2015-05-28 15:53:14 +02:00
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;;; GNU Guix --- Functional package management for GNU
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2018-05-31 12:34:06 +02:00
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;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
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2016-05-25 20:48:22 +02:00
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;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
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2017-11-17 22:07:23 +01:00
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;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
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2018-01-10 03:53:16 +01:00
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;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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2018-05-09 16:01:40 +02:00
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;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
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2018-02-01 15:07:58 +01:00
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;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
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;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
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2018-04-28 05:47:03 +02:00
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;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
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gnu: ocaml: Update to 4.7.0.
Update ocaml to the latest version and fixes dependent packages by
updating them or by adding new inputs, such as ocaml-num and ocamlbuild,
that were removed from the core ocaml package. Rename packages that
cannot be built with the new compiler with an ocaml4.02 prefix. Add
ocaml4.02 dependencies.
* gnu/packages/ocaml.scm (ocaml): Update to 4.7.0.
(ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir)
(ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip)
(ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest)
(ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree)
(ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned)
(ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult)
(ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner)
(ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools)
(ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log)
(ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos)
(ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf)
(ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake)
(ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis)
(ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq)
(ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format)
(ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi)
(ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages.
(opam): Update to 2.0.0.
(camlp4): Update to 4.07+1.
(camlp5): Update to 7.06.
(hevea): Update to 2.32.
(coq)[inputs]: Add ocaml-num.
(emacs-tuareg): Update to 2.2.0.
(ocaml-menhir)[native-inputs]: Add ocamlbuild.
(ocaml-lablgtk): Update to 2.18.6.
(unison)[inputs]: Use ocaml-4.02.
(ocaml-findlib): Update to 1.8.0.
(ocaml-ounit)[native-inputs]: Add ocamlbuild.
(ocamlmod): Update to 0.0.9.
(ocaml-frontc)[arguments]: Use ocaml-4.02.
(ocaml-qcheck)[native-inputs]: Add ocamlbuild.
(ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild.
(ocaml-stringext)[native-inputs]: Add ocamlbuild.
(ocaml-bisect): Update to 1.3.1.
(ocaml4.01-bisect): Downgrade to 1.3.
(ocaml-bitstring): Update to 3.1.0.
(ocaml-topkg)[native-inputs]: Add ocamlbuild.
(ocaml-rresult)[native-inputs]: Add ocamlbuild.
(ocaml-sqlite3)[native-inputs]: Add ocamlbuild.
(ocaml-csv)[native-inputs]: Add ocamlbuild.
(ocaml-mtime)[native-inputs]: Add ocamlbuild.
(ocaml-cmdliner)[native-inputs]: Add ocamlbuild.
(ocaml-fmt)[native-inputs]: Add ocamlbuild.
(ocaml-astring)[native-inputs]: Add ocamlbuild.
(ocaml-alcotest)[native-inputs]: Add ocamlbuild.
(ocaml-ppx-tools)[native-inputs]: Add ocamlbuild.
(ocaml-react)[native-inputs]: Add ocamlbuild.
(ocaml-ssl)[arguments]: Return #t in phases.
(ocaml-lwt): Update to 4.1.0.
(ocaml-logs)[native-inputs]: Add ocamlbuild.
(ocaml-fpath)[native-inputs]: Add ocamlbuild.
(ocaml-bos)[native-inputs]: Add ocamlbuild.
(ocaml-xmlm): Update to 1.3.0.
(ocaml-ulex): Update to 1.2.0.
(ocaml-uchar)[native-inputs]: Add ocamlbuild.
(ocaml-uutf): Update to 1.0.1.
(ocaml-jsonm): Update to 1.0.1.
(ocaml-ocurl): Update to 0.8.2.
(ocaml-base64)[native-inputs]: Add ocamlbuild.
(ocamlify)[native-inputs]: Use ocaml-4.02.
(omake): Update to 0.10.3.
(ocaml-batteries): Update to 2.9.0.
(ocaml-pcre)[native-inputs]: Add ocamlbuild.
(ocaml-expect): Update 0.0.6.
(ocaml4.02-fileutils): Update to 0.5.3.
(ocaml-oasis): Update 0.4.11.
(ocaml-js-build-tools)[native-inputs]: Add ocamlbuild.
(ocaml-bin-prot): Rename to ocaml4.02-bin-prot.
(ocaml-fieldslib): Rename to ocaml4.02-fieldslib.
(ocaml-ppx-core): Rename to ocaml4.02-ppx-core.
(ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp.
(ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver.
(ocaml-cppo): Update to 1.6.5.
(ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving.
(ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv.
(ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test.
(ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench.
(ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare.
(ocaml-sexplib): Rename to ocaml4.02-sexplib.
(ocaml-typerep): Rename to ocaml4.02-typerep.
(ocaml-variantslib): Rename to ocaml4.02-variantslib.
(ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv.
(ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv.
(ocaml-ppx-here): Rename to ocaml4.02-ppx-here.
(ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert.
(ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate.
(ocaml-ppx-let): Rename to ocaml4.02-ppx-let.
(ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv.
(ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value.
(ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang.
(ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot.
(ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail.
(ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf.
(ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message.
(ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv.
(ocaml-re): Update to 1.8.0.
(ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect.
(ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane.
(ocaml-core-kernel): Rename to ocaml4.02-core-kernel.
(ocaml-async-kernel): Rename to ocaml4.02-async-kernel.
(ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel.
(ocaml-core): Rename to ocaml4.02-core.
(ocaml-async-unix): Rename to ocaml4.02-async-unix.
(ocaml-async-extra): Rename to ocaml4.02-async-extra.
(ocaml-async): Rename to ocaml4.02-async.
(ocaml-ocplib-endian)[native-inputs]: Update to 1.0.
(ocaml-cstruct): Rename to ocaml4.02-cstruct.
(ocaml-hex): Rename to ocaml4.02-hex.
(ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm.
(ocaml-uri): Rename to ocaml4.02-uri.
(optcomp): Use ocaml-4.02.
(ocaml-piqilib): Update to 0.6.14.
(ocaml-uuidm)[native-inputs]: Add ocamlbuild.
(ocaml-graph): Update to 1.8.8.
(ocaml-piqi): Update to 0.7.6.
(bap): Update to 1.3.0.
(ocaml-camomile): Update to 1.0.1.
(ocaml-jbuilder): Use ocaml-4.02.
(ocaml-lambda-term): Update to 1.13.
(ocaml-utop): Update to 2.2.0.
(ocaml-integers)[native-inputs]: Add ocamlbuild.
(ocaml-ctypes): Update to 0.14.0.
(ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild.
(ocaml-tsdl)[native-inputs]: Add ocamlbuild.
* gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02.
* gnu/packages/maths.scm (cubicle): Update to 1.1.2.
* gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch:
Update patch.
* guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib)
(package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.
2018-11-17 17:55:44 +01:00
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;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
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2018-11-27 07:41:12 +01:00
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;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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2015-05-28 15:53:14 +02:00
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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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2016-05-23 12:52:00 +02:00
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#:use-module (guix svn-download)
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2015-08-14 16:48:52 +02:00
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#:use-module (guix build-system cmake)
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2015-05-28 15:53:14 +02:00
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#:use-module (guix build-system gnu)
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2017-03-17 12:24:13 +01:00
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#:use-module (guix build-system ocaml)
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2017-11-17 22:07:23 +01:00
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#:use-module (guix build-system python)
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2015-12-17 16:28:25 +01:00
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#:use-module (guix build-system r)
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2018-02-01 15:07:58 +01:00
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#:use-module (guix git-download)
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2015-06-02 15:10:37 +02:00
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#:use-module (gnu packages)
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2018-05-16 17:56:18 +02:00
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#:use-module (gnu packages algebra)
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2016-05-23 12:52:00 +02:00
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#:use-module (gnu packages autotools)
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2015-06-02 15:47:22 +02:00
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#:use-module (gnu packages boost)
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2017-11-17 22:07:23 +01:00
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#:use-module (gnu packages check)
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2015-06-02 15:47:22 +02:00
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#:use-module (gnu packages compression)
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2017-08-03 22:14:48 +02:00
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#:use-module (gnu packages cran)
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2016-05-23 12:52:00 +02:00
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#:use-module (gnu packages dejagnu)
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2015-06-02 15:47:22 +02:00
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#:use-module (gnu packages gcc)
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2016-08-13 12:26:10 +02:00
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#:use-module (gnu packages image)
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2015-06-02 15:47:22 +02:00
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#:use-module (gnu packages maths)
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2018-06-12 12:01:16 +02:00
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#:use-module (gnu packages mpi)
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2017-03-17 12:24:13 +01:00
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#:use-module (gnu packages ocaml)
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2018-06-27 03:02:00 +02:00
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#:use-module (gnu packages onc-rpc)
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2016-07-12 07:56:07 +02:00
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#:use-module (gnu packages perl)
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2015-08-14 16:48:52 +02:00
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#:use-module (gnu packages pkg-config)
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2015-06-02 15:47:22 +02:00
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#:use-module (gnu packages python)
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2015-08-14 16:48:52 +02:00
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages swig)
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2016-08-13 12:26:10 +02:00
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#:use-module (gnu packages xml)
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#:use-module (gnu packages xorg))
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2015-05-28 15:53:14 +02:00
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2018-02-01 15:07:58 +01:00
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(define-public fann
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;; The last release is >100 commits behind, so we package from git.
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(let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
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(package
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(name "fann")
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(version (string-append "2.2.0-1." (string-take commit 8)))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/libfann/fann.git")
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(commit commit)))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
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(build-system cmake-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out")))
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(with-directory-excursion (string-append (getcwd) "/tests")
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(invoke "./fann_tests"))))))))
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(home-page "http://leenissen.dk/fann/wp/")
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(synopsis "Fast Artificial Neural Network")
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(description
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"FANN is a free open source neural network library, which implements
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multilayer artificial neural networks in C with support for both fully
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connected and sparsely connected networks.")
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(license license:lgpl2.1))))
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2015-05-28 15:53:14 +02:00
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(define-public libsvm
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(package
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(name "libsvm")
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2018-01-10 03:53:16 +01:00
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(version "3.22")
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2015-05-28 15:53:14 +02:00
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(source
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(origin
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(method url-fetch)
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2018-01-10 03:53:16 +01:00
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(uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
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name "-" version ".tar.gz"))
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2015-05-28 15:53:14 +02:00
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(sha256
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(base32
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2018-01-10 03:53:16 +01:00
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"0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
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2015-05-28 15:53:14 +02:00
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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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2018-01-10 03:53:16 +01:00
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'install ; no ‘install’ target
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2015-05-28 15:53:14 +02:00
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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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2015-06-02 15:10:37 +02:00
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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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2018-01-10 03:53:16 +01:00
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'install ; no ‘install’ target
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2015-06-02 15:10:37 +02:00
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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/")))
|
|
|
|
|
(substitute* "python/svm.py"
|
|
|
|
|
(("../libsvm.so.2") "libsvm.so.2"))
|
|
|
|
|
(mkdir-p site)
|
|
|
|
|
(for-each (lambda (file)
|
|
|
|
|
(copy-file file (string-append site (basename file))))
|
|
|
|
|
(find-files "python" "\\.py"))
|
|
|
|
|
(copy-file "libsvm.so.2"
|
|
|
|
|
(string-append site "libsvm.so.2")))
|
|
|
|
|
#t)))))
|
|
|
|
|
(inputs
|
|
|
|
|
`(("python" ,python)))
|
|
|
|
|
(synopsis "Python bindings of libSVM")))
|
2015-06-02 15:47:22 +02:00
|
|
|
|
|
2016-05-23 12:52:00 +02:00
|
|
|
|
(define-public ghmm
|
|
|
|
|
;; The latest release candidate is several years and a couple of fixes have
|
|
|
|
|
;; been published since. This is why we download the sources from the SVN
|
|
|
|
|
;; repository.
|
|
|
|
|
(let ((svn-revision 2341))
|
|
|
|
|
(package
|
|
|
|
|
(name "ghmm")
|
|
|
|
|
(version (string-append "0.9-rc3-0." (number->string svn-revision)))
|
|
|
|
|
(source (origin
|
|
|
|
|
(method svn-fetch)
|
|
|
|
|
(uri (svn-reference
|
|
|
|
|
(url "http://svn.code.sf.net/p/ghmm/code/trunk")
|
|
|
|
|
(revision svn-revision)))
|
|
|
|
|
(file-name (string-append name "-" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
|
|
|
|
|
(build-system gnu-build-system)
|
|
|
|
|
(arguments
|
2016-10-03 19:12:08 +02:00
|
|
|
|
`(#:imported-modules (,@%gnu-build-system-modules
|
|
|
|
|
(guix build python-build-system))
|
|
|
|
|
#:phases
|
2016-05-23 12:52:00 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'enter-dir
|
|
|
|
|
(lambda _ (chdir "ghmm") #t))
|
2016-10-03 19:12:08 +02:00
|
|
|
|
(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")))
|
2016-05-23 12:52:00 +02:00
|
|
|
|
#t))
|
|
|
|
|
(add-after 'enter-dir 'fix-runpath
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
|
|
|
(substitute* "ghmmwrapper/setup.py"
|
|
|
|
|
(("^(.*)extra_compile_args = \\[" line indent)
|
|
|
|
|
(string-append indent
|
|
|
|
|
"extra_link_args = [\"-Wl,-rpath="
|
|
|
|
|
(assoc-ref outputs "out") "/lib\"],\n"
|
|
|
|
|
line
|
|
|
|
|
"\"-Wl,-rpath="
|
|
|
|
|
(assoc-ref outputs "out")
|
|
|
|
|
"/lib\", ")))
|
|
|
|
|
#t))
|
|
|
|
|
(add-after 'enter-dir 'disable-broken-tests
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* "tests/Makefile.am"
|
|
|
|
|
;; GHMM_SILENT_TESTS is assumed to be a command.
|
|
|
|
|
(("TESTS_ENVIRONMENT.*") "")
|
|
|
|
|
;; Do not build broken tests.
|
|
|
|
|
(("chmm .*") "")
|
|
|
|
|
(("read_fa .*") "")
|
|
|
|
|
(("mcmc .*") "")
|
|
|
|
|
(("label_higher_order_test.*$")
|
|
|
|
|
"label_higher_order_test\n"))
|
|
|
|
|
|
|
|
|
|
;; These Python unittests are broken as there is no gato.
|
|
|
|
|
;; See https://sourceforge.net/p/ghmm/support-requests/3/
|
|
|
|
|
(substitute* "ghmmwrapper/ghmmunittests.py"
|
|
|
|
|
(("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
|
|
|
|
|
line indent)
|
|
|
|
|
(string-append indent
|
|
|
|
|
"@unittest.skip(\"Disabled by Guix\")\n"
|
|
|
|
|
line)))
|
|
|
|
|
#t))
|
gnu: Put autoconf-related phases immediately after the 'unpack phase.
* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
2017-07-31 03:02:35 +02:00
|
|
|
|
(add-after 'disable-broken-tests 'autogen
|
2016-05-23 12:52:00 +02:00
|
|
|
|
(lambda _
|
2018-06-26 19:37:21 +02:00
|
|
|
|
(invoke "bash" "autogen.sh"))))))
|
2016-05-23 12:52:00 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("python" ,python-2) ; only Python 2 is supported
|
|
|
|
|
("libxml2" ,libxml2)))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("pkg-config" ,pkg-config)
|
|
|
|
|
("dejagnu" ,dejagnu)
|
|
|
|
|
("swig" ,swig)
|
|
|
|
|
("autoconf" ,autoconf)
|
|
|
|
|
("automake" ,automake)
|
|
|
|
|
("libtool" ,libtool)))
|
|
|
|
|
(home-page "http://ghmm.org")
|
|
|
|
|
(synopsis "Hidden Markov Model library")
|
|
|
|
|
(description
|
|
|
|
|
"The General Hidden Markov Model library (GHMM) is a C library with
|
|
|
|
|
additional Python bindings implementing a wide range of types of @dfn{Hidden
|
2017-04-16 18:06:57 +02:00
|
|
|
|
Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
|
2016-05-23 12:52:00 +02:00
|
|
|
|
training, HMM clustering, HMM mixtures.")
|
|
|
|
|
(license license:lgpl2.0+))))
|
|
|
|
|
|
2016-07-12 07:56:07 +02:00
|
|
|
|
(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)))
|
|
|
|
|
|
2017-03-17 12:24:13 +01:00
|
|
|
|
(define-public ocaml-mcl
|
|
|
|
|
(package
|
|
|
|
|
(name "ocaml-mcl")
|
|
|
|
|
(version "12-068oasis4")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"https://github.com/fhcrc/mcl/archive/"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
|
|
|
|
|
(build-system ocaml-build-system)
|
|
|
|
|
(arguments
|
gnu: ocaml: Update to 4.7.0.
Update ocaml to the latest version and fixes dependent packages by
updating them or by adding new inputs, such as ocaml-num and ocamlbuild,
that were removed from the core ocaml package. Rename packages that
cannot be built with the new compiler with an ocaml4.02 prefix. Add
ocaml4.02 dependencies.
* gnu/packages/ocaml.scm (ocaml): Update to 4.7.0.
(ocaml-4.02, ocamlbuild, camlp4-4.02, ocaml-num, ocaml4.02-menhir)
(ocaml4.02-lablgtk, ocaml4.02-findlib, ocaml4.02-ounit, ocaml4.02-camlzip)
(ocaml4.02-ocamlmod, ocaml4.02-zarith, ocaml4.02-qcheck, ocaml4.02-qtest)
(ocaml4.02-stringext, ocaml4.02-bisect, dune, ocaml-migrate-parsetree)
(ocaml-ppx-tools-versioned, ocaml-ppx-tools-versioned)
(ocaml4.02-bitstring, ocaml4.02-result, ocaml4.02-topkg, ocaml4.02-rresult)
(ocaml4.02-sqlite3, ocaml4.02-csv, ocaml4.02-mtime, ocaml4.02-cmdliner)
(ocaml4.02-fmt, ocaml4.02-astring, ocaml4.02-alcotest, ocaml4.02-ppx-tools)
(ocaml4.02-react, ocaml4.02-ssl, ocaml4.02-lwt, ocaml-lwt-log)
(ocaml4.02-lwt-log, ocaml4.02-logs, ocaml4.02-fpath, ocaml4.02-bos)
(ocaml4.02-xmlm, ocaml4.02-ulex, ocaml4.02-uchar, ocaml4.02-uutf)
(ocaml4.02-jsonm, ocaml4.02-ocurl, ocaml4.02-base64, ocaml4.02-omake)
(ocaml4.02-batteries, ocaml4.02-pcre, ocaml4.02-oasis)
(ocaml4.02-js-build-tools, ocaml4.02-cppo, ocaml-seq, ocaml4.02-seq)
(ocaml4.02-re, ocaml4.02-ocplib-endian, ocaml4.02-easy-format)
(ocaml4.02-piqilib, ocaml4.02-uuidm, ocaml4.02-graph, ocaml4.02-piqi)
(ocaml4.02-camomile, ocaml4.02-zed, ocaml4.02-lambda-term): New packages.
(opam): Update to 2.0.0.
(camlp4): Update to 4.07+1.
(camlp5): Update to 7.06.
(hevea): Update to 2.32.
(coq)[inputs]: Add ocaml-num.
(emacs-tuareg): Update to 2.2.0.
(ocaml-menhir)[native-inputs]: Add ocamlbuild.
(ocaml-lablgtk): Update to 2.18.6.
(unison)[inputs]: Use ocaml-4.02.
(ocaml-findlib): Update to 1.8.0.
(ocaml-ounit)[native-inputs]: Add ocamlbuild.
(ocamlmod): Update to 0.0.9.
(ocaml-frontc)[arguments]: Use ocaml-4.02.
(ocaml-qcheck)[native-inputs]: Add ocamlbuild.
(ocaml-qtest)[native-inputs]: Remove ocaml-findlib and add ocamlbuild.
(ocaml-stringext)[native-inputs]: Add ocamlbuild.
(ocaml-bisect): Update to 1.3.1.
(ocaml4.01-bisect): Downgrade to 1.3.
(ocaml-bitstring): Update to 3.1.0.
(ocaml-topkg)[native-inputs]: Add ocamlbuild.
(ocaml-rresult)[native-inputs]: Add ocamlbuild.
(ocaml-sqlite3)[native-inputs]: Add ocamlbuild.
(ocaml-csv)[native-inputs]: Add ocamlbuild.
(ocaml-mtime)[native-inputs]: Add ocamlbuild.
(ocaml-cmdliner)[native-inputs]: Add ocamlbuild.
(ocaml-fmt)[native-inputs]: Add ocamlbuild.
(ocaml-astring)[native-inputs]: Add ocamlbuild.
(ocaml-alcotest)[native-inputs]: Add ocamlbuild.
(ocaml-ppx-tools)[native-inputs]: Add ocamlbuild.
(ocaml-react)[native-inputs]: Add ocamlbuild.
(ocaml-ssl)[arguments]: Return #t in phases.
(ocaml-lwt): Update to 4.1.0.
(ocaml-logs)[native-inputs]: Add ocamlbuild.
(ocaml-fpath)[native-inputs]: Add ocamlbuild.
(ocaml-bos)[native-inputs]: Add ocamlbuild.
(ocaml-xmlm): Update to 1.3.0.
(ocaml-ulex): Update to 1.2.0.
(ocaml-uchar)[native-inputs]: Add ocamlbuild.
(ocaml-uutf): Update to 1.0.1.
(ocaml-jsonm): Update to 1.0.1.
(ocaml-ocurl): Update to 0.8.2.
(ocaml-base64)[native-inputs]: Add ocamlbuild.
(ocamlify)[native-inputs]: Use ocaml-4.02.
(omake): Update to 0.10.3.
(ocaml-batteries): Update to 2.9.0.
(ocaml-pcre)[native-inputs]: Add ocamlbuild.
(ocaml-expect): Update 0.0.6.
(ocaml4.02-fileutils): Update to 0.5.3.
(ocaml-oasis): Update 0.4.11.
(ocaml-js-build-tools)[native-inputs]: Add ocamlbuild.
(ocaml-bin-prot): Rename to ocaml4.02-bin-prot.
(ocaml-fieldslib): Rename to ocaml4.02-fieldslib.
(ocaml-ppx-core): Rename to ocaml4.02-ppx-core.
(ocaml-ppx-optcomp): Rename to ocaml4.02-ppx-optcomp.
(ocaml-ppx-driver): Rename to ocaml4.02-ppx-driver.
(ocaml-cppo): Update to 1.6.5.
(ocaml-ppx-deriving): Rename to ocaml4.02-ppx-deriving.
(ocaml-ppx-type-conv): Rename to ocaml4.02-ppx-type-conv.
(ocaml-ppx-inline-test): Rename to ocaml4.02-ppx-inline-test.
(ocaml-ppx-bench): Rename to ocaml4.02-ppx-bench.
(ocaml-ppx-compare): Rename to ocaml4.02-ppx-compare.
(ocaml-sexplib): Rename to ocaml4.02-sexplib.
(ocaml-typerep): Rename to ocaml4.02-typerep.
(ocaml-variantslib): Rename to ocaml4.02-variantslib.
(ocaml-ppx-sexp-conv): Rename to ocaml4.02-ppx-sexp-conv.
(ocaml-ppx-variants-conv): Rename to ocaml4.02-ppx-variants-conv.
(ocaml-ppx-here): Rename to ocaml4.02-ppx-here.
(ocaml-ppx-assert): Rename to ocaml4.02-ppx-assert.
(ocaml-ppx-enumerate): Rename to ocaml4.02-ppx-enumerate.
(ocaml-ppx-let): Rename to ocaml4.02-ppx-let.
(ocaml-ppx-typerep-conv): Rename to ocaml4.02-ppx-typerep-conv.
(ocaml-ppx-sexp-value): Rename to ocaml4.02-ppx-sexp-value.
(ocaml-ppx-pipebang): Rename to ocaml4.02-ppx-pipebang.
(ocaml-ppx-bin-prot): Rename to ocaml4.02-ppx-bin-prot.
(ocaml-ppx-fail): Rename to ocaml4.02-ppx-fail.
(ocaml-ppx-custom-printf): Rename to ocaml4.02-ppx-custom-printf.
(ocaml-ppx-sexp-message): Rename to ocaml4.02-ppx-sexp-message.
(ocaml-ppx-fields-conv): Rename to ocaml4.02-ppx-fields-conv.
(ocaml-re): Update to 1.8.0.
(ocaml-ppx-expect): Rename to ocaml4.02-ppx-expect.
(ocaml-ppx-jane): Rename to ocaml4.02-ppx-jane.
(ocaml-core-kernel): Rename to ocaml4.02-core-kernel.
(ocaml-async-kernel): Rename to ocaml4.02-async-kernel.
(ocaml-async-rpc-kernel): Rename to ocaml4.02-async-rpc-kernel.
(ocaml-core): Rename to ocaml4.02-core.
(ocaml-async-unix): Rename to ocaml4.02-async-unix.
(ocaml-async-extra): Rename to ocaml4.02-async-extra.
(ocaml-async): Rename to ocaml4.02-async.
(ocaml-ocplib-endian)[native-inputs]: Update to 1.0.
(ocaml-cstruct): Rename to ocaml4.02-cstruct.
(ocaml-hex): Rename to ocaml4.02-hex.
(ocaml-ezjsonm): Rename to ocaml4.02-ezjsonm.
(ocaml-uri): Rename to ocaml4.02-uri.
(optcomp): Use ocaml-4.02.
(ocaml-piqilib): Update to 0.6.14.
(ocaml-uuidm)[native-inputs]: Add ocamlbuild.
(ocaml-graph): Update to 1.8.8.
(ocaml-piqi): Update to 0.7.6.
(bap): Update to 1.3.0.
(ocaml-camomile): Update to 1.0.1.
(ocaml-jbuilder): Use ocaml-4.02.
(ocaml-lambda-term): Update to 1.13.
(ocaml-utop): Update to 2.2.0.
(ocaml-integers)[native-inputs]: Add ocamlbuild.
(ocaml-ctypes): Update to 0.14.0.
(ocaml-ocb-stubblr)[native-inputs]: Add ocamlbuild.
(ocaml-tsdl)[native-inputs]: Add ocamlbuild.
* gnu/packages/machine-learning.scm (ocaml-mcl): Use ocaml-4.02.
* gnu/packages/maths.scm (cubicle): Update to 1.1.2.
* gnu/packages/patches/ocaml-bisect-fix-camlp4-in-another-directory.patch:
Update patch.
* guix/build-system/ocaml.scm: (default-ocaml4.02, default-ocaml4.02-findlib)
(package-with-ocaml4.02, strip-ocaml4.02-variant): New variables.
2018-11-17 17:55:44 +01:00
|
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`(#:ocaml ,ocaml-4.02
|
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#:findlib ,ocaml4.02-findlib
|
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#:phases
|
2017-03-17 12:24:13 +01:00
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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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2017-03-17 22:17:07 +01:00
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(define-public ocaml4.01-mcl
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(package-with-ocaml4.01 ocaml-mcl))
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2015-06-02 15:47:22 +02:00
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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
|
2018-11-27 07:41:12 +01:00
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"https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
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"/randomjungle/randomjungle-" version ".tar_.gz"))
|
2015-06-02 15:47:22 +02:00
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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
|
2016-05-25 20:48:22 +02:00
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`(("gfortran" ,gfortran)
|
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("gfortran:lib" ,gfortran "lib")))
|
2016-09-23 08:22:09 +02:00
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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"))
|
2018-11-27 07:41:12 +01:00
|
|
|
|
(home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
|
2015-06-02 15:47:22 +02:00
|
|
|
|
(synopsis "Implementation of the Random Forests machine learning method")
|
|
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|
|
(description
|
|
|
|
|
"Random Jungle is an implementation of Random Forests. It is supposed to
|
|
|
|
|
analyse high dimensional data. In genetics, it can be used for analysing big
|
|
|
|
|
Genome Wide Association (GWA) data. Random Forests is a powerful machine
|
|
|
|
|
learning method. Most interesting features are variable selection, missing
|
|
|
|
|
value imputation, classifier creation, generalization error estimation and
|
|
|
|
|
sample proximities between pairs of cases.")
|
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|
|
(license license:gpl3+)))
|
2015-08-14 16:48:52 +02:00
|
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|
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|
|
|
|
(define-public shogun
|
|
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|
|
(package
|
|
|
|
|
(name "shogun")
|
2018-05-16 17:56:18 +02:00
|
|
|
|
(version "6.1.3")
|
2015-08-14 16:48:52 +02:00
|
|
|
|
(source
|
|
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|
(origin
|
|
|
|
|
(method url-fetch)
|
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|
|
(uri (string-append
|
|
|
|
|
"ftp://shogun-toolbox.org/shogun/releases/"
|
|
|
|
|
(version-major+minor version)
|
|
|
|
|
"/sources/shogun-" version ".tar.bz2"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-05-16 17:56:18 +02:00
|
|
|
|
"1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
|
2015-08-14 16:48:52 +02:00
|
|
|
|
(modules '((guix build utils)
|
|
|
|
|
(ice-9 rdelim)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; Remove non-free sources and files referencing them
|
|
|
|
|
(for-each delete-file
|
|
|
|
|
(find-files "src/shogun/classifier/svm/"
|
|
|
|
|
"SVMLight\\.(cpp|h)"))
|
|
|
|
|
(for-each delete-file
|
|
|
|
|
(find-files "examples/undocumented/libshogun/"
|
|
|
|
|
(string-append
|
|
|
|
|
"(classifier_.*svmlight.*|"
|
|
|
|
|
"evaluation_cross_validation_locked_comparison).cpp")))
|
|
|
|
|
;; Remove non-free functions.
|
|
|
|
|
(define (delete-ifdefs file)
|
|
|
|
|
(with-atomic-file-replacement file
|
|
|
|
|
(lambda (in out)
|
|
|
|
|
(let loop ((line (read-line in 'concat))
|
|
|
|
|
(skipping? #f))
|
|
|
|
|
(if (eof-object? line)
|
|
|
|
|
#t
|
|
|
|
|
(let ((skip-next?
|
|
|
|
|
(or (and skipping?
|
|
|
|
|
(not (string-prefix?
|
|
|
|
|
"#endif //USE_SVMLIGHT" line)))
|
|
|
|
|
(string-prefix?
|
|
|
|
|
"#ifdef USE_SVMLIGHT" line))))
|
|
|
|
|
(when (or (not skipping?)
|
|
|
|
|
(and skipping? (not skip-next?)))
|
|
|
|
|
(display line out))
|
|
|
|
|
(loop (read-line in 'concat) skip-next?)))))))
|
2018-05-16 17:56:18 +02:00
|
|
|
|
(for-each delete-ifdefs
|
|
|
|
|
(append
|
|
|
|
|
(find-files "src/shogun/classifier/mkl"
|
|
|
|
|
"^MKLClassification\\.cpp")
|
|
|
|
|
(find-files "src/shogun/classifier/svm"
|
|
|
|
|
"^SVMLightOneClass\\.(cpp|h)")
|
|
|
|
|
(find-files "src/shogun/multiclass"
|
|
|
|
|
"^ScatterSVM\\.(cpp|h)")
|
|
|
|
|
(find-files "src/shogun/kernel/"
|
|
|
|
|
"^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
|
|
|
|
|
(find-files "src/shogun/regression/svr"
|
|
|
|
|
"^(MKLRegression|SVRLight)\\.(cpp|h)")
|
|
|
|
|
(find-files "src/shogun/transfer/domain_adaptation"
|
2018-05-30 03:20:47 +02:00
|
|
|
|
"^DomainAdaptationSVM\\.(cpp|h)")))
|
gnu: All snippets report errors using exceptions, else return #t.
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
2018-03-16 12:47:34 +01:00
|
|
|
|
#t))))
|
2015-08-14 16:48:52 +02:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
'(#:tests? #f ;no check target
|
|
|
|
|
#:phases
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'delete-broken-symlinks
|
|
|
|
|
(lambda _
|
|
|
|
|
(for-each delete-file '("applications/arts/data"
|
|
|
|
|
"applications/asp/data"
|
|
|
|
|
"applications/easysvm/data"
|
|
|
|
|
"applications/msplicer/data"
|
|
|
|
|
"applications/ocr/data"
|
2018-05-16 17:56:18 +02:00
|
|
|
|
"examples/meta/data"
|
|
|
|
|
"examples/undocumented/data"))
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
#t))
|
|
|
|
|
(add-after 'unpack 'change-R-target-path
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
2018-05-16 17:56:18 +02:00
|
|
|
|
(substitute* '("src/interfaces/r/CMakeLists.txt"
|
|
|
|
|
"examples/meta/r/CMakeLists.txt")
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(("\\$\\{R_COMPONENT_LIB_PATH\\}")
|
|
|
|
|
(string-append (assoc-ref outputs "out")
|
|
|
|
|
"/lib/R/library/")))
|
|
|
|
|
#t))
|
|
|
|
|
(add-after 'unpack 'fix-octave-modules
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
2018-05-16 17:56:18 +02:00
|
|
|
|
(substitute* "src/interfaces/octave/CMakeLists.txt"
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
|
2018-05-16 17:56:18 +02:00
|
|
|
|
"include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
|
|
|
|
|
;; change target directory
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
|
|
|
|
|
(string-append (assoc-ref outputs "out")
|
|
|
|
|
"/share/octave/packages")))
|
2018-05-16 17:56:18 +02:00
|
|
|
|
(substitute* '("src/interfaces/octave/swig_typemaps.i"
|
|
|
|
|
"src/interfaces/octave/sg_print_functions.cpp")
|
|
|
|
|
;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
|
|
|
|
|
(("octave/config\\.h") "octave/octave-config.h")
|
|
|
|
|
(("octave/oct-obj.h") "octave/ovl.h"))
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
#t))
|
2018-05-16 17:56:18 +02:00
|
|
|
|
(add-after 'unpack 'move-rxcpp
|
|
|
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
|
|
|
(let ((rxcpp-dir "shogun/third-party/rxcpp"))
|
|
|
|
|
(mkdir-p rxcpp-dir)
|
|
|
|
|
(install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
|
|
|
|
|
#t)))
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(add-before 'build 'set-HOME
|
2015-08-14 16:48:52 +02:00
|
|
|
|
;; $HOME needs to be set at some point during the build phase
|
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-07-29 17:28:42 +02:00
|
|
|
|
(lambda _ (setenv "HOME" "/tmp") #t)))
|
2015-08-14 16:48:52 +02:00
|
|
|
|
#:configure-flags
|
|
|
|
|
(list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
|
|
|
|
|
"-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
|
2018-05-16 17:56:18 +02:00
|
|
|
|
"-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
|
|
|
|
|
;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
|
|
|
|
|
;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
|
|
|
|
|
;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
|
|
|
|
|
;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
|
|
|
|
|
"-DINTERFACE_OCTAVE=ON"
|
|
|
|
|
"-DINTERFACE_PYTHON=ON"
|
|
|
|
|
"-DINTERFACE_R=ON")))
|
2015-08-14 16:48:52 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("python" ,python)
|
|
|
|
|
("numpy" ,python-numpy)
|
2017-03-17 09:42:22 +01:00
|
|
|
|
("r-minimal" ,r-minimal)
|
2015-08-14 16:48:52 +02:00
|
|
|
|
("octave" ,octave)
|
|
|
|
|
("swig" ,swig)
|
2018-05-16 17:56:18 +02:00
|
|
|
|
("eigen" ,eigen)
|
2015-08-14 16:48:52 +02:00
|
|
|
|
("hdf5" ,hdf5)
|
|
|
|
|
("atlas" ,atlas)
|
|
|
|
|
("arpack" ,arpack-ng)
|
|
|
|
|
("lapack" ,lapack)
|
|
|
|
|
("glpk" ,glpk)
|
|
|
|
|
("libxml2" ,libxml2)
|
|
|
|
|
("lzo" ,lzo)
|
|
|
|
|
("zlib" ,zlib)))
|
|
|
|
|
(native-inputs
|
2018-05-16 17:56:18 +02:00
|
|
|
|
`(("pkg-config" ,pkg-config)
|
|
|
|
|
("rxcpp" ,rxcpp)))
|
2015-11-02 14:08:45 +01:00
|
|
|
|
;; Non-portable SSE instructions are used so building fails on platforms
|
|
|
|
|
;; other than x86_64.
|
|
|
|
|
(supported-systems '("x86_64-linux"))
|
2015-08-14 16:48:52 +02:00
|
|
|
|
(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+)))
|
2015-12-17 16:28:25 +01:00
|
|
|
|
|
2018-05-09 16:01:40 +02:00
|
|
|
|
(define-public rxcpp
|
|
|
|
|
(package
|
|
|
|
|
(name "rxcpp")
|
|
|
|
|
(version "4.0.0")
|
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
|
|
|
|
|
version ".tar.gz"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
|
|
|
|
"0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
|
|
|
|
|
(file-name (string-append name "-" version ".tar.gz"))))
|
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
|
|
|
|
`(#:phases
|
|
|
|
|
(modify-phases %standard-phases
|
|
|
|
|
(add-after 'unpack 'remove-werror
|
|
|
|
|
(lambda _
|
|
|
|
|
(substitute* (find-files ".")
|
|
|
|
|
(("-Werror") ""))
|
|
|
|
|
#t))
|
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _
|
|
|
|
|
(invoke "ctest"))))))
|
|
|
|
|
(native-inputs
|
|
|
|
|
`(("catch" ,catch-framework)))
|
|
|
|
|
(home-page "http://reactivex.io/")
|
|
|
|
|
(synopsis "Reactive Extensions for C++")
|
|
|
|
|
(description
|
|
|
|
|
"The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
|
|
|
|
|
values-distributed-in-time. ReactiveX is a library for composing asynchronous
|
|
|
|
|
and event-based programs by using observable sequences.
|
|
|
|
|
|
|
|
|
|
It extends the observer pattern to support sequences of data and/or events and
|
|
|
|
|
adds operators that allow you to compose sequences together declaratively while
|
|
|
|
|
abstracting away concerns about things like low-level threading,
|
|
|
|
|
synchronization, thread-safety, concurrent data structures, and non-blocking
|
|
|
|
|
I/O.")
|
|
|
|
|
(license license:asl2.0)))
|
|
|
|
|
|
2015-12-17 16:28:25 +01:00
|
|
|
|
(define-public r-adaptivesparsity
|
|
|
|
|
(package
|
|
|
|
|
(name "r-adaptivesparsity")
|
2018-09-05 19:49:33 +02:00
|
|
|
|
(version "1.6")
|
2015-12-17 16:28:25 +01:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "AdaptiveSparsity" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-09-05 19:49:33 +02:00
|
|
|
|
"0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
|
2015-12-17 16:28:25 +01:00
|
|
|
|
(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
|
2018-09-05 19:49:33 +02:00
|
|
|
|
`(("r-mass" ,r-mass)
|
|
|
|
|
("r-matrix" ,r-matrix)
|
|
|
|
|
("r-rcpp" ,r-rcpp)
|
2015-12-17 16:28:25 +01:00
|
|
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
2017-09-22 11:46:21 +02:00
|
|
|
|
(inputs
|
|
|
|
|
`(("armadillo" ,armadillo)))
|
gnu, doc: Use HTTPS for cran.r-project.org home pages.
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
2017-12-24 01:01:21 +01:00
|
|
|
|
(home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
|
2015-12-17 16:28:25 +01:00
|
|
|
|
(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+)))
|
2016-03-31 17:05:27 +02:00
|
|
|
|
|
2016-11-24 15:18:06 +01:00
|
|
|
|
(define-public r-kernlab
|
|
|
|
|
(package
|
|
|
|
|
(name "r-kernlab")
|
2018-09-05 19:50:14 +02:00
|
|
|
|
(version "0.9-27")
|
2016-11-24 15:18:06 +01:00
|
|
|
|
(source
|
|
|
|
|
(origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (cran-uri "kernlab" version))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2018-09-05 19:50:14 +02:00
|
|
|
|
"1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
|
2016-11-24 15:18:06 +01:00
|
|
|
|
(build-system r-build-system)
|
gnu, doc: Use HTTPS for cran.r-project.org home pages.
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
2017-12-24 01:01:21 +01:00
|
|
|
|
(home-page "https://cran.r-project.org/web/packages/kernlab")
|
2016-11-24 15:18:06 +01:00
|
|
|
|
(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)))
|
|
|
|
|
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(define-public dlib
|
|
|
|
|
(package
|
|
|
|
|
(name "dlib")
|
2017-09-21 20:04:36 +02:00
|
|
|
|
(version "19.7")
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(source (origin
|
|
|
|
|
(method url-fetch)
|
|
|
|
|
(uri (string-append
|
|
|
|
|
"http://dlib.net/files/dlib-" version ".tar.bz2"))
|
|
|
|
|
(sha256
|
|
|
|
|
(base32
|
2017-09-21 20:04:36 +02:00
|
|
|
|
"1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(modules '((guix build utils)))
|
|
|
|
|
(snippet
|
|
|
|
|
'(begin
|
|
|
|
|
;; Delete ~13MB of bundled dependencies.
|
|
|
|
|
(delete-file-recursively "dlib/external")
|
2017-02-20 02:08:27 +01:00
|
|
|
|
(delete-file-recursively "docs/dlib/external")
|
|
|
|
|
#t))))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(build-system cmake-build-system)
|
|
|
|
|
(arguments
|
2017-12-19 15:25:12 +01:00
|
|
|
|
`(#:phases
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(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))
|
2016-09-09 02:51:23 +02:00
|
|
|
|
(add-after 'disable-asserts 'disable-failing-tests
|
|
|
|
|
(lambda _
|
|
|
|
|
;; One test times out on MIPS, so we need to disable it.
|
2017-02-20 02:08:27 +01:00
|
|
|
|
;; Others are flaky on some platforms.
|
2016-09-09 02:51:23 +02:00
|
|
|
|
(let* ((system ,(or (%current-target-system)
|
|
|
|
|
(%current-system)))
|
|
|
|
|
(disabled-tests (cond
|
|
|
|
|
((string-prefix? "mips64" system)
|
|
|
|
|
'("object_detector" ; timeout
|
|
|
|
|
"data_io"))
|
|
|
|
|
((string-prefix? "armhf" system)
|
2017-02-25 12:09:25 +01:00
|
|
|
|
'("learning_to_track"))
|
2016-09-09 02:51:23 +02:00
|
|
|
|
((string-prefix? "i686" system)
|
2017-02-20 02:08:27 +01:00
|
|
|
|
'("optimization"))
|
2016-09-09 02:51:23 +02:00
|
|
|
|
(else '()))))
|
|
|
|
|
(for-each
|
|
|
|
|
(lambda (test)
|
|
|
|
|
(substitute* "dlib/test/makefile"
|
2017-02-20 02:08:27 +01:00
|
|
|
|
(((string-append "SRC \\+= " test "\\.cpp")) "")))
|
|
|
|
|
disabled-tests)
|
|
|
|
|
#t)))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(replace 'check
|
|
|
|
|
(lambda _
|
|
|
|
|
;; No test target, so we build and run the unit tests here.
|
2016-08-27 18:23:58 +02:00
|
|
|
|
(let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(with-directory-excursion test-dir
|
2018-06-26 19:39:29 +02:00
|
|
|
|
(invoke "make" "-j" (number->string (parallel-job-count)))
|
|
|
|
|
(invoke "./dtest" "--runall"))
|
|
|
|
|
#t)))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(add-after 'install 'delete-static-library
|
|
|
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
2017-02-20 02:08:27 +01:00
|
|
|
|
(delete-file (string-append (assoc-ref outputs "out")
|
|
|
|
|
"/lib/libdlib.a"))
|
|
|
|
|
#t)))))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(native-inputs
|
2018-06-27 03:02:00 +02:00
|
|
|
|
`(("pkg-config" ,pkg-config)
|
|
|
|
|
;; For tests.
|
|
|
|
|
("libnsl" ,libnsl)))
|
2016-08-13 12:26:10 +02:00
|
|
|
|
(inputs
|
2016-08-23 22:17:14 +02:00
|
|
|
|
`(("giflib" ,giflib)
|
2016-09-09 02:51:23 +02:00
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("lapack" ,lapack)
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2016-08-13 12:26:10 +02:00
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("libjpeg" ,libjpeg)
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("libpng" ,libpng)
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("libx11" ,libx11)
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("openblas" ,openblas)
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("zlib" ,zlib)))
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(synopsis
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"Toolkit for making machine learning and data analysis applications in C++")
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(description
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"Dlib is a modern C++ toolkit containing machine learning algorithms and
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tools. It is used in both industry and academia in a wide range of domains
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including robotics, embedded devices, mobile phones, and large high performance
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computing environments.")
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(home-page "http://dlib.net")
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(license license:boost1.0)))
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2017-11-17 22:07:23 +01:00
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(define-public python-scikit-learn
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(package
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(name "python-scikit-learn")
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2018-09-12 19:04:02 +02:00
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(version "0.19.2")
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2017-11-17 22:07:23 +01:00
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(source
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(origin
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2018-09-12 19:04:02 +02:00
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/scikit-learn/scikit-learn.git")
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(commit version)))
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(file-name (git-file-name name version))
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2017-11-17 22:07:23 +01:00
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(sha256
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(base32
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2018-09-12 19:04:02 +02:00
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"1dk9hdj01c0bny4ps78b7869fjw9gr6qklxf6wyql8h6nh4k19xm"))
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2017-12-14 09:45:21 +01:00
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(patches (search-patches
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2018-09-12 19:04:02 +02:00
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"python-scikit-learn-fix-test-non-determinism.patch"))))
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2017-11-17 22:07:23 +01:00
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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2018-09-12 19:04:02 +02:00
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(add-after 'build 'build-ext
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(lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
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(replace 'check
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(lambda _
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;; Restrict OpenBLAS threads to prevent segfaults while testing!
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(setenv "OPENBLAS_NUM_THREADS" "1")
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;; Disable tests that require network access
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(delete-file "sklearn/datasets/tests/test_mldata.py")
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(delete-file "sklearn/datasets/tests/test_rcv1.py")
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(invoke "pytest" "sklearn")
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#t))
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;; FIXME: This fails with permission denied
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(delete 'reset-gzip-timestamps))))
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2017-11-17 22:07:23 +01:00
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(inputs
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`(("openblas" ,openblas)))
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(native-inputs
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2018-09-12 19:04:02 +02:00
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`(("python-pytest" ,python-pytest)
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("python-pandas" ,python-pandas) ;for tests
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2017-11-17 22:07:23 +01:00
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("python-cython" ,python-cython)))
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(propagated-inputs
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`(("python-numpy" ,python-numpy)
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("python-scipy" ,python-scipy)))
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(home-page "http://scikit-learn.org/")
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(synopsis "Machine Learning in Python")
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(description
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2018-09-12 19:04:02 +02:00
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"Scikit-learn provides simple and efficient tools for data mining and
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data analysis.")
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2017-11-17 22:07:23 +01:00
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(license license:bsd-3)))
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(define-public python2-scikit-learn
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2018-09-20 15:53:20 +02:00
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(let ((parent (package-with-python2 python-scikit-learn)))
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(package (inherit parent)
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(arguments
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(substitute-keyword-arguments (package-arguments parent)
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((#:phases phases)
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`(modify-phases ,phases
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(replace 'check
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(lambda _
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;; Restrict OpenBLAS threads to prevent segfaults while testing!
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(setenv "OPENBLAS_NUM_THREADS" "1")
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;; Some tests expect to be able to write to HOME.
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(setenv "HOME" "/tmp")
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;; Disable tests that require network access
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(delete-file "sklearn/datasets/tests/test_kddcup99.py")
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(delete-file "sklearn/datasets/tests/test_mldata.py")
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(delete-file "sklearn/datasets/tests/test_rcv1.py")
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(invoke "pytest" "sklearn")
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#t)))))))))
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2018-04-28 05:47:03 +02:00
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(define-public python-autograd
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(let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
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(revision "0")
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(version (git-version "0.0.0" revision commit)))
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(package
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(name "python-autograd")
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(home-page "https://github.com/HIPS/autograd")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url home-page)
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(commit commit)))
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(sha256
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(base32
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"189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
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(file-name (git-file-name name version))))
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(version version)
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(build-system python-build-system)
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(native-inputs
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`(("python-nose" ,python-nose)
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("python-pytest" ,python-pytest)))
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(propagated-inputs
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`(("python-future" ,python-future)
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("python-numpy" ,python-numpy)))
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(arguments
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`(#:phases (modify-phases %standard-phases
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(replace 'check
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(lambda _
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(invoke "py.test" "-v"))))))
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(synopsis "Efficiently computes derivatives of NumPy code")
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(description "Autograd can automatically differentiate native Python and
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NumPy code. It can handle a large subset of Python's features, including loops,
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ifs, recursion and closures, and it can even take derivatives of derivatives
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of derivatives. It supports reverse-mode differentiation
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(a.k.a. backpropagation), which means it can efficiently take gradients of
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scalar-valued functions with respect to array-valued arguments, as well as
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forward-mode differentiation, and the two can be composed arbitrarily. The
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main intended application of Autograd is gradient-based optimization.")
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(license license:expat))))
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(define-public python2-autograd
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(package-with-python2 python-autograd))
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2018-06-12 12:01:16 +02:00
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(define-public lightgbm
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(package
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(name "lightgbm")
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(version "2.0.12")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/Microsoft/LightGBM/archive/v"
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version ".tar.gz"))
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(sha256
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(base32
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"132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
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(file-name (string-append name "-" version ".tar.gz"))))
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(native-inputs
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`(("python-pytest" ,python-pytest)
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("python-nose" ,python-nose)))
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(inputs
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`(("openmpi" ,openmpi)))
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(propagated-inputs
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`(("python-numpy" ,python-numpy)
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("python-scipy" ,python-scipy)))
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(arguments
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`(#:configure-flags
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'("-DUSE_MPI=ON")
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#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda* (#:key outputs #:allow-other-keys)
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(with-directory-excursion ,(string-append "../LightGBM-" version)
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(invoke "pytest" "tests/c_api_test/test_.py")))))))
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(build-system cmake-build-system)
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(home-page "https://github.com/Microsoft/LightGBM")
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(synopsis "Gradient boosting framework based on decision tree algorithms")
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(description "LightGBM is a gradient boosting framework that uses tree
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based learning algorithms. It is designed to be distributed and efficient with
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the following advantages:
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@itemize
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@item Faster training speed and higher efficiency
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@item Lower memory usage
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@item Better accuracy
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@item Parallel and GPU learning supported (not enabled in this package)
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@item Capable of handling large-scale data
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@end itemize\n")
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(license license:expat)))
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2018-06-12 12:02:15 +02:00
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(define-public vowpal-wabbit
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;; Language bindings not included.
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(package
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(name "vowpal-wabbit")
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(version "8.5.0")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/JohnLangford/vowpal_wabbit/archive/"
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version ".tar.gz"))
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(sha256
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(base32
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"0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
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(file-name (string-append name "-" version ".tar.gz"))))
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(inputs
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`(("boost" ,boost)
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("zlib" ,zlib)))
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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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(build-system gnu-build-system)
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(home-page "https://github.com/JohnLangford/vowpal_wabbit")
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(synopsis "Fast machine learning library for online learning")
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(description "Vowpal Wabbit is a machine learning system with techniques
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such as online, hashing, allreduce, reductions, learning2search, active, and
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interactive learning.")
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(license license:bsd-3)))
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