient tools for data -mining and data analysis.") + "Scikit-learn provides simple and efficient tools for data mining and +data analysis.") (license license:bsd-3))) (define-public python2-scikit-learn |