From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 1/3] gnu: octave: Update to 4.4.0. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 May 2018 23:12:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 31479@debbugs.gnu.org Cc: Kei Kebreau X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.15265122727742 (code B ref -1); Wed, 16 May 2018 23:12:01 +0000 Received: (at submit) by debbugs.gnu.org; 16 May 2018 23:11:12 +0000 Received: from localhost ([127.0.0.1]:37711 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5Zf-00020o-SW for submit@debbugs.gnu.org; Wed, 16 May 2018 19:11:12 -0400 Received: from eggs.gnu.org ([208.118.235.92]:58720) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5Ze-00020Z-5t for submit@debbugs.gnu.org; Wed, 16 May 2018 19:11:10 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJ5ZY-0001p0-Ba for submit@debbugs.gnu.org; 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Wed, 16 May 2018 19:10:59 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 8DCCC2102F for ; Thu, 17 May 2018 01:10:48 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526512248; bh=6ks/x8USl37qEBJTF3NJ3HzynsI1q8XczcZmQ8OBCc4=; h=From:To:Cc:Subject:Date:From; b=ZPZAzcG7NrpLIMxpaIxTWg93E/ckNQHfB9C1Rw//nDCaXOkp+gNe8vnK08q1XR9zb tai0IHWjPmpfx7YWqrAZpKoiIrM8FUBJpl2ReLdmFJjEcqdPzG9t3cHlZObzi2kK7I qnQmL9pMjA2OsL+yn3fe7gwXrU94LmNBbL7HkFtKWrsHmDvZZhzMk2PIgwm+AqnYUi +czPuq+oSSKC8Le4zL9Kt2J/t6pmbrvsJCNNl0ZqTsfLAOeJYkXq7FE+MV9zbGzj5C Tznq+RkfbtdTAjETA6AW5WouvrHfrN4P168XzXx/lVVOEonY9IoBgif2vJqbDjjIY4 dRL3KRFR6Fkwg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40mVXl1vw0z9rxH; Thu, 17 May 2018 01:10:46 +0200 (CEST) From: Kei Kebreau Date: Wed, 16 May 2018 19:10:33 -0400 Message-Id: <20180516231033.1680-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.17.0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) * gnu/packages/maths.scm (octave): Update to 4.4.0. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2e6f79ad5..e9a6ceaab 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1323,7 +1323,7 @@ can solve two kinds of problems: (define-public octave (package (name "octave") - (version "4.2.2") + (version "4.4.0") (source (origin (method url-fetch) @@ -1331,7 +1331,7 @@ can solve two kinds of problems: version ".tar.lz")) (sha256 (base32 - "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp")))) + "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) -- 2.17.0 From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 2/3] gnu: Add rxcpp. References: <20180516231033.1680-1-kkebreau@posteo.net> In-Reply-To: <20180516231033.1680-1-kkebreau@posteo.net> Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 May 2018 23:21:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 31479@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15265128308582 (code B ref 31479); Wed, 16 May 2018 23:21:02 +0000 Received: (at 31479) by debbugs.gnu.org; 16 May 2018 23:20:30 +0000 Received: from localhost ([127.0.0.1]:37721 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5iZ-0002EE-Pv for submit@debbugs.gnu.org; Wed, 16 May 2018 19:20:29 -0400 Received: from mout01.posteo.de ([185.67.36.65]:54372) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5iV-0002Dp-3p for 31479@debbugs.gnu.org; Wed, 16 May 2018 19:20:20 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id E9C2F20DFA for <31479@debbugs.gnu.org>; Thu, 17 May 2018 01:20:12 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526512813; bh=fdBlzKF/SzbLWbmfeoc+yuaA4lXVNkvHZF2PsaYS6Aw=; h=From:To:Cc:Subject:Date:From; b=CXIAQLH5DFJHKYIk1A1FL5fCgEo4hde77T9XJjeNDxmaZrvs65Tl4dVw8InA54flm t8kFy4hmW21CrCjRctRtviNPcU7AniyOT2gYF3Yt/dZ/EehRe3TgpBSkQu4T+g54YW eyJzW4uVsxAu1mD7IWAKOGgUN8qsPT4MoC6Fuc5U8GMdtYgfxEGD3WZL61cpZbSkFA x5a2JikzEC6tS6yTaQHzrTmxo2BFLbsRCukbFAFUx5AYpT83vVf/ME59TR1mVYAb9G FJB76VaZzHw5Fd8JFrTWcFj7aw4ZzPSobJ7IX6cpPB9mrFGy6OxvZpTO3bJnu39Rxf hgJHiUj7a2ZWA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40mVlb5lHLz9rxH; Thu, 17 May 2018 01:20:11 +0200 (CEST) From: Kei Kebreau Date: Wed, 16 May 2018 19:19:56 -0400 Message-Id: <20180516231957.1827-1-kkebreau@posteo.net> X-Mailer: git-send-email 2.17.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/machine-learning.scm (rxcpp): New variable. --- gnu/packages/machine-learning.scm | 42 +++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index f0d35484e..6536d861e 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2016, 2017 Marius Bakke ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2018 Tobias Geerinckx-Rice +;;; Copyright © 2018 Kei Kebreau ;;; Copyright © 2018 Mark Meyer ;;; Copyright © 2018 Ben Woodcroft ;;; Copyright © 2018 Fis Trivial @@ -501,6 +502,47 @@ tools. This enables both rapid prototyping of data pipelines and extensibility in terms of new algorithms.") (license license:gpl3+))) +(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))) + (define-public r-adaptivesparsity (package (name "r-adaptivesparsity") -- 2.17.0 From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 May 2018 23:21:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 31479@debbugs.gnu.org Cc: Kei Kebreau Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15265128308588 (code B ref 31479); Wed, 16 May 2018 23:21:02 +0000 Received: (at 31479) by debbugs.gnu.org; 16 May 2018 23:20:30 +0000 Received: from localhost ([127.0.0.1]:37723 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5ig-0002EN-1e for submit@debbugs.gnu.org; Wed, 16 May 2018 19:20:30 -0400 Received: from mout01.posteo.de ([185.67.36.65]:41751) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5iX-0002Dw-2V for 31479@debbugs.gnu.org; Wed, 16 May 2018 19:20:23 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 5E8A520DFA for <31479@debbugs.gnu.org>; Thu, 17 May 2018 01:20:15 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526512815; bh=Su6mcM0hrZMqOanh/pP7hR+WiFATNxpPe1AMAAt7SW0=; h=From:To:Cc:Subject:Date:From; b=g4YSK27BMum2aGKvXRp+UHcTwaNAuy7Iw5PmgcZ+9yZmBrOYEVOfwklw1oBJYoel7 q5eGhoYWpHtS32fxDy+zXLCJZC2kUTdWaUCZe4kIgud6caVqEz5jKJi0WIk927NlrX G/p8qwZuQfD25fo8boITU8Rr0z4Gdpz2v0XaN3XG2oioi9FeQt3jSnVRiMjPeTdbHU tIY6hfvZTI1waaSlGFAP/gpfowKBlUdNNRrx+AbzdcoToc/VPNDBWBK7SDF6oOrbBn 9Zx6tnowfdYNY+Bjxrkv5zZAGHdkS7QQNu1gZ+E6DyJbSTVWBX61tv60XGMrQxMWIy cegTMRoR37PWQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40mVlf5RVSz9rxH; Thu, 17 May 2018 01:20:14 +0200 (CEST) From: Kei Kebreau Date: Wed, 16 May 2018 19:19:57 -0400 Message-Id: <20180516231957.1827-2-kkebreau@posteo.net> X-Mailer: git-send-email 2.17.0 In-Reply-To: <20180516231957.1827-1-kkebreau@posteo.net> References: <20180516231957.1827-1-kkebreau@posteo.net> X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/machine-learning.scm (shogun): Update to 6.1.3. [arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase. Rewrite file lists given to substitute* in 'change-R-target-path' and 'fix-octave-modules' phases. Add 'move-rxcpp' phase. Rewrite configure-flags for the update. [inputs]: Add eigen. [native-inputs]: Add rxcpp. --- gnu/packages/machine-learning.scm | 60 ++++++++++++++----------------- 1 file changed, 27 insertions(+), 33 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 6536d861e..e79aa6692 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -37,6 +37,7 @@ #:use-module (guix build-system r) #:use-module (guix git-download) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -367,7 +368,7 @@ sample proximities between pairs of cases.") (define-public shogun (package (name "shogun") - (version "4.0.0") + (version "6.1.3") (source (origin (method url-fetch) @@ -377,7 +378,7 @@ sample proximities between pairs of cases.") "/sources/shogun-" version ".tar.bz2")) (sha256 (base32 - "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")) + "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp")) (modules '((guix build utils) (ice-9 rdelim))) (snippet @@ -423,62 +424,54 @@ sample proximities between pairs of cases.") "applications/easysvm/data" "applications/msplicer/data" "applications/ocr/data" - "examples/documented/data" - "examples/documented/matlab_static" - "examples/documented/octave_static" - "examples/undocumented/data" - "examples/undocumented/matlab_static" - "examples/undocumented/octave_static" - "tests/integration/data" - "tests/integration/matlab_static" - "tests/integration/octave_static" - "tests/integration/python_modular/tests")) + "examples/meta/data" + "examples/undocumented/data")) #t)) (add-after 'unpack 'change-R-target-path (lambda* (#:key outputs #:allow-other-keys) - (substitute* '("src/interfaces/r_modular/CMakeLists.txt" - "src/interfaces/r_static/CMakeLists.txt" - "examples/undocumented/r_modular/CMakeLists.txt") + (substitute* '("src/interfaces/r/CMakeLists.txt" + "examples/meta/r/CMakeLists.txt") (("\\$\\{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) - (substitute* '("src/interfaces/octave_modular/CMakeLists.txt" - "src/interfaces/octave_static/CMakeLists.txt") + (substitute* "src/interfaces/octave/CMakeLists.txt" (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") - "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")) - - ;; change target directory - (substitute* "src/interfaces/octave_modular/CMakeLists.txt" + "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave") + ;; change target directory (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") (string-append (assoc-ref outputs "out") "/share/octave/packages"))) #t)) + (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))) (add-before 'build 'set-HOME ;; $HOME needs to be set at some point during the build phase (lambda _ (setenv "HOME" "/tmp") #t))) #:configure-flags (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE" "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT - ;;"-DJavaModular=ON" ;requires unpackaged jblas - ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray - ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist - ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file - "-DOctaveModular=ON" - "-DOctaveStatic=ON" - "-DPythonModular=ON" - "-DPythonStatic=ON" - "-DRModular=ON" - "-DRStatic=ON" - "-DCmdLineStatic=ON"))) + "-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"))) (inputs `(("python" ,python) ("numpy" ,python-numpy) ("r-minimal" ,r-minimal) ("octave" ,octave) ("swig" ,swig) + ("eigen" ,eigen) ("hdf5" ,hdf5) ("atlas" ,atlas) ("arpack" ,arpack-ng) @@ -488,7 +481,8 @@ sample proximities between pairs of cases.") ("lzo" ,lzo) ("zlib" ,zlib))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("rxcpp" ,rxcpp))) ;; Non-portable SSE instructions are used so building fails on platforms ;; other than x86_64. (supported-systems '("x86_64-linux")) -- 2.17.0 From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 May 2018 23:25:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15265130678984 (code B ref 31479); Wed, 16 May 2018 23:25:01 +0000 Received: (at 31479) by debbugs.gnu.org; 16 May 2018 23:24:27 +0000 Received: from localhost ([127.0.0.1]:37732 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5mU-0002Kq-Ti for submit@debbugs.gnu.org; Wed, 16 May 2018 19:24:27 -0400 Received: from mout01.posteo.de ([185.67.36.65]:36270) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJ5mT-0002Kc-0q for 31479@debbugs.gnu.org; Wed, 16 May 2018 19:24:25 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 5A18D20DE5 for <31479@debbugs.gnu.org>; Thu, 17 May 2018 01:24:19 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526513059; bh=QcHocTN3794in7qcoi22+OkaRpyvkw4KYZQJ36dzHpA=; h=From:To:Subject:Date:From; b=Tfhjr9/cFRRoM1G3ObIC7oIsrxVs/DK1vTWZH55cciMPZIJzrwsIThB+V41Il48uZ h7wm+L/wSMf92OrULadPa1K6gyevY2zfCQYzZIUsamvDAcejn/GKrRuA2rBVlBtYme zPaYde2BbWE632/lPyC0R6big8ScLz6A5mv+KeoQ3NtYKcpKAxDjmJbEdL+Qbh58p9 hy0QukiKn8uTB7uihun2KfGUHnIHdVxO7+3AW/JkRPSkUBwUywVcBydz7cA2VT7jtO ZHt7fhux02eqZ5lS4dfoT9FDBB8Tqyyu+iK9xcIEcx4tMauzHEjMOlPLDYneqla1ZU QXxRdLvgLZQyw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40mVrL2f0Wz9rxK for <31479@debbugs.gnu.org>; Thu, 17 May 2018 01:24:18 +0200 (CEST) From: Kei Kebreau References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> Date: Wed, 16 May 2018 19:24:01 -0400 In-Reply-To: <20180516231957.1827-2-kkebreau@posteo.net> (Kei Kebreau's message of "Wed, 16 May 2018 19:19:57 -0400") Message-ID: <874lj7w5f2.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Kei Kebreau writes: > * gnu/packages/machine-learning.scm (shogun): Update to 6.1.3. > [arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase. > Rewrite file lists given to substitute* in 'change-R-target-path' and > 'fix-octave-modules' phases. Add 'move-rxcpp' phase. Rewrite configure-flags > for the update. > [inputs]: Add eigen. > [native-inputs]: Add rxcpp. > --- > gnu/packages/machine-learning.scm | 60 ++++++++++++++----------------- > 1 file changed, 27 insertions(+), 33 deletions(-) > > diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm > index 6536d861e..e79aa6692 100644 > --- a/gnu/packages/machine-learning.scm > +++ b/gnu/packages/machine-learning.scm > @@ -37,6 +37,7 @@ > #:use-module (guix build-system r) > #:use-module (guix git-download) > #:use-module (gnu packages) > + #:use-module (gnu packages algebra) > #:use-module (gnu packages autotools) > #:use-module (gnu packages boost) > #:use-module (gnu packages check) > @@ -367,7 +368,7 @@ sample proximities between pairs of cases.") > (define-public shogun > (package > (name "shogun") > - (version "4.0.0") > + (version "6.1.3") > (source > (origin > (method url-fetch) > @@ -377,7 +378,7 @@ sample proximities between pairs of cases.") > "/sources/shogun-" version ".tar.bz2")) > (sha256 > (base32 > - "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")) > + "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp")) > (modules '((guix build utils) > (ice-9 rdelim))) > (snippet > @@ -423,62 +424,54 @@ sample proximities between pairs of cases.") > "applications/easysvm/data" > "applications/msplicer/data" > "applications/ocr/data" > - "examples/documented/data" > - "examples/documented/matlab_static" > - "examples/documented/octave_static" > - "examples/undocumented/data" > - "examples/undocumented/matlab_static" > - "examples/undocumented/octave_static" > - "tests/integration/data" > - "tests/integration/matlab_static" > - "tests/integration/octave_static" > - "tests/integration/python_modular/tests")) > + "examples/meta/data" > + "examples/undocumented/data")) > #t)) > (add-after 'unpack 'change-R-target-path > (lambda* (#:key outputs #:allow-other-keys) > - (substitute* '("src/interfaces/r_modular/CMakeLists.txt" > - "src/interfaces/r_static/CMakeLists.txt" > - "examples/undocumented/r_modular/CMakeLists.txt") > + (substitute* '("src/interfaces/r/CMakeLists.txt" > + "examples/meta/r/CMakeLists.txt") > (("\\$\\{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) > - (substitute* '("src/interfaces/octave_modular/CMakeLists.txt" > - "src/interfaces/octave_static/CMakeLists.txt") > + (substitute* "src/interfaces/octave/CMakeLists.txt" > (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") > - "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")) > - > - ;; change target directory > - (substitute* "src/interfaces/octave_modular/CMakeLists.txt" > + "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave") > + ;; change target directory > (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") > (string-append (assoc-ref outputs "out") > "/share/octave/packages"))) > #t)) > + (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))) > (add-before 'build 'set-HOME > ;; $HOME needs to be set at some point during the build phase > (lambda _ (setenv "HOME" "/tmp") #t))) > #:configure-flags > (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE" > "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT > - ;;"-DJavaModular=ON" ;requires unpackaged jblas > - ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray > - ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist > - ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file > - "-DOctaveModular=ON" > - "-DOctaveStatic=ON" > - "-DPythonModular=ON" > - "-DPythonStatic=ON" > - "-DRModular=ON" > - "-DRStatic=ON" > - "-DCmdLineStatic=ON"))) > + "-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"))) > (inputs > `(("python" ,python) > ("numpy" ,python-numpy) > ("r-minimal" ,r-minimal) > ("octave" ,octave) > ("swig" ,swig) > + ("eigen" ,eigen) > ("hdf5" ,hdf5) > ("atlas" ,atlas) > ("arpack" ,arpack-ng) > @@ -488,7 +481,8 @@ sample proximities between pairs of cases.") > ("lzo" ,lzo) > ("zlib" ,zlib))) > (native-inputs > - `(("pkg-config" ,pkg-config))) > + `(("pkg-config" ,pkg-config) > + ("rxcpp" ,rxcpp))) > ;; Non-portable SSE instructions are used so building fails on platforms > ;; other than x86_64. > (supported-systems '("x86_64-linux")) These patches are really just to upgrade Octave, but the old Shogun couldn't find the new version of Octave. The shogun update patch is a WIP, but I don't have enough RAM (only 3.8GB) to make it through Shogun's build process reliably. Could someone else help out with this patch? --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlr8vZEACgkQ5qXuPBlG eg1QyQ//fLGrQuyCXRtG7w7kWz/Lc8J5bWNPbwR6X4uUCK6DlwxdiBe4sgZlzbgf e7a5MBmazE5FSRV3YGnQiZOykHPBU3DzuZ45YgMIQO/2MBU7tgja52GZLUPtHEYc uYUeoNs2OIF7PEV0iBaMNEQUElJUSlFWW/Jju8VJPKniSVy/FC53Jm6ZG0e9+oSX Pqbo0fqfpSTlJQvSh3oG0f5it1JjC0Pmxd2J7B2/OE2rbU0tKbburPJkVXoTuvya 0SN1E/9rCBQGTisppyu/lklJ5DoC2R0l/+2sDSXHsAXP3MHw3XBLisJNQuimKYxL z1EZtVvwL5UrVp1QtmyaAxESEWBcR/tsvtO4kg55354Ri3YaY63ZFvz/4WYMGT/t VIXPDC4IvTq16zdi48rZcH5VMB9XtwLsuM2OaLGYdqVfbzxDHzlY2iieYAr/y6ic qiLhyfsPB+Y0NhdkpV4jh8xkoQGcnnVh8mMK4M91Pgoedu8uYxpNhiPl9Lbkp8LC v6wyT2lzHxfw/5Yy9NcZqMnrxdDJRvckFyPmoF6He37Sia0Kcylziw8ymcDrf1d0 CvUnu5t2f2TMdAIG4ihUGrw36W6QOMUx//io2NHJuegyZVixDzasFO0DjcLwF8dw 36P5FSZgU2oN03nW2ve1G4MPSC26zuBxvJq0wbJWHAYCIGb+ABg= =NR03 -----END PGP SIGNATURE----- --=-=-=-- From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 1/3] gnu: octave: Update to 4.4.0. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 17 May 2018 11:25:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15265562768382 (code B ref 31479); Thu, 17 May 2018 11:25:02 +0000 Received: (at 31479) by debbugs.gnu.org; 17 May 2018 11:24:36 +0000 Received: from localhost ([127.0.0.1]:37978 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJH1P-0002B8-UJ for submit@debbugs.gnu.org; Thu, 17 May 2018 07:24:36 -0400 Received: from eggs.gnu.org ([208.118.235.92]:48613) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJH1O-0002Av-4k for 31479@debbugs.gnu.org; Thu, 17 May 2018 07:24:34 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJH1F-0000GZ-J7 for 31479@debbugs.gnu.org; Thu, 17 May 2018 07:24:28 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:45250) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fJH1F-0000GT-FD; Thu, 17 May 2018 07:24:25 -0400 Received: from [193.50.110.196] (port=49784 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fJH1E-0002mO-WB; Thu, 17 May 2018 07:24:25 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20180516231033.1680-1-kkebreau@posteo.net> Date: Thu, 17 May 2018 13:24:23 +0200 In-Reply-To: <20180516231033.1680-1-kkebreau@posteo.net> (Kei Kebreau's message of "Wed, 16 May 2018 19:10:33 -0400") Message-ID: <87h8n634pk.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Kei Kebreau skribis: > * gnu/packages/maths.scm (octave): Update to 4.4.0. LGTM, thanks! Ludo'. From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 2/3] gnu: Add rxcpp. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 17 May 2018 11:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15265563738545 (code B ref 31479); Thu, 17 May 2018 11:27:02 +0000 Received: (at 31479) by debbugs.gnu.org; 17 May 2018 11:26:13 +0000 Received: from localhost ([127.0.0.1]:37984 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJH2z-0002Dl-BJ for submit@debbugs.gnu.org; Thu, 17 May 2018 07:26:13 -0400 Received: from eggs.gnu.org ([208.118.235.92]:48971) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJH2y-0002DZ-9M for 31479@debbugs.gnu.org; Thu, 17 May 2018 07:26:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJH2q-0001IO-0P for 31479@debbugs.gnu.org; Thu, 17 May 2018 07:26:07 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:45298) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fJH2p-0001I6-Sl; Thu, 17 May 2018 07:26:03 -0400 Received: from [193.50.110.196] (port=50002 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fJH2p-0002wB-Cw; Thu, 17 May 2018 07:26:03 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20180516231033.1680-1-kkebreau@posteo.net> <20180516231957.1827-1-kkebreau@posteo.net> Date: Thu, 17 May 2018 13:26:01 +0200 In-Reply-To: <20180516231957.1827-1-kkebreau@posteo.net> (Kei Kebreau's message of "Wed, 16 May 2018 19:19:56 -0400") Message-ID: <87d0xu34mu.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Kei Kebreau skribis: > * gnu/packages/machine-learning.scm (rxcpp): New variable. [...] > + (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 asynch= ronous > +and event-based programs by using observable sequences. LGTM! Probably machine-learning.scm is not the best place for it, but I can=E2=80= =99t think of a better place. Thanks, Ludo=E2=80=99. From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Jonathan Brielmaier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 17 May 2018 11:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 31479@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.152655716917168 (code B ref -1); Thu, 17 May 2018 11:40:02 +0000 Received: (at submit) by debbugs.gnu.org; 17 May 2018 11:39:29 +0000 Received: from localhost ([127.0.0.1]:37994 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJHFm-0004Sn-Re for submit@debbugs.gnu.org; Thu, 17 May 2018 07:39:29 -0400 Received: from eggs.gnu.org ([208.118.235.92]:52705) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJHFk-0004Sa-R9 for submit@debbugs.gnu.org; Thu, 17 May 2018 07:39:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJHFe-0000fo-SD for submit@debbugs.gnu.org; Thu, 17 May 2018 07:39:19 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:36581) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fJHFe-0000fP-Oz for submit@debbugs.gnu.org; Thu, 17 May 2018 07:39:18 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:43642) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fJHFa-0007Jj-0I for guix-patches@gnu.org; Thu, 17 May 2018 07:39:18 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJHFX-0000Zv-DH for guix-patches@gnu.org; Thu, 17 May 2018 07:39:14 -0400 Received: from mout.web.de ([212.227.17.12]:53507) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1fJHFX-0000Z4-2W for guix-patches@gnu.org; Thu, 17 May 2018 07:39:11 -0400 Received: from [10.161.59.95] ([195.135.221.2]) by smtp.web.de (mrweb103 [213.165.67.124]) with ESMTPSA (Nemesis) id 0MCqkB-1fAig30jIJ-009izj for ; Thu, 17 May 2018 13:39:08 +0200 References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> <874lj7w5f2.fsf@posteo.net> From: Jonathan Brielmaier Message-ID: <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> Date: Thu, 17 May 2018 13:39:07 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.0 MIME-Version: 1.0 In-Reply-To: <874lj7w5f2.fsf@posteo.net> Content-Type: text/plain; charset=utf-8 Content-Language: en-US Content-Transfer-Encoding: 7bit X-Provags-ID: V03:K1:roLLZc8vahiJ4/5nwVsel7yC1NGMtfa2CHKUKLWhPFcDewKhuRC GL7USX/IH79LQbCLJgQxl/ajw7SxgJG1viZGTll9bpbE2iPBkhELngugA933gKGWZbKvrdJ hafoDBAxuoylFWp7/tchPeTt0NXpSQNpWi4keRtztTM/JPfvmCTFgbJP4/IcSBg4oNb0RhX BnpQaPMsFVE+pdJ7WeWjA== X-UI-Out-Filterresults: notjunk:1;V01:K0:qjkpXoW739o=:eP2NIMARizgjnZ16Cfte3z 9PC+43rcjNQq6dFjZlC8dpSHDEpoxSFRPhhWijpEdMDFtM01EpakwWxyL0Q1aAAcqHVC28Imy 2E+SJLCyNfrPjSJFrzE4n9m2ZwF4Djs2mUYATZUDd9bPV2GstsRmULD7sJKwqp6sBM6hjJDwp o/LezPDGPtkvRAjjPVq65ZYhU5j+I1avTTGXawbzIqU6LEZFFBu4mjrFF06EUGuUS59e6hSTz XVwT9rLLsKD7vr1+5dxr39oL2TA4xnSIwPylZG4ea/4h9t+38dp6c+E29gTGLFhM2WVjJFUi9 C4Lo1VbNFmQPA0ON+EVNs2wjwl8j06skyY3mpWODVJgdd7D1a0K5swUOviBm2LJG7NxVFOh6q DOM/itJiLeOifcTpLIiu108Q/1vVziU0XGZYqddoEew95HSmqgKO7mTsIMBjbeFnDjLmGZx+H alLP4jDRD547kHKdqmnfaE/6ZE8Ob+NCsIbvlPGOv94IMGJyX9f9rdz84FZe91F3QqN14DAac v6HbhN4mySBHafD2Qwlhxe9P2RqfkDrfMfM47tLtm7pUTf7IJhLhrlWBRfRugw6ML31ou+QBQ ilC9k4WhicdpEla2tvuT5sCMusQf+/gmxFgQYtRxoKydoTuY1j/vxzixhrEXd5PFsN7OcksCB 2ogjCfJloahBaYTXBimvprjFPrJh1MIJmbAFHEimEliPeg0DFyEf98ZM1nq+KompqGBnBdojn 81vkYhkxoG7pfzQtD/h1r1uuarxfw75MTMKPZgS924rZi/4NZimiT8Fu4lI5+eBCUSCT1ISi0 m4S+AoV X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.1 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.1 (-----) On 17/05/2018 01:24, Kei Kebreau wrote: > > These patches are really just to upgrade Octave, but the old Shogun > couldn't find the new version of Octave. The shogun update patch is a > WIP, but I don't have enough RAM (only 3.8GB) to make it through Shogun's > build process reliably. Could someone else help out with this patch? > I build shogun now, lets see how it goes :) From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Jonathan Brielmaier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 18 May 2018 06:00:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 31479@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.152662314724339 (code B ref -1); Fri, 18 May 2018 06:00:01 +0000 Received: (at submit) by debbugs.gnu.org; 18 May 2018 05:59:07 +0000 Received: from localhost ([127.0.0.1]:39052 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJYPz-0006KU-0c for submit@debbugs.gnu.org; Fri, 18 May 2018 01:59:07 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39343) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJYPx-0006K0-Fd for submit@debbugs.gnu.org; Fri, 18 May 2018 01:59:05 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJYPq-0003SI-TI for submit@debbugs.gnu.org; Fri, 18 May 2018 01:59:00 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,FREEMAIL_FROM autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:41720) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fJYPq-0003SA-Of for submit@debbugs.gnu.org; Fri, 18 May 2018 01:58:58 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58547) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fJYPp-0001p0-BQ for guix-patches@gnu.org; Fri, 18 May 2018 01:58:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fJYPl-0003Q0-C5 for guix-patches@gnu.org; Fri, 18 May 2018 01:58:57 -0400 Received: from mout.web.de ([217.72.192.78]:56245) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1fJYPl-0003PP-1z for guix-patches@gnu.org; Fri, 18 May 2018 01:58:53 -0400 Received: from [10.161.59.95] ([195.135.221.2]) by smtp.web.de (mrweb102 [213.165.67.124]) with ESMTPSA (Nemesis) id 0McWnE-1f1t2R18fw-00Hi9v for ; Fri, 18 May 2018 07:58:51 +0200 References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> <874lj7w5f2.fsf@posteo.net> <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> From: Jonathan Brielmaier Message-ID: <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> Date: Fri, 18 May 2018 07:58:50 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:60.0) Gecko/20100101 Thunderbird/60.0 MIME-Version: 1.0 In-Reply-To: <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> Content-Type: multipart/mixed; boundary="------------04CB17B79655649C4E65E153" Content-Language: en-US X-Provags-ID: V03:K1:FopSvLHYvth9lOnHzLECBSPZFjV6QtCV4M8WIfJgJKwPxRhdjx8 cNL++eplri7rftqcTXTbnMsyqf9vrQy1FYE3/x/y64oC3fhLJ03D6ASD9mnDByJIeUdtOnv 9DLPhGRaftw2Pj15Vrre30Lm1ScaunlJmLTJXH1QXcYqtoHyiENJpmiymSZSo6PC1otchmV +s3nzCnEgKHiWT+UN0uJw== X-UI-Out-Filterresults: notjunk:1;V01:K0:+gqB5MOJoFA=:eJaLupncIQ4ctjPRiFGzvQ 1e2KLtj+imMjsZodM0QpKdlVZwdyJiZlCURMIJPvBTyv48GiU8GHa5xIxXOaNdlhzNlIp27Sb 7yGdCBzlvXij5zuKUQfBd8NdDhdNRMNPOXmeF+R9RkIU65A1Mwuahzf1tVqy3eF4r+jYs8cBa pVrLzU3SvUN9eZB59Zsdyfh3URAFEAOHqKfcwpQmuifpNvYKbV9I/5cQ1vaBadKZp8ql4JEND JzCK4nVMHESLnxHulF6OG2DeqgpX5h+/01bzJO2G8N6BCA7VXhvPhjT7nMyxv4ba0XO4/Xfe5 /Gk1UdE0FXBoaf7M2uo4K49YBzTAsHHlfmCjnsQRecKDa6P39hwCVMB61CZpwBjAQSe4MGgrC qfpHlKvX8P9AsuCtv88qtRmxfvf7AVwXJw1pTxbVbQVZ/cLyovwp0H6O0BE7P0iRxpBDOWqbz G/K5+Mm2a+wPnD7HNpNol4RhLNJoTVPEdsSuQjpY8dTgOeiHkcfIpqM+mHH1QXZhWxev3EHeb 0Nv0RSGMM9xXZAskxX8TnruiqmQQ6iBxC7JXLOjXffPs8NeIFmrlz15oX14whxuY/tOjLyqU9 z0PVXxA+GJLuU1Zh3LLejHCmaeXDZvTEUT/wL8B7OykO7Ujo4ZLcqg5nnwZC7ryOEMvkNT1iT uD0tG6o61NImNtpseASGc+TBsuuIBzWMEJtffPzqnuWlCurLfDpDKLhSeyrYz7qGHQWihlVMi vSThST/a167NJswhDPg4m5gDSZHZTJ7mUyWy5JS/snfXccK8O7rDYXn1mAc= X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.1 (----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.1 (-----) This is a multi-part message in MIME format. --------------04CB17B79655649C4E65E153 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit On 17/05/2018 13:39, Jonathan Brielmaier wrote: > On 17/05/2018 01:24, Kei Kebreau wrote: >> >> These patches are really just to upgrade Octave, but the old Shogun >> couldn't find the new version of Octave. The shogun update patch is a >> WIP, but I don't have enough RAM (only 3.8GB) to make it through Shogun's >> build process reliably. Could someone else help out with this patch? >> > > I build shogun now, lets see how it goes :) Unfortunately there was a build error for shogun. I attached the build log where it fails. It has something to do with the eigen library... --------------04CB17B79655649C4E65E153 Content-Type: text/plain; charset=UTF-8; name="shogun_build.txt" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="shogun_build.txt" JCAvcHJlLWluc3QtZW52IGd1aXggYnVpbGQgc2hvZ3VuClsuLi5dClsgNTAlXSBCdWlsZGlu ZyBDWFggb2JqZWN0IHNyYy9zaG9ndW4vQ01ha2VGaWxlcy9saWJzaG9ndW4uZGlyL21hdGhl bWF0aWNzL2xpbmFsZy9yYXRhcHByb3gvbG9nZGV0L29wZnVuYy9EZW5zZU1hdHJpeEV4YWN0 TG9nLmNwcC5vCmNkIC90bXAvZ3VpeC1idWlsZC1zaG9ndW4tNi4xLjMuZHJ2LTAvYnVpbGQv c3JjL3Nob2d1biAmJiAvZ251L3N0b3JlL2NmZG42OXNwamM0NHg0c2QwYWNyd2h4cTZ5YXkz cmJjLWdjYy01LjUuMC9iaW4vYysrICAgIC1JL3RtcC9ndWl4LWJ1aWxkLXNob2d1bi02LjEu My5kcnYtMC9zaG9ndW4tNi4xLjMvc3JjIC1JL3RtcC9ndWl4LWJ1aWxkLXNob2d1bi02LjEu My5kcnYtMC9idWlsZC9zcmMgLUkvdG1wL2d1aXgtYnVpbGQtc2hvZ3VuLTYuMS4zLmRydi0w L3Nob2d1bi02LjEuMy9zcmMvZ3BsIC1pc3lzdGVtIC9nbnUvc3RvcmUvaXd6bjN2aHdtemt2 aHE3c3FzNmM0YmpwMnhsZDE3a2MtZWlnZW4tMy4zLjQvaW5jbHVkZS9laWdlbjMgLWlzeXN0 ZW0gL2dudS9zdG9yZS81czlhbTFkZ244M3dqNXE1a3dmY2FzcXdzOHpkODV6ei1yeGNwcC00 LjAuMCAtSS9nbnUvc3RvcmUvbWxseXZmeTM5bnB6cmE5ODRqc21jbThrc24zeDgwOTQtZ2xw ay00LjY1L2luY2x1ZGUgLUkvZ251L3N0b3JlL3dudzBndjVoZ21obHczanoxcGd3NG4wMTdi aGo5ZjJ6LWFycGFjay1uZy0zLjUuMC9saWIvLi4vaW5jbHVkZSAtSS9nbnUvc3RvcmUvbXY5 bTZieGRoaWpobGZ2eHBqYTNrbTZ2NTk5YjRwdjUtbGlieG1sMi0yLjkuNy9pbmNsdWRlL2xp YnhtbDIgLUkvZ251L3N0b3JlLzI3anJ2d2JnNXhhOWxhNmp3bnF6NnlzNGs3cGZ5eWtsLWhk ZjUtMS44LjE5L2luY2x1ZGUgLUkvZ251L3N0b3JlLzloZDM4Ymt3OGJxOGdxNmxjdjZ2ZDh4 anBjc2J5emxtLXpsaWItMS4yLjExL2luY2x1ZGUgLUkvZ251L3N0b3JlLzc3bDhzeGg5cHkx MzNjeTFwOWt5cHNoamk0cTl3djB3LWJ6aXAyLTEuMC42L2luY2x1ZGUgLUkvZ251L3N0b3Jl L2tnYWY2NzFhOWE3NmswcWwxcHd3anhqYmo4MHgyMm1qLXh6LTUuMi4zL2luY2x1ZGUgLUkv Z251L3N0b3JlLzMzbTg2eWNhazUwdmgycDBxN3FiMGJ5aDk5MGhya2puLWx6by0yLjEwL2lu Y2x1ZGUgIC1XYWxsIC1Xbm8tdW51c2VkLXBhcmFtZXRlciAtV2Zvcm1hdCAtV2Zvcm1hdC1z ZWN1cml0eSAtV3BhcmVudGhlc2VzIC1Xc2hhZG93IC1Xbm8tdW5rbm93bi1wcmFnbWFzIC1X bm8tZGVwcmVjYXRlZCAgLU8yIC1nIC1ETkRFQlVHIC1mUElDICAgLWZvcGVubXAgLXN0ZD1j KysxMSAtbyBDTWFrZUZpbGVzL2xpYnNob2d1bi5kaXIvbWF0aGVtYXRpY3MvbGluYWxnL3Jh dGFwcHJveC9sb2dkZXQvb3BmdW5jL0RlbnNlTWF0cml4RXhhY3RMb2cuY3BwLm8gLWMgL3Rt cC9ndWl4LWJ1aWxkLXNob2d1bi02LjEuMy5kcnYtMC9zaG9ndW4tNi4xLjMvc3JjL3Nob2d1 bi9tYXRoZW1hdGljcy9saW5hbGcvcmF0YXBwcm94L2xvZ2RldC9vcGZ1bmMvRGVuc2VNYXRy aXhFeGFjdExvZy5jcHAKL3RtcC9ndWl4LWJ1aWxkLXNob2d1bi02LjEuMy5kcnYtMC9zaG9n dW4tNi4xLjMvc3JjL3Nob2d1bi9tYXRoZW1hdGljcy9saW5hbGcvcmF0YXBwcm94L2xvZ2Rl dC9vcGZ1bmMvRGVuc2VNYXRyaXhFeGFjdExvZy5jcHA6MTU6NDU6IGZhdGFsIGVycm9yOiB1 bnN1cHBvcnRlZC9FaWdlbi9NYXRyaXhGdW5jdGlvbnM6IE5vIHN1Y2ggZmlsZSBvciBkaXJl Y3RvcnkKY29tcGlsYXRpb24gdGVybWluYXRlZC4KbWFrZVsyXTogKioqIFtzcmMvc2hvZ3Vu L0NNYWtlRmlsZXMvbGlic2hvZ3VuLmRpci9idWlsZC5tYWtlOjExNDU2OiBzcmMvc2hvZ3Vu L0NNYWtlRmlsZXMvbGlic2hvZ3VuLmRpci9tYXRoZW1hdGljcy9saW5hbGcvcmF0YXBwcm94 L2xvZ2RldC9vcGZ1bmMvRGVuc2VNYXRyaXhFeGFjdExvZy5jcHAub10gRXJyb3IgMQptYWtl WzJdOiAqKiogV2FpdGluZyBmb3IgdW5maW5pc2hlZCBqb2JzLi4uLgptYWtlWzJdOiBMZWF2 aW5nIGRpcmVjdG9yeSAnL3RtcC9ndWl4LWJ1aWxkLXNob2d1bi02LjEuMy5kcnYtMC9idWls ZCcKbWFrZVsxXTogKioqIFtDTWFrZUZpbGVzL01ha2VmaWxlMjoxMjY6IHNyYy9zaG9ndW4v Q01ha2VGaWxlcy9saWJzaG9ndW4uZGlyL2FsbF0gRXJyb3IgMgptYWtlWzFdOiBMZWF2aW5n IGRpcmVjdG9yeSAnL3RtcC9ndWl4LWJ1aWxkLXNob2d1bi02LjEuMy5kcnYtMC9idWlsZCcK bWFrZTogKioqIFtNYWtlZmlsZToxNTM6IGFsbF0gRXJyb3IgMgpwaGFzZSBgYnVpbGQnIGZh aWxlZCBhZnRlciA0OTMuNyBzZWNvbmRzCmJ1aWxkZXIgZm9yIGAvZ251L3N0b3JlL21qbm1o emR4Nnptd2N2c3BtbGpzcmp3MmFhemZ2bnY3LXNob2d1bi02LjEuMy5kcnYnIGZhaWxlZCB3 aXRoIGV4aXQgY29kZSAxCkAgYnVpbGQtZmFpbGVkIC9nbnUvc3RvcmUvbWpubWh6ZHg2em13 Y3ZzcG1sanNyancyYWF6ZnZudjctc2hvZ3VuLTYuMS4zLmRydiAtIDEgYnVpbGRlciBmb3Ig YC9nbnUvc3RvcmUvbWpubWh6ZHg2em13Y3ZzcG1sanNyancyYWF6ZnZudjctc2hvZ3VuLTYu MS4zLmRydicgZmFpbGVkIHdpdGggZXhpdCBjb2RlIDEKZ3VpeCBidWlsZDogZXJyb3I6IGJ1 aWxkIGZhaWxlZDogYnVpbGQgb2YgYC9nbnUvc3RvcmUvbWpubWh6ZHg2em13Y3ZzcG1sanNy ancyYWF6ZnZudjctc2hvZ3VuLTYuMS4zLmRydicgZmFpbGVkCg== --------------04CB17B79655649C4E65E153-- From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 18 May 2018 17:10:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Jonathan Brielmaier Cc: 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.152666337028629 (code B ref 31479); Fri, 18 May 2018 17:10:01 +0000 Received: (at 31479) by debbugs.gnu.org; 18 May 2018 17:09:30 +0000 Received: from localhost ([127.0.0.1]:40023 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJisk-0007Rh-Fc for submit@debbugs.gnu.org; Fri, 18 May 2018 13:09:30 -0400 Received: from mout01.posteo.de ([185.67.36.65]:45510) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fJisi-0007RQ-Rt for 31479@debbugs.gnu.org; Fri, 18 May 2018 13:09:29 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id A79C8211B5 for <31479@debbugs.gnu.org>; Fri, 18 May 2018 19:09:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526663362; bh=DDpIW7/QB13TcVYYIxTRlwch7nAVuzDgQSGQ7JJlz1Q=; h=From:To:Cc:Subject:Date:From; b=AIA1sm1BtCg9Mw7eGa9v3EPFd+jFiEHXId/ppgeirC5lZ8ndqZBtibMBbP0LG2Xd3 h30LZ6PGM47HXOdio71d0XKpL7sPXTS7BHVqGiBFdbqvIBHxhau95mipqM8tTnAK8I 1pYfU2LxjV/CTwnTzRuPlsN4/B/NSwnnsOomEZS/CD/jqMgIYf+txatL43/Vk+eNEz 5MBhenXnA523pfZYWsyNyzKEj+J1SGmgUO8FuRmMM9GIyTXXhZDPklC0DAMIP1Ta55 TcjINdHrOk99IBnM06dALX7NGdcuLJNIDpB0N5yjAOLenNU8XPPXXN9jetHFhje2X3 bKLEAWVl2k3sg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40nZQn0B8Mz9rxS; Fri, 18 May 2018 19:09:20 +0200 (CEST) From: Kei Kebreau References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> <874lj7w5f2.fsf@posteo.net> <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> Date: Fri, 18 May 2018 13:08:57 -0400 In-Reply-To: <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> (Jonathan Brielmaier's message of "Fri, 18 May 2018 07:58:50 +0200") Message-ID: <87muww6gd2.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Jonathan Brielmaier writes: > On 17/05/2018 13:39, Jonathan Brielmaier wrote: >> On 17/05/2018 01:24, Kei Kebreau wrote: >>> >>> These patches are really just to upgrade Octave, but the old Shogun >>> couldn't find the new version of Octave. The shogun update patch is a >>> WIP, but I don't have enough RAM (only 3.8GB) to make it through Shogun= 's >>> build process reliably. Could someone else help out with this patch? >>> >>=20 >> I build shogun now, lets see how it goes :) > > Unfortunately there was a build error for shogun. I attached the build > log where it fails. It has something to do with the eigen library... > > > > $ /pre-inst-env guix build shogun > [...] > [ 50%] Building CXX object src/shogun/CMakeFiles/libshogun.dir/mathematic= s/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp.o > cd /tmp/guix-build-shogun-6.1.3.drv-0/build/src/shogun && /gnu/store/cfdn= 69spjc44x4sd0acrwhxq6yay3rbc-gcc-5.5.0/bin/c++ -I/tmp/guix-build-shogun-= 6.1.3.drv-0/shogun-6.1.3/src -I/tmp/guix-build-shogun-6.1.3.drv-0/build/src= -I/tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/gpl -isystem /gnu/st= ore/iwzn3vhwmzkvhq7sqs6c4bjp2xld17kc-eigen-3.3.4/include/eigen3 -isystem /g= nu/store/5s9am1dgn83wj5q5kwfcasqws8zd85zz-rxcpp-4.0.0 -I/gnu/store/mllyvfy3= 9npzra984jsmcm8ksn3x8094-glpk-4.65/include -I/gnu/store/wnw0gv5hgmhlw3jz1pg= w4n017bhj9f2z-arpack-ng-3.5.0/lib/../include -I/gnu/store/mv9m6bxdhijhlfvxp= ja3km6v599b4pv5-libxml2-2.9.7/include/libxml2 -I/gnu/store/27jrvwbg5xa9la6j= wnqz6ys4k7pfyykl-hdf5-1.8.19/include -I/gnu/store/9hd38bkw8bq8gq6lcv6vd8xjp= csbyzlm-zlib-1.2.11/include -I/gnu/store/77l8sxh9py133cy1p9kypshji4q9wv0w-b= zip2-1.0.6/include -I/gnu/store/kgaf671a9a76k0ql1pwwjxjbj80x22mj-xz-5.2.3/i= nclude -I/gnu/store/33m86ycak50vh2p0q7qb0byh990hrkjn-lzo-2.10/include -Wal= l -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -= Wno-unknown-pragmas -Wno-deprecated -O2 -g -DNDEBUG -fPIC -fopenmp -std= =3Dc++11 -o CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/op= func/DenseMatrixExactLog.cpp.o -c /tmp/guix-build-shogun-6.1.3.drv-0/shogun= -6.1.3/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExa= ctLog.cpp > /tmp/guix-build-shogun-6.1.3.drv-0/shogun-6.1.3/src/shogun/mathematics/li= nalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp:15:45: fatal error: un= supported/Eigen/MatrixFunctions: No such file or directory > compilation terminated. > make[2]: *** [src/shogun/CMakeFiles/libshogun.dir/build.make:11456: src/s= hogun/CMakeFiles/libshogun.dir/mathematics/linalg/ratapprox/logdet/opfunc/D= enseMatrixExactLog.cpp.o] Error 1 > make[2]: *** Waiting for unfinished jobs.... > make[2]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build' > make[1]: *** [CMakeFiles/Makefile2:126: src/shogun/CMakeFiles/libshogun.d= ir/all] Error 2 > make[1]: Leaving directory '/tmp/guix-build-shogun-6.1.3.drv-0/build' > make: *** [Makefile:153: all] Error 2 > phase `build' failed after 493.7 seconds > builder for `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.drv= ' failed with exit code 1 > @ build-failed /gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.3.d= rv - 1 builder for `/gnu/store/mjnmhzdx6zmwcvspmljsrjw2aazfvnv7-shogun-6.1.= 3.drv' failed with exit code 1 > guix build: error: build failed: build of `/gnu/store/mjnmhzdx6zmwcvspmlj= srjw2aazfvnv7-shogun-6.1.3.drv' failed So it turns out that Eigen's source code comes with some functions that are officially unsupported by the developers but still available for use. Guix just doesn't install them. I've attached a patch that *should* properly install the unsupported files to Eigen's include path. Also, thanks for helping with this shogun patch! --=-=-= Content-Type: text/plain Content-Disposition: attachment; filename=0003-gnu-eigen-Install-unsupported-header-files.patch Content-Transfer-Encoding: quoted-printable From=20eed3dcce3714bc16ccb378d261d9e1bd8db3c249 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 18 May 2018 12:46:57 -0400 Subject: [PATCH 3/4] gnu: eigen: Install unsupported header files. * gnu/packages/algebra.scm (eigen)[arguments]: Add 'install-unsupported' ph= ase. Use invoke instead of system*. =2D-- gnu/packages/algebra.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 03a61be47..51be58ee2 100644 =2D-- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -750,6 +750,14 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transf= orm} (DHT).") #:build-type "Release" =20 #:phases (modify-phases %standard-phases + (add-after 'install 'install-unsupported + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (include (string-append out "/include/eigen3"= ))) + (copy-recursively "unsupported" + (string-append include + "/unsupported")) + #t))) (replace 'check (lambda _ (let* ((cores (parallel-job-count)) @@ -757,11 +765,11 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Trans= form} (DHT).") (setenv "EIGEN_SEED" "1") ;for reproducibility ;; First build the tests, in parallel. See ;; . =2D (and (zero? (system* "make" "buildtests" dash-j)) + (and (invoke "make" "buildtests" dash-j) =20 ;; Then run 'CTest' with -V so we get more ;; details upon failure. =2D (zero? (system* "ctest" "-V" dash-j))))))))) + (invoke "ctest" "-V" dash-j)))))))) (home-page "http://eigen.tuxfamily.org") (synopsis "C++ template library for linear algebra") (description =2D-=20 2.17.0 --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlr/CKoACgkQ5qXuPBlG eg2V7RAAmVC+dENQkqavr41b3GDjdkFiA2hqaphm8st2mG6KphgnlXbTHM8x7MIB vnvo+PIKoRRZu9pieGY9pYVQxkaByRM+SaLw9ip4dc8aJ8bCmYJbYCUzsmdFM9Qx MdOXc7wGm/jnbsxMmiiWicfEXm2ZCm7pAYIBgjJomy2YPFJoId3F64YhBYmLNyzg U1S3JGMjtaZzVDK1Oyl88OscQJwKgM0RPLFwvXHP8WzVvSPLM7OoKRGAtR8nK6fB hVc7LwAMVqYCtN1VPaeEbeAWnVMMjinFwlETsXRfWrHbUkrWjP0er3VyEK+oQWef rc1Z3RbElhgakSt8g3gFq//JH4Sfl0WiKvf7szk9XGcqAp7fsLGQ6Ny6NxAu8Z4D vFfO6XPrPkkStL2yAN83vqFQrzoLho79VxfZ2KAUJePjXXYmqnJR1k2KJ9ZRfP2/ oLqrHfkw1EIdZydRlUzf3qGpJ2EW6tS0BLOj6tHqxNQHr1i8cWoCXee4WVlgTtno OCmgIy/ro4KNv8ftYH13Tp99RiR78i6LJNuXyJldt5C1M/ri6V+mUzHPl9p5NSbd MF+Hmf7YNXjB1K2jcP8Tx49ghUnOUcL/vNx4XDEn8rYOkvZWVdkV4Pgjoo8Kp2Ks Ov+msIBtLaCqjSZJnsmK9avmTxau4xr+tmgK2WLOSCXImsVruPI= =D7iJ -----END PGP SIGNATURE----- --==-=-=-- From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 19 May 2018 20:19:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: Ricardo Wurmus , Jonathan Brielmaier , 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15267611031229 (code B ref 31479); Sat, 19 May 2018 20:19:01 +0000 Received: (at 31479) by debbugs.gnu.org; 19 May 2018 20:18:23 +0000 Received: from localhost ([127.0.0.1]:41350 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fK8J5-0000Jk-9p for submit@debbugs.gnu.org; Sat, 19 May 2018 16:18:23 -0400 Received: from eggs.gnu.org ([208.118.235.92]:41979) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fK8J4-0000JZ-09 for 31479@debbugs.gnu.org; Sat, 19 May 2018 16:18:22 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fK8Iy-00050f-1p for 31479@debbugs.gnu.org; Sat, 19 May 2018 16:18:16 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:49904) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fK8Im-0004q5-Fu; Sat, 19 May 2018 16:18:04 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=36898 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fK8Im-0008LW-37; Sat, 19 May 2018 16:18:04 -0400 From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> <874lj7w5f2.fsf@posteo.net> <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> <87muww6gd2.fsf@posteo.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 30 =?UTF-8?Q?Flor=C3=A9al?= an 226 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Sat, 19 May 2018 22:18:02 +0200 In-Reply-To: <87muww6gd2.fsf@posteo.net> (Kei Kebreau's message of "Fri, 18 May 2018 13:08:57 -0400") Message-ID: <87fu2npfgl.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Hello, Kei Kebreau skribis: > So it turns out that Eigen's source code comes with some functions that > are officially unsupported by the developers but still available for > use. Guix just doesn't install them. I've attached a patch that *should* > properly install the unsupported files to Eigen's include path. Ricardo has a similar patch in the Tensorflow series: https://bugs.gnu.org/31386 Could the two of you see how the two patches should be merged? :-) Thanks, Ludo=E2=80=99. From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 20 May 2018 18:33:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Cc: Ricardo Wurmus , Jonathan Brielmaier , 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.152684112213172 (code B ref 31479); Sun, 20 May 2018 18:33:02 +0000 Received: (at 31479) by debbugs.gnu.org; 20 May 2018 18:32:02 +0000 Received: from localhost ([127.0.0.1]:42118 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fKT7h-0003QD-Uk for submit@debbugs.gnu.org; Sun, 20 May 2018 14:32:02 -0400 Received: from mout01.posteo.de ([185.67.36.65]:59649) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fKT7f-0003Pq-UM for 31479@debbugs.gnu.org; Sun, 20 May 2018 14:32:00 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id AC3EB21134 for <31479@debbugs.gnu.org>; Sun, 20 May 2018 20:31:53 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1526841113; bh=QHeVvzWtbHbiHjize4KwScewLzYneHdU8Cxl4LOUF0I=; h=From:To:Cc:Subject:Date:From; b=mziVR9dKHus1JF8caltvmjajcXvn340lrignP+F6FFHnXbmJTkWHBIPCxya7dfyPZ 0ZxqCvOev81IyR+MtM+4DfxyqiGs+8g0CzE5GZeAlJyby8Et/nQXgQRayYZii5weEb K9iyMFOWfL+GlorR0lDXNsnVK5O2udKaHGcOcFr7VreZ1USJ6G0QE7vuL7bQPCK34V GbE6FajvV0s/Q0JjFlabmms+sE3KQewAhiahmC+/WfGO1OfWvnm6t1qsC0QWDgffPO 3LpoWEESXe18W0R9akWL3ZPDx7byExOyMXB/15Nf8Qh3TJOXJyh1HmzP+xDse7z0sm D+JxkZOBlKO+g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40pr936gsYz9rxF; Sun, 20 May 2018 20:31:51 +0200 (CEST) From: Kei Kebreau In-Reply-To: <87fu2npfgl.fsf@gnu.org> ("Ludovic \=\?utf-8\?Q\?Court\=C3\=A8s\=22'\?\= \=\?utf-8\?Q\?s\?\= message of "Sat, 19 May 2018 22:18:02 +0200") References: <20180516231957.1827-1-kkebreau@posteo.net> <20180516231957.1827-2-kkebreau@posteo.net> <874lj7w5f2.fsf@posteo.net> <0ccd42b9-0856-0b45-c85b-a792d3b38ab4@web.de> <0e99a56a-bfb8-5c53-2408-9f202a116eb1@web.de> <87muww6gd2.fsf@posteo.net> <87fu2npfgl.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) Date: Sun, 20 May 2018 14:31:48 -0400 Message-ID: <87h8n25gbv.fsf@posteo.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable ludo@gnu.org (Ludovic Court=C3=A8s) writes: > Hello, > > Kei Kebreau skribis: > >> So it turns out that Eigen's source code comes with some functions that >> are officially unsupported by the developers but still available for >> use. Guix just doesn't install them. I've attached a patch that *should* >> properly install the unsupported files to Eigen's include path. > > Ricardo has a similar patch in the Tensorflow series: > > https://bugs.gnu.org/31386 > > Could the two of you see how the two patches should be merged? :-) > > Thanks, > Ludo=E2=80=99. Hi, Thanks for the heads up! Looking at Ricardo's patch, it looks like the same goal is accomplished in a cleaner fashion. I'll test it today and report back results. I've been working on shogun during the past few days and it may soon be finished. --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlsBvxUACgkQ5qXuPBlG eg29kQ//fTcqbia8NUMLQiEM2Qz8LxwFQotOdpDTsFWGRXnDr5ErL/VSaTrYLgqt mW4vuFOYLrcKqpHoPOLEz5TrTnBVgX0yptd2AnfwuLoHRXU+Owf9zvcdrRi275tK CGFSPM43v2AZHspCkODZPUk25tSHAFuSEMOQi3XnVRGs9S3S0xFqo+9+Ej3rQaxu 5tKwDo84K8YE5aCJln/KzvV9i0AtJQLDmNbGaZ/Xz+B6ni7T1EpnDjW8r1VKMdwU EyPZEaF6fBeFiEKittDH8akT5p4YmitXyZLQQuqfXk3acSypSdhXfEDeBLyXp07s 15E4yFBEAq4exFMxvhQdrtqi2m2MrLXVjRWYNG/0RYmIxylMTeaW9HRHLWsKUJz5 5JareUfcbzdEfyy4Cv9XkVclUGe9wEwGc07jBevafq5oEx7OiqkEwe8sWLzNFDup Ox+l3Abt1Scxl3GaR+RzebKNgwl/JLjKvHZks9r1Hm0iHDKxF2fh0mfKd9avyvP1 84Z6btBp/8sil0yxm8Pq/DF4LYaKriErMXfgmPw/5l/1G4emwkFrQFEo+9woSwga 5tGfjWy6vcVW9fRfpG0g5WMXqDGK0bnfKJD+Vprg8d4aLrcShNrVQrn1GFr8Liyn o3makzJSu1WFMU4JR7flzVEY/QBWy7uHTNTklJF6bB0DtVOUQ7s= =p2Pj -----END PGP SIGNATURE----- --=-=-=-- From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. References: <20180516231033.1680-1-kkebreau@posteo.net> In-Reply-To: <20180516231033.1680-1-kkebreau@posteo.net> Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 24 May 2018 09:10:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.152715296431894 (code B ref 31479); Thu, 24 May 2018 09:10:02 +0000 Received: (at 31479) by debbugs.gnu.org; 24 May 2018 09:09:24 +0000 Received: from localhost ([127.0.0.1]:45967 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fLmFQ-0008IM-2e for submit@debbugs.gnu.org; Thu, 24 May 2018 05:09:24 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:45930) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fLmFO-0008ID-1c for 31479@debbugs.gnu.org; Thu, 24 May 2018 05:09:22 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id DBCBD3806C8; Thu, 24 May 2018 11:09:20 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :message-id:date:date:subject:subject:from:from:user-agent :received:received:received:received; s=mdc; t=1527152960; x= 1528967361; bh=VUSUxBfUHnN5nMUypl8FOXgUWwoCTnMbX8V1bh0CrtY=; b=I bYBqBJouyLwHhFNzN+Op1wISWa6FjrOQ7DkErl4MRS7FhD5zQvclvlOwiPLNscm2 HdgOHfvKpxVSEXchHFwBJxcRUNB9qEKWjWLP8S3Xz4MHagCggLlelxSegV6oRyeJ EF8kbYM9c7953glKp1rAcCWrVY+tA021l3Ue0S38dE= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 5Kf4nZyciYo7; Thu, 24 May 2018 11:09:20 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Thu, 24 May 2018 11:09:20 +0200 (CEST) Received: from SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) by HTCATWO.mdc-berlin.net (141.80.180.190) with Microsoft SMTP Server (TLS) id 14.3.399.0; Thu, 24 May 2018 11:09:19 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server id 14.3.399.0; Thu, 24 May 2018 11:09:19 +0200 User-agent: mu4e 1.0; emacs 25.3.1 From: Ricardo Wurmus X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 24 May 2018 11:09:09 +0200 Message-ID: <87a7spcte2.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.2.1013-23864.001 X-TM-AS-Result: No-3.005100-8.000000-10 X-TMASE-MatchedRID: wQVy7q402w1jDV//SvkH3vOS+SRxjgFwELbqrOgWzyeqXPmD6/Pqg6bi YSDCIuiCdmjn29714VMAHrqTu1TQpw3DNjTHgjBsgOqr/r0d+Cy6hgVvSdGKo8lgi/vLS272A5H e1kDS+OLnzlXMYw4XMKHUf3pt8cg10C1sQRfQzEHEQdG7H66TyN+E/XGDLHcMMJtOxDfqY7Ut5s 9Gu30MLk6Nls0PlDqWru2MD/AMrB/rg3GUTFfH/6u95xKJliOFJW0nk2KEj4IJlJAL7mk5yWEP0 swrSBlzD/EiZwqh/WBl2xuA1t/ICypPUAInKdYv9avTT1aTf3caXqAnCd/q6g== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.005100-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.2.1013-23864.001 X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Hi Kei, please also note that Shogun contains references to proprietary software. It has support for SVMLight, which is non-free software. It includes a script to remove all references to and adapters for SVMLight, but unfortunately we cannot run shell scripts in a snippet. Changing this requires changing the “package” syntax to delay evaluation more. Until then we need to remove the non-free bits in code, which is what the current snippet does, but the code would need to be adjusted for version 6.1.3. Thanks for taking this on! -- Ricardo From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 27 May 2018 01:23:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: ludo@gnu.org, 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15273841367728 (code B ref 31479); Sun, 27 May 2018 01:23:01 +0000 Received: (at 31479) by debbugs.gnu.org; 27 May 2018 01:22:16 +0000 Received: from localhost ([127.0.0.1]:50040 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fMkNr-00020R-0y for submit@debbugs.gnu.org; Sat, 26 May 2018 21:22:14 -0400 Received: from mout01.posteo.de ([185.67.36.65]:56977) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fMkNh-0001zp-T4 for 31479@debbugs.gnu.org; Sat, 26 May 2018 21:22:06 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 9BB1D20E2F for <31479@debbugs.gnu.org>; Sun, 27 May 2018 03:21:51 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1527384111; bh=mhvx0k9hqKS2au3wQAelIyUHzjTQjxdEQSnWjTiCm2M=; h=From:To:Cc:Subject:Date:From; b=cPJjb13JgJBO+8UZZWepSY2zHjtiPwk3oOr2D98YCQHuvOjqmA2I7vz38zN2n4cjR xMEYJGvbgWOs4j+HxcdBYqDzKJcv5i0ao8gmWmwVXTfazNSqJi+Dq3eDpi9OYPQlbG TKR4uDXB2DLBaZIwRcUGkpfIyl9nnm4FC7S5rFVK+rz1RSHZMY6BLzNjyxvgUl8uEz uJMg69O8V83bvtDlUL6Xmk+9B9nBpsY8Ni7KlZf/tRiqkZmQfzAYaxxPyNfGfiKBnP J1U+WqDXgK8DOaFz83a3/cyS5xnuyLfN11/svFL+jURSS/2AiwtimBOKTIFxb2NeE3 WHfnK+CMgXlIA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40thzK4ktLz9rxG; Sun, 27 May 2018 03:21:49 +0200 (CEST) From: Kei Kebreau References: <20180516231033.1680-1-kkebreau@posteo.net> <87a7spcte2.fsf@mdc-berlin.de> Date: Sat, 26 May 2018 21:21:43 -0400 In-Reply-To: <87a7spcte2.fsf@mdc-berlin.de> (Ricardo Wurmus's message of "Thu, 24 May 2018 11:09:09 +0200") Message-ID: <87po1hnba0.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 0.7 (/) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Ricardo Wurmus writes: > Hi Kei, > > please also note that Shogun contains references to proprietary > software. It has support for SVMLight, which is non-free software. It > includes a script to remove all references to and adapters for SVMLight, > but unfortunately we cannot run shell scripts in a snippet. Changing > this requires changing the =E2=80=9Cpackage=E2=80=9D syntax to delay eval= uation more. > > Until then we need to remove the non-free bits in code, which is what > the current snippet does, but the code would need to be adjusted for > version 6.1.3. > > Thanks for taking this on! > > -- > Ricardo Thank you for the tip! I've attached the four patches that make it possible to build Shogun 6.1.3 successfully, and I'm just looking through the source code to remove the proprietary bits. P.S. Ricardo, you'll notice the eigen patch is actually yours from another patchset! I verified that it works as expected. --=-=-= Content-Type: text/plain Content-Disposition: attachment; filename=0001-gnu-octave-Update-to-4.4.0.patch Content-Transfer-Encoding: quoted-printable From=200243faa33cc2c33ed7160ab754ad45ceff626eb2 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Sat, 5 May 2018 10:21:38 -0400 Subject: [PATCH 1/5] gnu: octave: Update to 4.4.0. * gnu/packages/maths.scm (octave): Update to 4.4.0. =2D-- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a36d2333e..97f847665 100644 =2D-- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1332,7 +1332,7 @@ can solve two kinds of problems: (define-public octave (package (name "octave") =2D (version "4.2.2") + (version "4.4.0") (source (origin (method url-fetch) @@ -1340,7 +1340,7 @@ can solve two kinds of problems: version ".tar.lz")) (sha256 (base32 =2D "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp")))) + "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) =2D-=20 2.17.0 --=-=-= Content-Type: text/plain; charset=utf-8 Content-Disposition: attachment; filename=0002-gnu-Add-rxcpp.patch Content-Transfer-Encoding: quoted-printable From=2050b6630e06f434237c1014765444d01a38f40e61 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Wed, 9 May 2018 10:01:40 -0400 Subject: [PATCH 2/5] gnu: Add rxcpp. * gnu/packages/machine-learning.scm (rxcpp): New variable. =2D-- gnu/packages/machine-learning.scm | 42 +++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learn= ing.scm index f0d35484e..6536d861e 100644 =2D-- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -4,6 +4,7 @@ ;;; Copyright =C2=A9 2016, 2017 Marius Bakke ;;; Copyright =C2=A9 2016 Hartmut Goebel ;;; Copyright =C2=A9 2018 Tobias Geerinckx-Rice +;;; Copyright =C2=A9 2018 Kei Kebreau ;;; Copyright =C2=A9 2018 Mark Meyer ;;; Copyright =C2=A9 2018 Ben Woodcroft ;;; Copyright =C2=A9 2018 Fis Trivial @@ -501,6 +502,47 @@ tools. This enables both rapid prototyping of data pi= pelines and extensibility in terms of new algorithms.") (license license:gpl3+))) =20 +(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 f= or +values-distributed-in-time. ReactiveX is a library for composing asynchro= nous +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-blocki= ng +I/O.") + (license license:asl2.0))) + (define-public r-adaptivesparsity (package (name "r-adaptivesparsity") =2D-=20 2.17.0 --=-=-= Content-Type: text/plain Content-Disposition: attachment; filename=0003-gnu-eigen-Include-unsupported-features.patch Content-Transfer-Encoding: quoted-printable From=20593edb81de8b6ad064d388aa39896ef8667e06bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 8 May 2018 16:59:07 +0200 Subject: [PATCH 3/5] gnu: eigen: Include unsupported features. * gnu/packages/algebra.scm (eigen)[source]: Do not build the tests for unsupported features, but include the files. Signed-off-by: Kei Kebreau =2D-- gnu/packages/algebra.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 210b734b9..ff8478c50 100644 =2D-- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -732,9 +732,10 @@ Sine Transform} (DST) and @dfn{Discrete Hartley Transf= orm} (DHT).") ;; but maintainers say it's a known issue and it's unsuppor= ted ;; anyway, so just skip them. '(begin + (substitute* "unsupported/CMakeLists.txt" + (("add_subdirectory\\(test.*") + "# Do not build the tests for unsupported features.\n= ")) (substitute* "CMakeLists.txt" =2D (("add_subdirectory\\(unsupported\\)") =2D "# Do not build the tests for unsupported features.= \n") ;; Work around ;; . (("\"include/eigen3\"") =2D-=20 2.17.0 --=-=-= Content-Type: text/plain Content-Disposition: attachment; filename=0004-gnu-swig-Patch-for-Octave-4.4.patch Content-Transfer-Encoding: quoted-printable From=201d714096fd7f37eddfb87dfe3a933588e55ab77f Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Fri, 25 May 2018 22:25:21 -0400 Subject: [PATCH 4/5] gnu: swig: Patch for Octave 4.4. * gnu/packages/swig.scm (swig)[source]: Add patch. * gnu/packages/patches/swig-octave-patches.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. =2D-- gnu/local.mk | 1 + .../patches/swig-octave-patches.patch | 1119 +++++++++++++++++ gnu/packages/swig.scm | 5 +- 3 files changed, 1124 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/swig-octave-patches.patch diff --git a/gnu/local.mk b/gnu/local.mk index 4cdbaec1d..6ae25c1f3 100644 =2D-- a/gnu/local.mk +++ b/gnu/local.mk @@ -1102,6 +1102,7 @@ dist_patch_DATA =3D \ %D%/packages/patches/steghide-fixes.patch \ %D%/packages/patches/strace-kernel-4.16.patch \ %D%/packages/patches/superlu-dist-scotchmetis.patch \ + %D%/packages/patches/swig-octave-patches.patch \ %D%/packages/patches/swish-e-search.patch \ %D%/packages/patches/swish-e-format-security.patch \ %D%/packages/patches/synfigstudio-fix-ui-with-gtk3.patch \ diff --git a/gnu/packages/patches/swig-octave-patches.patch b/gnu/packages/= patches/swig-octave-patches.patch new file mode 100644 index 000000000..9fb64a7b1 =2D-- /dev/null +++ b/gnu/packages/patches/swig-octave-patches.patch @@ -0,0 +1,1119 @@ +This patch represents the recently added support for Octave version 4.4 fo= und +here: + +https://github.com/swig/swig/commit/12c66f9b7d884020e896ce92b9783bc3bac95d= 2d + +diff -urN swig-3.0.12.old/CHANGES.current swig-3.0.12.new/CHANGES.current +--- swig-3.0.12.old/CHANGES.current 2017-01-27 18:52:02.000000000 -0500 ++++ swig-3.0.12.new/CHANGES.current 2018-05-26 08:40:06.501850058 -0400 +@@ -4,6 +4,14 @@ + Issue # numbers mentioned below can be found on Github. For more details,= add + the issue number to the end of the URL: https://github.com/swig/swig/issu= es/ +=20 ++Version 4.0.0 (in progress) ++=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D ++ ++2018-05-12: kwwette ++ [Octave] add support for version 4.4 ++ - Should not introduce any user-visible incompatibilities ++ ++ + Version 3.0.12 (27 Jan 2017) + =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D +=20 +diff -urN swig-3.0.12.old/Examples/Makefile.in swig-3.0.12.new/Examples/Ma= kefile.in +--- swig-3.0.12.old/Examples/Makefile.in 2017-01-27 18:52:02.000000000 -05= 00 ++++ swig-3.0.12.new/Examples/Makefile.in 2018-05-26 08:39:16.510124553 -04= 00 +@@ -463,7 +463,7 @@ + # ----------------------------------------------------------------- +=20 + octave_run: +- OCTAVE_HISTFILE=3D/dev/null $(RUNTOOL) $(OCTAVE) $(OCTAVE_SCRIPT) $(RUNP= IPE) ++ env OCTAVE_PATH=3D OCTAVE_HISTFILE=3D/dev/null $(RUNTOOL) $(OCTAVE) $(OC= TAVE_SCRIPT) $(RUNPIPE) +=20 + # ----------------------------------------------------------------- + # Version display +diff -urN swig-3.0.12.old/Examples/octave/module_load/runme.m swig-3.0.12.= new/Examples/octave/module_load/runme.m +--- swig-3.0.12.old/Examples/octave/module_load/runme.m 2017-01-27 18:52:0= 2.000000000 -0500 ++++ swig-3.0.12.new/Examples/octave/module_load/runme.m 2018-05-26 08:39:1= 6.518124669 -0400 +@@ -5,63 +5,73 @@ +=20 + # load module + clear all; ++assert(exist("swigexample") =3D=3D 3); + swigexample; ++assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +-assert(exist("swigexample","var")); + clear all ++assert(exist("swigexample") =3D=3D 3); + swigexample; ++assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +-assert(exist("swigexample","var")); + clear all +=20 + # load module in a function globally before base context + clear all; +-function testme ++function testme_1 ++ assert(exist("swigexample") =3D=3D 3); + swigexample; ++ assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +- assert(exist("swigexample","var")); + endfunction +-testme +-testme ++testme_1 ++testme_1 ++assert(exist("swigexample") =3D=3D 3); + swigexample; ++assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +-assert(exist("swigexample","var")); + clear all +-function testme ++function testme_2 ++ assert(exist("swigexample") =3D=3D 3); + swigexample; ++ assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +- assert(exist("swigexample","var")); + endfunction +-testme +-testme ++testme_2 ++testme_2 ++assert(exist("swigexample") =3D=3D 3); + swigexample; ++assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +-assert(exist("swigexample","var")); + clear all +=20 + # load module in a function globally after base context + clear all; ++assert(exist("swigexample") =3D=3D 3); + swigexample; ++assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +-assert(exist("swigexample","var")); +-function testme ++function testme_3 ++ assert(exist("swigexample") =3D=3D 3); + swigexample; ++ assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +- assert(exist("swigexample","var")); + endfunction +-testme +-testme ++testme_3 ++testme_3 + clear all ++assert(exist("swigexample") =3D=3D 3); + swigexample; ++assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +-assert(exist("swigexample","var")); +-function testme ++function testme_4 ++ assert(exist("swigexample") =3D=3D 3); + swigexample; ++ assert(isglobal("swigexample")); + assert(cvar.ivar =3D=3D ifunc); +- assert(exist("swigexample","var")); + endfunction +-testme +-testme ++testme_4 ++testme_4 + clear all +=20 + # octave 3.0.5 randomly crashes on the remaining tests +@@ -71,13 +81,16 @@ +=20 + # load module with no cvar + clear all; ++who; ++assert(exist("swigexample2") =3D=3D 3); + swigexample2; ++assert(isglobal("swigexample2")); + assert(swigexample2.ivar =3D=3D ifunc); +-assert(exist("swigexample2","var")); +-assert(!isglobal("cvar")) ++assert(!exist("cvar", "var")); + clear all ++assert(exist("swigexample2") =3D=3D 3); + swigexample2; ++assert(isglobal("swigexample2")); + assert(swigexample2.ivar =3D=3D ifunc); +-assert(exist("swigexample2","var")); +-assert(!isglobal("cvar")) ++assert(!exist("cvar", "var")); + clear all +diff -urN swig-3.0.12.old/Examples/test-suite/octave/Makefile.in swig-3.0.= 12.new/Examples/test-suite/octave/Makefile.in +--- swig-3.0.12.old/Examples/test-suite/octave/Makefile.in 2017-01-27 18:5= 2:02.000000000 -0500 ++++ swig-3.0.12.new/Examples/test-suite/octave/Makefile.in 2018-05-26 08:3= 9:16.511124567 -0400 +@@ -59,7 +59,7 @@ + # a file is found which has _runme.m appended after the testcase name. + run_testcase =3D \ + if [ -f $(SCRIPTDIR)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then \ +- env LD_LIBRARY_PATH=3D.:$$LD_LIBRARY_PATH OCTAVE_PATH=3D$(srcdir):$$OC= TAVE_PATH $(RUNTOOL) $(OCTAVE) $(SCRIPTDIR)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX= ); \ ++ env LD_LIBRARY_PATH=3D.:$$LD_LIBRARY_PATH OCTAVE_PATH=3D$(srcdir) OCTA= VE_HISTFILE=3D/dev/null $(RUNTOOL) $(OCTAVE) $(SCRIPTDIR)/$(SCRIPTPREFIX)$*= $(SCRIPTSUFFIX); \ + fi +=20 + # Clean: remove the generated .m file +diff -urN swig-3.0.12.old/Examples/test-suite/octave/Makefile.in.orig swig= -3.0.12.new/Examples/test-suite/octave/Makefile.in.orig +--- swig-3.0.12.old/Examples/test-suite/octave/Makefile.in.orig 1969-12-31= 19:00:00.000000000 -0500 ++++ swig-3.0.12.new/Examples/test-suite/octave/Makefile.in.orig 2017-01-27= 18:52:02.000000000 -0500 +@@ -0,0 +1,92 @@ ++####################################################################### ++# Makefile for octave test-suite ++####################################################################### ++ ++LANGUAGE =3D octave ++OCTAVE =3D @OCTAVE@ ++SCRIPTSUFFIX =3D _runme.m ++ ++srcdir =3D @srcdir@ ++top_srcdir =3D @top_srcdir@ ++top_builddir =3D @top_builddir@ ++ ++CPP_TEST_CASES +=3D \ ++ li_std_pair_extra \ ++ li_std_string_extra \ ++ octave_cell_deref\ ++ octave_dim ++ ++CPP_TEST_BROKEN +=3D \ ++ implicittest \ ++ li_implicit \ ++ li_std_set \ ++ li_std_stream ++ ++#C_TEST_CASES +=3D ++ ++# ++# This test only works with modern C compilers ++# ++#C_TEST_CASES +=3D \ ++# complextest ++ ++include $(srcdir)/../common.mk ++ ++# Overridden variables here ++LIBS =3D -L. ++CSRCS =3D octave_empty.c ++ ++# Custom tests - tests with additional commandline options ++# none! ++ ++# Rules for the different types of tests ++%.cpptest: ++ $(setup) ++ +$(swig_and_compile_cpp) ++ $(run_testcase) ++ ++%.ctest: ++ $(setup) ++ +$(swig_and_compile_c) ++ $(run_testcase) ++ ++%.multicpptest: ++ $(setup) ++ +$(swig_and_compile_multi_cpp) ++ $(run_testcase) ++ ++# Runs the testcase. A testcase is only run if ++# a file is found which has _runme.m appended after the testcase name. ++run_testcase =3D \ ++ if [ -f $(SCRIPTDIR)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then \ ++ env LD_LIBRARY_PATH=3D.:$$LD_LIBRARY_PATH OCTAVE_PATH=3D$(srcdir):$$OC= TAVE_PATH $(RUNTOOL) $(OCTAVE) $(SCRIPTDIR)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX= ); \ ++ fi ++ ++# Clean: remove the generated .m file ++%.clean: ++ @rm -f hugemod.h hugemod_a.i hugemod_b.i hugemod_a.m hugemod_b.m hugemod= _runme.m ++ @rm -f $*.m; ++ ++clean: ++ $(MAKE) -f $(top_builddir)/$(EXAMPLES)/Makefile SRCDIR=3D'$(SRCDIR)' oct= ave_clean ++ ++cvsignore: ++ @echo '*wrap* *.mc *.so *.dll *.exp *.lib' ++ @echo Makefile ++ @for i in ${CPP_TEST_CASES} ${C_TEST_CASES}; do echo $$i.m; done ++ @for i in ${CPP_TEST_CASES} ${C_TEST_CASES}; do if grep -q $${i}_runme.m= CVS/Entries ; then echo $${i}_runme.m; fi; done ++ @echo clientdata_prop_a.m ++ @echo clientdata_prop_b.m ++ @echo imports_a.m ++ @echo imports_b.m ++ @echo mod_a.m mod_b.m ++ @echo hugemod.h hugemod_a.i hugemod_b.i hugemod_a.m hugemod_b.m hugemod_= runme.m ++ @echo template_typedef_import.m ++ ++ ++hugemod: ++ perl hugemod.pl ++ $(MAKE) hugemod_a.cpptest ++ $(MAKE) hugemod_b.cpptest ++ time $(OCTAVE) hugemod_runme.m ++ time $(OCTAVE) hugemod_runme.m +diff -urN swig-3.0.12.old/Examples/test-suite/register_par.i swig-3.0.12.n= ew/Examples/test-suite/register_par.i +--- swig-3.0.12.old/Examples/test-suite/register_par.i 2017-01-27 18:52:02= .000000000 -0500 ++++ swig-3.0.12.new/Examples/test-suite/register_par.i 2018-05-26 08:40:28= .146164544 -0400 +@@ -2,5 +2,5 @@ +=20 + // bug # 924413 + %inline { +- void clear_tree_flags(register struct tree *tp, register int i) {} ++ void clear_tree_flags(register struct swig_tree *tp, register int i) {} + } +diff -urN swig-3.0.12.old/Examples/test-suite/register_par.i.orig swig-3.0= .12.new/Examples/test-suite/register_par.i.orig +--- swig-3.0.12.old/Examples/test-suite/register_par.i.orig 1969-12-31 19:= 00:00.000000000 -0500 ++++ swig-3.0.12.new/Examples/test-suite/register_par.i.orig 2018-05-26 08:= 39:16.518124669 -0400 +@@ -0,0 +1,6 @@ ++%module register_par ++ ++// bug # 924413 ++%inline { ++ void clear_tree_flags(register struct tree *tp, register int i) {} ++} +diff -urN swig-3.0.12.old/Examples/test-suite/register_par.i.rej swig-3.0.= 12.new/Examples/test-suite/register_par.i.rej +--- swig-3.0.12.old/Examples/test-suite/register_par.i.rej 1969-12-31 19:0= 0:00.000000000 -0500 ++++ swig-3.0.12.new/Examples/test-suite/register_par.i.rej 2018-05-26 08:3= 9:16.518124669 -0400 +@@ -0,0 +1,15 @@ ++--- Examples/test-suite/register_par.i +++++ Examples/test-suite/register_par.i ++@@ -1,10 +1,10 @@ ++ %module register_par ++=20 ++ %{ ++-struct tree; +++struct swig_tree; ++ %} ++=20 ++ // bug # 924413 ++ %inline { ++- void clear_tree_flags(register struct tree *tp, register int i) {} +++ void clear_tree_flags(register struct swig_tree *tp, register int i) {} ++ } +diff -urN swig-3.0.12.old/Lib/octave/octcontainer.swg swig-3.0.12.new/Lib/= octave/octcontainer.swg +--- swig-3.0.12.old/Lib/octave/octcontainer.swg 2017-01-27 18:52:02.000000= 000 -0500 ++++ swig-3.0.12.new/Lib/octave/octcontainer.swg 2018-05-26 08:39:16.488124= 234 -0400 +@@ -567,7 +567,11 @@ + if (seq) *seq =3D p; + return SWIG_OLDOBJ; + } ++%#if SWIG_OCTAVE_PREREQ(4,4,0) ++ } else if (obj.iscell()) { ++%#else + } else if (obj.is_cell()) { ++%#endif + try { + OctSequence_Cont octseq(obj); + if (seq) { +diff -urN swig-3.0.12.old/Lib/octave/octprimtypes.swg swig-3.0.12.new/Lib/= octave/octprimtypes.swg +--- swig-3.0.12.old/Lib/octave/octprimtypes.swg 2017-01-27 18:52:02.000000= 000 -0500 ++++ swig-3.0.12.new/Lib/octave/octprimtypes.swg 2018-05-26 08:39:16.492124= 292 -0400 +@@ -18,7 +18,11 @@ + SWIGINTERN int + SWIG_AsVal_dec(bool)(const octave_value& ov, bool *val) + { ++%#if SWIG_OCTAVE_PREREQ(4,4,0) ++ if (!ov.islogical()) ++%#else + if (!ov.is_bool_type()) ++%#endif + return SWIG_ERROR; + if (val) + *val =3D ov.bool_value(); +@@ -214,7 +218,13 @@ + SWIGINTERN int + SWIG_AsCharPtrAndSize(octave_value ov, char** cptr, size_t* psize, int *a= lloc) + { +- if (ov.is_cell() && ov.rows() =3D=3D 1 && ov.columns() =3D=3D 1) ++ if ( ++%#if SWIG_OCTAVE_PREREQ(4,4,0) ++ ov.iscell() ++%#else ++ ov.is_cell() ++%#endif ++ && ov.rows() =3D=3D 1 && ov.columns() =3D=3D 1) + ov =3D ov.cell_value()(0); + if (!ov.is_string()) + return SWIG_TypeError; +diff -urN swig-3.0.12.old/Lib/octave/octrun.swg swig-3.0.12.new/Lib/octave= /octrun.swg +--- swig-3.0.12.old/Lib/octave/octrun.swg 2017-01-27 18:52:02.000000000 -0= 500 ++++ swig-3.0.12.new/Lib/octave/octrun.swg 2018-05-26 08:39:16.509124538 -0= 400 +@@ -151,6 +151,67 @@ + const swig_type_info **base; + }; +=20 ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ // in Octave 4.4 behaviour of octave_builtin() appears to have changed = and 'self' argument is no longer passed ++ // to function (maybe because this is now a 'method'??) so need to crea= te our own octave_function subclass ++#define SWIG_OCTAVE_BOUND_FUNC(func, args) octave_value(new octave_swig_b= ound_func(func, args)) ++ class octave_swig_bound_func : public octave_function { ++ public: ++ ++ octave_swig_bound_func(void) : octave_function(), method(0), first_ar= gs() ++ { } ++ ++ octave_swig_bound_func(octave_function* _method, octave_value_list _f= irst_args) ++ : octave_function("", ""), method(_method), first_args(_first_args) ++ { } ++ ++ octave_swig_bound_func(const octave_swig_bound_func& f) =3D delete; ++ ++ octave_swig_bound_func& operator=3D (const octave_swig_bound_func& f)= =3D delete; ++ ++ ~octave_swig_bound_func(void) =3D default; ++ ++ bool is_function(void) const { return true; } ++ ++ octave_function* function_value(bool =3D false) { return this; } ++ ++ octave_value_list call(octave::tree_evaluator& tw, int nargout =3D 0,= const octave_value_list& args =3D octave_value_list()) { ++ octave_value_list all_args; ++ all_args.append(first_args); ++ all_args.append(args); ++ return method->call(tw, nargout, all_args); ++ } ++ ++ octave_value subsref(const std::string &ops, const std::list < octave= _value_list > &idx) { ++ octave_value_list ovl =3D subsref(ops, idx, 1); ++ return ovl.length() ? ovl(0) : octave_value(); ++ } ++ ++ octave_value_list subsref(const std::string &ops, const std::list < o= ctave_value_list > &idx, int nargout) { ++ assert(ops.size() > 0); ++ assert(ops.size() =3D=3D idx.size()); ++ if (ops !=3D "(") ++ error("invalid function call"); ++ octave::tree_evaluator& tw =3D octave::interpreter::the_interpreter= ()->get_evaluator(); ++ return call(tw, nargout, *idx.begin()); ++ } ++ ++ protected: ++ ++ octave_function* method; ++ octave_value_list first_args; ++ ++ std::set dispatch_classes; ++ ++ private: ++ ++ DECLARE_OV_TYPEID_FUNCTIONS_AND_DATA ++ }; ++ DEFINE_OV_TYPEID_FUNCTIONS_AND_DATA(octave_swig_bound_func, "octave_swi= g_bound_func", "octave_swig_bound_func"); ++#else ++#define SWIG_OCTAVE_BOUND_FUNC(func, args) octave_value(func) ++#endif ++ + // octave_swig_type plays the role of both the shadow class and the cla= ss=20 + // representation within Octave, since there is no support for classes. + // +@@ -323,13 +384,17 @@ + } +=20 + octave_value_list member_deref(member_value_pair *m, const octave_val= ue_list &args) { +- if (m->second.is_defined()) +- return m->second; +- else if (m->first) { ++ if (m->second.is_defined()) { ++ if (m->second.is_function() || m->second.is_function_handle()) { ++ return SWIG_OCTAVE_BOUND_FUNC(m->second.function_value(), args); ++ } else { ++ return m->second; ++ } ++ } else if (m->first) { + if (m->first->get_method) + return m->first->get_method(args, 1); + else if (m->first->method) +- return octave_value(new octave_builtin(m->first->method)); ++ return SWIG_OCTAVE_BOUND_FUNC(new octave_builtin(m->first->meth= od), args); + } + error("undefined member"); + return octave_value_list(); +@@ -383,7 +448,11 @@ + return dim_vector(1,1); +=20 + // Return value should be cell or matrix of integers ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ if (out.iscell()) { ++#else + if (out.is_cell()) { ++#endif + const Cell & c=3Dout.cell_value(); + int ndim =3D c.rows(); + if (ndim=3D=3D1 && c.columns()!=3D1) ndim =3D c.columns(); +@@ -401,7 +470,11 @@ + if (error_state) return dim_vector(1,1); + } + return d; ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ } else if (out.is_matrix_type() || out.isnumeric() ) { ++#else + } else if (out.is_matrix_type() || out.is_numeric_type() ) { ++#endif + if (out.rows()=3D=3D1 || out.columns()=3D=3D1) { + Array a =3D out.int_vector_value(); + if (error_state) return dim_vector(1,1); +@@ -476,8 +549,12 @@ + } + types.insert(types.end(), rhs.types.begin(), rhs.types.end()); + members.insert(rhs.members.begin(), rhs.members.end()); ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ assign(rhs.swig_type_name(), rhs.as_value()); ++#else + rhs.types.clear(); + rhs.members.clear(); ++#endif + } +=20 + typedef member_map::const_iterator swig_member_const_iterator; +@@ -848,7 +925,14 @@ + octave_function *fcn =3D is_valid_function(symbol, std::string(), f= alse); + if (!fcn) + return false; ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::tree_evaluator& tw =3D octave::interpreter::the_interpreter= ()->get_evaluator(); ++ octave_value_list retval =3D fcn->call(tw, 1, args); ++ if (retval.length() =3D=3D 1) ++ ret =3D retval(0); ++#else + ret =3D fcn->do_multi_index_op(1, args)(0); ++#endif + return true; + } +=20 +@@ -1238,7 +1322,13 @@ + } +=20 + SWIGRUNTIME octave_swig_type *swig_value_deref(octave_value ov) { +- if (ov.is_cell() && ov.rows() =3D=3D 1 && ov.columns() =3D=3D 1) ++ if ( ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ ov.iscell() ++#else ++ ov.is_cell() ++#endif ++ && ov.rows() =3D=3D 1 && ov.columns() =3D=3D 1) + ov =3D ov.cell_value()(0); + return swig_value_deref(*ov.internal_rep()); + } +@@ -1261,12 +1351,24 @@ + SWIGRUNTIME octave_value swig_binary_op_##name(const octave_base_value&lh= s,const octave_base_value &rhs) { \ + return octave_swig_type::dispatch_binary_op(lhs,rhs,#name); \ + } ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++#define swigreg_unary_op(name) \ ++if (!octave_value_typeinfo::lookup_unary_op(octave_value::op_##name,tid))= \ ++typeinfo.register_unary_op(octave_value::op_##name,tid,swig_unary_op_##na= me); ++#else + #define swigreg_unary_op(name) \ + if (!octave_value_typeinfo::lookup_unary_op(octave_value::op_##name,tid))= \ + octave_value_typeinfo::register_unary_op(octave_value::op_##name,tid,swig= _unary_op_##name); ++#endif ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++#define swigreg_binary_op(name) \ ++if (!octave_value_typeinfo::lookup_binary_op(octave_value::op_##name,tid1= ,tid2)) \ ++typeinfo.register_binary_op(octave_value::op_##name,tid1,tid2,swig_binary= _op_##name); ++#else + #define swigreg_binary_op(name) \ + if (!octave_value_typeinfo::lookup_binary_op(octave_value::op_##name,tid1= ,tid2)) \ + octave_value_typeinfo::register_binary_op(octave_value::op_##name,tid1,ti= d2,swig_binary_op_##name); ++#endif +=20 + swig_unary_op(not); + swig_unary_op(uplus); +@@ -1300,6 +1402,9 @@ + swig_binary_op(el_or); +=20 + SWIGRUNTIME void SWIG_InstallUnaryOps(int tid) { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::type_info& typeinfo =3D octave::interpreter::the_interpreter(= )->get_type_info(); ++#endif + swigreg_unary_op(not); + swigreg_unary_op(uplus); + swigreg_unary_op(uminus); +@@ -1309,6 +1414,9 @@ + swigreg_unary_op(decr); + } + SWIGRUNTIME void SWIG_InstallBinaryOps(int tid1, int tid2) { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::type_info& typeinfo =3D octave::interpreter::the_interpreter(= )->get_type_info(); ++#endif + swigreg_binary_op(add); + swigreg_binary_op(sub); + swigreg_binary_op(mul); +@@ -1357,7 +1465,13 @@ + } +=20 + SWIGRUNTIME int SWIG_Octave_ConvertPtrAndOwn(octave_value ov, void **ptr,= swig_type_info *type, int flags, int *own) { +- if (ov.is_cell() && ov.rows() =3D=3D 1 && ov.columns() =3D=3D 1) ++ if ( ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ ov.iscell() ++#else ++ ov.is_cell() ++#endif ++ && ov.rows() =3D=3D 1 && ov.columns() =3D=3D 1) + ov =3D ov.cell_value()(0); + if (!ov.is_defined() || + (ov.is_matrix_type() && ov.rows() =3D=3D 0 && ov.columns() =3D=3D 0= ) ) { +@@ -1390,14 +1504,30 @@ + } +=20 + SWIGRUNTIMEINLINE octave_value SWIG_Octave_GetGlobalValue(std::string nam= e) { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::symbol_table& symtab =3D octave::interpreter::the_interpreter()= ->get_symbol_table(); ++ return symtab.global_varval(name); ++#else + return get_global_value(name, true); ++#endif + } +=20 + SWIGRUNTIME void SWIG_Octave_SetGlobalValue(std::string name, const octav= e_value& value) { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::symbol_table& symtab =3D octave::interpreter::the_interpreter()= ->get_symbol_table(); ++ symtab.global_assign(name, value); ++#else + set_global_value(name, value); ++#endif + } +=20 + SWIGRUNTIME void SWIG_Octave_LinkGlobalValue(std::string name) { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::symbol_table& symtab =3D octave::interpreter::the_interpreter()= ->get_symbol_table(); ++ octave::symbol_scope symscope =3D octave::interpreter::the_interpreter(= )->get_current_scope(); ++ symscope.assign(name, symtab.global_varval(name)); ++ symscope.mark_global(name); ++#else + #if !SWIG_OCTAVE_PREREQ(3,2,0) + link_to_global_variable(curr_sym_tab->lookup(name, true)); + #else +@@ -1406,6 +1536,7 @@ + #endif + symbol_table::mark_global(name); + #endif ++#endif + } +=20 + SWIGRUNTIME swig_module_info *SWIG_Octave_GetModule(void *clientdata) { +diff -urN swig-3.0.12.old/Lib/octave/octruntime.swg swig-3.0.12.new/Lib/oc= tave/octruntime.swg +--- swig-3.0.12.old/Lib/octave/octruntime.swg 2017-01-27 18:52:02.00000000= 0 -0500 ++++ swig-3.0.12.new/Lib/octave/octruntime.swg 2018-05-26 08:39:16.50712450= 9 -0400 +@@ -139,7 +139,11 @@ + #endif + #if SWIG_OCTAVE_PREREQ(4,2,0) + try { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::feval(name, octave_value_list(), 0); ++#else + feval(name, octave_value_list(), 0); ++#endif + retn =3D true; + } catch (octave::execution_exception&) { } + #else +@@ -170,7 +174,7 @@ + frame.protect_var(discard_error_messages); discard_error_mes= sages =3D true; + frame.protect_var(discard_warning_messages); discard_warning_m= essages =3D true; + #else +- unwind_protect::begin_frame("SWIG_Octave_LoadModule"); ++ unwind_protect::begin_frame("SWIG_Octave_InstallFunction"); + unwind_protect_int(error_state); error_state =3D 0; + unwind_protect_int(warning_state); warning_state =3D= 0; + unwind_protect_bool(discard_error_messages); discard_error_mes= sages =3D true; +@@ -181,7 +185,11 @@ + args.append(octloadfcn->fcn_file_name()); + #if SWIG_OCTAVE_PREREQ(4,2,0) + try { ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::feval("autoload", args, 0); ++#else + feval("autoload", args, 0); ++#endif + retn =3D true; + } catch (octave::execution_exception&) { } + #else +@@ -312,6 +320,8 @@ + Loads the SWIG-generated module `" SWIG_name_d "'.\n\ + @end deftypefn"; +=20 ++void __swig_atexit__(void) { ::_Exit(0); } ++ + DEFUN_DLD( SWIG_name, args, nargout, SWIG_name_usage ) { +=20 + static octave_swig_type* module_ns =3D 0; +@@ -322,7 +332,9 @@ + // version 3.4.*, but reappeared in 4.2.*, so turn on for all versions = after 3.2.*. + // can be turned off with macro definition. + #ifndef SWIG_OCTAVE_NO_SEGFAULT_HACK +-#if SWIG_OCTAVE_PREREQ(3,2,0) ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ atexit(__swig_atexit__); ++#elif SWIG_OCTAVE_PREREQ(3,2,0) + octave_exit =3D ::_Exit; + #endif + #endif +@@ -351,15 +363,54 @@ + "__swig_atexit__; " + "atexit(\"__swig_atexit__\", false); " + "atexit(\"__swig_atexit__\")"); ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::feval("evalin", eval_args, 0); ++#else + feval("evalin", eval_args, 0); + #endif ++#endif +=20 ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ { ++ octave::type_info& typeinfo =3D octave::interpreter::the_interprete= r()->get_type_info(); ++ string_vector types =3D typeinfo.installed_type_names(); ++ bool register_octave_swig_ref =3D true; ++ bool register_octave_swig_packed =3D true; ++ bool register_octave_swig_bound_func =3D true; ++ for (int i =3D 0; i < types.numel(); ++i) { ++ if (types(i) =3D=3D octave_swig_ref::static_type_name()) { ++ register_octave_swig_ref =3D false; ++ } ++ if (types(i) =3D=3D octave_swig_packed::static_type_name()) { ++ register_octave_swig_packed =3D false; ++ } ++ if (types(i) =3D=3D octave_swig_bound_func::static_type_name()) { ++ register_octave_swig_bound_func =3D false; ++ } ++ } ++ if (register_octave_swig_ref) { ++ octave_swig_ref::register_type(); ++ } ++ if (register_octave_swig_packed) { ++ octave_swig_packed::register_type(); ++ } ++ if (register_octave_swig_bound_func) { ++ octave_swig_bound_func::register_type(); ++ } ++ } ++#else + octave_swig_ref::register_type(); + octave_swig_packed::register_type(); ++#endif + SWIG_InitializeModule(0); + SWIG_PropagateClientData(); +=20 ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::call_stack& stack =3D octave::interpreter::the_interpreter()-= >get_call_stack(); ++ octave_function *me =3D stack.current(); ++#else + octave_function *me =3D octave_call_stack::current(); ++#endif +=20 + if (!SWIG_Octave_InstallFunction(me, "subclass")) { + return octave_value_list(); +@@ -426,10 +477,12 @@ + } + } +=20 +-#if !SWIG_OCTAVE_PREREQ(3,2,0) +- mlock(me->name()); +-#else ++#if SWIG_OCTAVE_PREREQ(4,4,0) ++ octave::interpreter::the_interpreter()->mlock(); ++#elif SWIG_OCTAVE_PREREQ(3,2,0) + mlock(); ++#else ++ mlock(me->name()); + #endif +=20 + } +diff -urN swig-3.0.12.old/Lib/octave/std_pair.i swig-3.0.12.new/Lib/octave= /std_pair.i +--- swig-3.0.12.old/Lib/octave/std_pair.i 2017-01-27 18:52:02.000000000 -0= 500 ++++ swig-3.0.12.new/Lib/octave/std_pair.i 2018-05-26 08:39:16.489124248 -0= 400 +@@ -38,7 +38,13 @@ + } +=20 + static int asval(const octave_value& obj, std::pair *val) { +- if (obj.is_cell()) { ++ if ( ++%#if SWIG_OCTAVE_PREREQ(4,4,0) ++ obj.iscell() ++%#else ++ obj.is_cell() ++%#endif ++ ) { + Cell c=3Dobj.cell_value(); + if (c.numel()<2) { + error("pair from Cell array requires at least two elements"); +@@ -96,7 +102,13 @@ + } +=20 + static int asptr(const octave_value& obj, std::pair **val) { +- if (obj.is_cell()) { ++ if ( ++%#if SWIG_OCTAVE_PREREQ(4,4,0) ++ obj.iscell() ++%#else ++ obj.is_cell() ++%#endif ++ ) { + Cell c=3Dobj.cell_value(); + if (c.numel()<2) { + error("pair from Cell array requires at least two elements"); +diff -urN swig-3.0.12.old/.travis.yml swig-3.0.12.new/.travis.yml +--- swig-3.0.12.old/.travis.yml 2017-01-27 18:52:02.000000000 -0500 ++++ swig-3.0.12.new/.travis.yml 2018-05-26 08:39:16.520124698 -0400 +@@ -92,6 +92,11 @@ + dist: trusty + - compiler: gcc + os: linux ++ env: SWIGLANG=3Doctave SWIGJOBS=3D-j2 VER=3D4.4 CPP11=3D1 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux + env: SWIGLANG=3Dperl5 + sudo: required + dist: trusty +diff -urN swig-3.0.12.old/.travis.yml.orig swig-3.0.12.new/.travis.yml.orig +--- swig-3.0.12.old/.travis.yml.orig 1969-12-31 19:00:00.000000000 -0500 ++++ swig-3.0.12.new/.travis.yml.orig 2017-01-27 18:52:02.000000000 -0500 +@@ -0,0 +1,334 @@ ++language: cpp ++matrix: ++ include: ++ - compiler: clang ++ os: linux ++ env: SWIGLANG=3D ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3D ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3D ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3D SWIG_CC=3Dgcc-5 SWIG_CXX=3Dg++-5 CPP11=3D1 ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3D SWIG_CC=3Dgcc-6 SWIG_CXX=3Dg++-6 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dcsharp ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dd ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dgo ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dgo VER=3D1.5 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dguile ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Djava ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Djavascript ENGINE=3Dnode ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Djavascript ENGINE=3Djsc ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Djavascript ENGINE=3Dv8 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dlua ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dlua VER=3D5.3 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Doctave SWIGJOBS=3D-j2 # 3.8 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Doctave SWIGJOBS=3D-j2 VER=3D4.0 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Doctave SWIGJOBS=3D-j2 VER=3D4.2 CPP11=3D1 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dperl5 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dphp5 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dphp VER=3D7.0 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dphp VER=3D7.1 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython VER=3D2.4 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython VER=3D2.5 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython VER=3D2.6 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython # 2.7 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython PY3=3D3 VER=3D3.2 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython PY3=3D3 VER=3D3.3 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython PY3=3D3 VER=3D3.4 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython PY3=3D3 VER=3D3.5 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-builtin VER=3D2.6 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-builtin ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-builtin PY3=3D3 VER=3D3.4 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-builtin PY3=3D3 VER=3D3.5 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-builtin PY3=3D3 VER=3D3.5 S= WIGOPTPY3=3D ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-O ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-classic ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dr ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Druby VER=3D1.9.3 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Druby VER=3D2.0.0 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Druby VER=3D2.3.0 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dscilab ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dtcl ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3Dcsharp SWIG_CC=3Dgcc-5 SWIG_CXX=3Dg++-5 CPP11=3D1 ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3Djava SWIG_CC=3Dgcc-5 SWIG_CXX=3Dg++-5 CPP11=3D1 ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3Dpython SWIG_CC=3Dgcc-5 SWIG_CXX=3Dg++-5 CPP11=3D1 ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3Dcsharp SWIG_CC=3Dgcc-6 SWIG_CXX=3Dg++-6 CPP14=3D1 ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3Djava SWIG_CC=3Dgcc-6 SWIG_CXX=3Dg++-6 CPP14=3D1 ++ sudo: required ++ dist: trusty ++ - os: linux ++ env: SWIGLANG=3Dpython SWIG_CC=3Dgcc-6 SWIG_CXX=3Dg++-6 CPP14=3D1 ++ sudo: required ++ dist: trusty ++ - compiler: gcc ++ os: osx ++ env: SWIGLANG=3D ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3D ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dcsharp ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dgo ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dguile ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Djava ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dlua ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dperl5 ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dphp5 ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dpython ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dpython PY3=3D3 ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Druby ++ - compiler: clang ++ os: osx ++ env: SWIGLANG=3Dtcl ++ ++ allow_failures: ++ # Lots of failing tests currently ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Docaml ++ sudo: required ++ dist: trusty ++ # Not quite working yet ++ - compiler: gcc ++ os: linux ++ env: SWIGLANG=3Dpython SWIG_FEATURES=3D-O ++ sudo: required ++ dist: trusty ++before_install: ++ - date -u ++ - uname -a ++ - if test "$TRAVIS_OS_NAME" =3D "linux"; then lscpu && cat /proc/cpuinf= o | grep "model name" && cat /proc/meminfo | grep MemTotal; fi ++ - if test "$TRAVIS_OS_NAME" =3D "osx"; then sysctl -a | grep brand_stri= ng; fi ++ # Travis overrides CC environment with compiler predefined values ++ - if test -n "$SWIG_CC"; then export CC=3D"$SWIG_CC"; fi ++ - if test -n "$SWIG_CXX"; then export CXX=3D"$SWIG_CXX"; fi ++install: ++ - if test "$TRAVIS_OS_NAME" =3D "linux"; then source Tools/travis-linux= -install.sh; fi ++ - if test "$TRAVIS_OS_NAME" =3D "osx"; then source Tools/travis-osx-ins= tall.sh; fi ++ - if test -n "$CPP11"; then CONFIGOPTS+=3D(--enable-cpp11-testing --wit= hout-maximum-compile-warnings "CXXFLAGS=3D-std=3Dc++11 -Wall -Wextra" "CFLA= GS=3D-std=3Dc11 -Wall -Wextra") && export CSTD=3Dc11 && export CPPSTD=3Dc++= 11; fi ++ - if test -n "$CPP14"; then CONFIGOPTS+=3D(--enable-cpp11-testing --wit= hout-maximum-compile-warnings "CXXFLAGS=3D-std=3Dc++14 -Wall -Wextra" "CFLA= GS=3D-std=3Dc11 -Wall -Wextra") && export CSTD=3Dc11 && export CPPSTD=3Dc++= 14; fi ++ - ls -la $(which $CC) ++ - ls -la $(which $CXX) ++ - $CC --version ++ - $CXX --version ++script: ++ - echo 'Configuring...' && echo -en 'travis_fold:start:script.1\\r' ++ - if test -n "$SWIGLANG"; then CONFIGOPTS+=3D(--without-alllang --with-= $WITHLANG); fi ++ - echo "${CONFIGOPTS[@]}" ++ - ./autogen.sh && mkdir -p build/build && cd build/build && ../../confi= gure "${CONFIGOPTS[@]}" ++ - echo -en 'travis_fold:end:script.1\\r' ++ - make -s $SWIGJOBS ++ - ./swig -version && ./swig -pcreversion ++ - if test -z "$SWIGLANG"; then make -s $SWIGJOBS check-ccache; fi ++ - if test -z "$SWIGLANG"; then make -s $SWIGJOBS check-errors-test-suit= e; fi ++ - echo 'Installing...' && echo -en 'travis_fold:start:script.2\\r' ++ - if test -z "$SWIGLANG"; then sudo make -s install && swig -version &&= ccache-swig -V; fi ++ - echo -en 'travis_fold:end:script.2\\r' ++ # Stricter compile flags for examples. Various headers and SWIG generat= ed code prevents full use of -pedantic. ++ - if test -n "$SWIGLANG"; then cflags=3D$($TRAVIS_BUILD_DIR/Tools/testf= lags.py --language $SWIGLANG --cflags --std=3D$CSTD --compiler=3D$CC) && ec= ho $cflags; fi ++ - if test -n "$SWIGLANG"; then cxxflags=3D$($TRAVIS_BUILD_DIR/Tools/tes= tflags.py --language $SWIGLANG --cxxflags --std=3D$CPPSTD --compiler=3D$CC)= && echo $cxxflags; fi ++ - if test -n "$SWIGLANG"; then make -s check-$SWIGLANG-version; fi ++ - if test -n "$SWIGLANG"; then make check-$SWIGLANG-enabled; fi ++ - if test -n "$SWIGLANG"; then make $SWIGJOBS check-$SWIGLANG-examples = CFLAGS=3D"$cflags" CXXFLAGS=3D"$cxxflags"; fi ++ - if test -n "$SWIGLANG"; then make $SWIGJOBS check-$SWIGLANG-test-suit= e CFLAGS=3D"$cflags" CXXFLAGS=3D"$cxxflags"; fi ++ - echo 'Cleaning...' && echo -en 'travis_fold:start:script.3\\r' ++ - make check-maintainer-clean && ../../configure $CONFIGOPTS ++ - echo -en 'travis_fold:end:script.3\\r' diff --git a/gnu/packages/swig.scm b/gnu/packages/swig.scm index b931db412..34163aa9e 100644 =2D-- a/gnu/packages/swig.scm +++ b/gnu/packages/swig.scm @@ -22,6 +22,7 @@ #:use-module (guix download) #:use-module (guix licenses) #:use-module (guix build-system gnu) + #:use-module (gnu packages) #:use-module (gnu packages pcre) #:use-module (gnu packages guile) #:use-module (gnu packages boost) @@ -39,7 +40,9 @@ name "-" version ".tar.gz")) (sha256 (base32 =2D "0kf99ygrjs5616gsqhz1l7bib3a12izmxi7g48bwblbymr3z9ybw")))) + "0kf99ygrjs5616gsqhz1l7bib3a12izmxi7g48bwblbymr3z9ybw")) + (patches + (search-patches "swig-octave-patches.patch")))) (build-system gnu-build-system) (arguments '(#:phases =2D-=20 2.17.0 --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlsKCCcACgkQ5qXuPBlG eg3OeA//f+i6/J61ZaI2Me3kRqRp973nnM5hUkSLitdNinqA/pLUEWqB2+NeSysm h+32d32eZInx+KIEtg2x+isxSGln8I0l2N+CbhHKhWQyXtC7deaXjqlCP9gMhxUT BUSWVe325M+3AS7nlw2Q0S8yo/zXGu86o7cbYd6I0uqSsU+KfuACIuVEmvPlFP1g 8mKEolhLyEsULp+Ag0cXxTYEKihCfXtlBEH1TbtikB3UmfZylouFerYk4TcfFfZE 2DLTH1GH6rWKwuG/BXBV0Za5cICL81tes7EsiV0WvKQj5vgP7gIBoG7L2nv4hCaG wUsHeZAbDMqfS2gs0wh8F+qiXz8cDjABJGQJG6lDPgTZSs11Rp0JCU88y94/R9uL 8RwKM0wPIBWUMqkl8HHfmSp3yjq8vdnR0OH4EgVyI2DYEtoDcJOiTvLm+CEyx/zU oULp59qnkIz+8sZCEFWmzjh8knyRvGK3Dr4p4tImihsz//dN6WCi9nIPXF54Rl3m fC9cQV39iVKgviI+wBtyMD6x2B4+HyeOdy+DE/ruonswYfJ/ZqMPFSEzk6vhuhMZ 3yJQhNhFRrBzuy4n/g/WFYZ9aqNF0FfGvp8mJF7iJQd//76jvIb1IqjxDnFWMZ/r wKgw8rsTNCjG/OqkvCdUlAy1ZU5ApukPOn0cpUhPfIIVDUsEsxQ= =YbBO -----END PGP SIGNATURE----- --==-=-=-- From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 29 May 2018 20:57:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: ludo@gnu.org, 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15276273633196 (code B ref 31479); Tue, 29 May 2018 20:57:01 +0000 Received: (at 31479) by debbugs.gnu.org; 29 May 2018 20:56:03 +0000 Received: from localhost ([127.0.0.1]:54364 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fNlf0-0000pT-MF for submit@debbugs.gnu.org; Tue, 29 May 2018 16:56:03 -0400 Received: from mout01.posteo.de ([185.67.36.65]:56397) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fNlez-0000oz-3e for 31479@debbugs.gnu.org; Tue, 29 May 2018 16:56:02 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id C17D721039 for <31479@debbugs.gnu.org>; Tue, 29 May 2018 22:55:54 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1527627354; bh=xcryQOPyTyFOizPLIoEM0hUeViwSrV8quHRTISp+WTY=; h=From:To:Cc:Subject:Date:From; b=qbVgzv84h1rUcul95mhUJIrVeZMXIUHDOjRIJzI/gAxEZFtEG7d1y5Y+nRdPBiBs8 9OyGDsCuyY6rvbk7FL3Jrb8fG1vDPPz+9a01kt01OSuVE9vo1utmtLQlGwvBxXDViH toWGj7/D7V44EuLKvKMvcFde0IkyGJl36ZEAwyYVO2pQfYit5/FLXhr7WZEKX5Cq36 K3MYr6rc/BdLYsMsGxW77pYYNijKJIg0x2kvWuDyEqLcxckxCZhCwJmDwcYRhKdfPo PWlgv1wUZPlbBtu2ofGxr55NpHBQqbxrU+EdcDTaqeTh5Vj9GAzxMhMvILA02k/vam opXYZen3eNbmg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40wQx50Hvsz9rxF; Tue, 29 May 2018 22:55:52 +0200 (CEST) From: Kei Kebreau References: <20180516231033.1680-1-kkebreau@posteo.net> <87a7spcte2.fsf@mdc-berlin.de> <87po1hnba0.fsf@posteo.net> Date: Tue, 29 May 2018 16:55:51 -0400 In-Reply-To: <87po1hnba0.fsf@posteo.net> (Kei Kebreau's message of "Sat, 26 May 2018 21:21:43 -0400") Message-ID: <87h8mqkwq0.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="==-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --==-=-= Content-Type: multipart/mixed; boundary="=-=-=" --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Kei Kebreau writes: > Ricardo Wurmus writes: > >> Hi Kei, >> >> please also note that Shogun contains references to proprietary >> software. It has support for SVMLight, which is non-free software. It >> includes a script to remove all references to and adapters for SVMLight, >> but unfortunately we cannot run shell scripts in a snippet. Changing >> this requires changing the =E2=80=9Cpackage=E2=80=9D syntax to delay eva= luation more. >> >> Until then we need to remove the non-free bits in code, which is what >> the current snippet does, but the code would need to be adjusted for >> version 6.1.3. >> >> Thanks for taking this on! >> >> -- >> Ricardo > > Thank you for the tip! > > I've attached the four patches that make it possible to build Shogun > 6.1.3 successfully, and I'm just looking through the source code to > remove the proprietary bits. > > P.S. Ricardo, you'll notice the eigen patch is actually yours from > another patchset! I verified that it works as expected. The shogun patch below builds successfully for me! If no corrections need to be made, I'll push this patch series to master! --=-=-= Content-Type: text/plain Content-Disposition: attachment; filename=0005-gnu-Update-shogun-to-6.1.3.patch Content-Transfer-Encoding: quoted-printable From=202c41c81ad77ee20c89c3056908c13635ee3f5e10 Mon Sep 17 00:00:00 2001 From: Kei Kebreau Date: Wed, 16 May 2018 11:56:18 -0400 Subject: [PATCH 5/5] gnu: Update shogun to 6.1.3. * gnu/packages/machine-learning.scm (shogun): Update to 6.1.3. [source]: Update snippet to remove proprietary software. [arguments]: Rewrite list of symlinks in 'delete-broken-symlinks' phase. Rewrite file lists given to substitute* in 'change-R-target-path' and 'fix-octave-modules' phases. Adjust 'fix-octave-modules' for the update. Add 'move-rxcpp' phase. Rewrite configure-flags for the update. [inputs]: Add eigen. [native-inputs]: Add rxcpp. =2D-- gnu/packages/machine-learning.scm | 81 ++++++++++++++++++------------- 1 file changed, 46 insertions(+), 35 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learn= ing.scm index 6536d861e..e135ee0ee 100644 =2D-- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -37,6 +37,7 @@ #:use-module (guix build-system r) #:use-module (guix git-download) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -367,7 +368,7 @@ sample proximities between pairs of cases.") (define-public shogun (package (name "shogun") =2D (version "4.0.0") + (version "6.1.3") (source (origin (method url-fetch) @@ -377,7 +378,7 @@ sample proximities between pairs of cases.") "/sources/shogun-" version ".tar.bz2")) (sha256 (base32 =2D "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb")) + "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp")) (modules '((guix build utils) (ice-9 rdelim))) (snippet @@ -409,8 +410,20 @@ sample proximities between pairs of cases.") (and skipping? (not skip-next?))) (display line out)) (loop (read-line in 'concat) skip-next?))))))) =2D (for-each delete-ifdefs (find-files "src/shogun/kernel/" =2D "^Kernel\\.(cpp|h)")))))) + (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" + "^DomainAdaptationSVM\\.(cpp|h)"))))))) (build-system cmake-build-system) (arguments '(#:tests? #f ;no check target @@ -423,62 +436,59 @@ sample proximities between pairs of cases.") "applications/easysvm/data" "applications/msplicer/data" "applications/ocr/data" =2D "examples/documented/data" =2D "examples/documented/matlab_static" =2D "examples/documented/octave_static" =2D "examples/undocumented/data" =2D "examples/undocumented/matlab_stati= c" =2D "examples/undocumented/octave_stati= c" =2D "tests/integration/data" =2D "tests/integration/matlab_static" =2D "tests/integration/octave_static" =2D "tests/integration/python_modular/t= ests")) + "examples/meta/data" + "examples/undocumented/data")) #t)) (add-after 'unpack 'change-R-target-path (lambda* (#:key outputs #:allow-other-keys) =2D (substitute* '("src/interfaces/r_modular/CMakeLists.txt" =2D "src/interfaces/r_static/CMakeLists.txt" =2D "examples/undocumented/r_modular/CMakeLists.= txt") + (substitute* '("src/interfaces/r/CMakeLists.txt" + "examples/meta/r/CMakeLists.txt") (("\\$\\{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) =2D (substitute* '("src/interfaces/octave_modular/CMakeLists.tx= t" =2D "src/interfaces/octave_static/CMakeLists.txt= ") + (substitute* "src/interfaces/octave/CMakeLists.txt" (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") =2D "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INC= LUDE_DIRS}/octave")) =2D =2D ;; change target directory =2D (substitute* "src/interfaces/octave_modular/CMakeLists.txt" + "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLU= DE_DIRS}/octave") + ;; change target directory (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}") (string-append (assoc-ref outputs "out") "/share/octave/packages"))) + (substitute* '("src/interfaces/octave/swig_typemaps.i" + "src/interfaces/octave/sg_print_functions.cpp") + ;; "octave/config.h" and "octave/oct-obj.h" deprecated in O= ctave. + (("octave/config\\.h") "octave/octave-config.h") + (("octave/oct-obj.h") "octave/ovl.h")) #t)) + (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))) (add-before 'build 'set-HOME ;; $HOME needs to be set at some point during the build phase (lambda _ (setenv "HOME" "/tmp") #t))) #:configure-flags (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=3DTRUE" "-DUSE_SVMLIGHT=3DOFF" ;disable proprietary SVMLIGHT =2D ;;"-DJavaModular=3DON" ;requires unpackaged jblas =2D ;;"-DRubyModular=3DON" ;requires unpackaged ruby-narray =2D ;;"-DPerlModular=3DON" ;"FindPerlLibs" does not exist =2D ;;"-DLuaModular=3DON" ;fails because lua doesn't build pkg= config file =2D "-DOctaveModular=3DON" =2D "-DOctaveStatic=3DON" =2D "-DPythonModular=3DON" =2D "-DPythonStatic=3DON" =2D "-DRModular=3DON" =2D "-DRStatic=3DON" =2D "-DCmdLineStatic=3DON"))) + "-DBUILD_META_EXAMPLES=3DOFF" ;requires unpackaged ctags + ;;"-DINTERFACE_JAVA=3DON" ;requires unpackaged jblas + ;;"-DINTERFACE_RUBY=3DON" ;requires unpackaged ruby-narray + ;;"-DINTERFACE_PERL=3DON" ;"FindPerlLibs" does not exist + ;;"-DINTERFACE_LUA=3DON" ;fails because lua doesn't build pk= gconfig file + "-DINTERFACE_OCTAVE=3DON" + "-DINTERFACE_PYTHON=3DON" + "-DINTERFACE_R=3DON"))) (inputs `(("python" ,python) ("numpy" ,python-numpy) ("r-minimal" ,r-minimal) ("octave" ,octave) ("swig" ,swig) + ("eigen" ,eigen) ("hdf5" ,hdf5) ("atlas" ,atlas) ("arpack" ,arpack-ng) @@ -488,7 +498,8 @@ sample proximities between pairs of cases.") ("lzo" ,lzo) ("zlib" ,zlib))) (native-inputs =2D `(("pkg-config" ,pkg-config))) + `(("pkg-config" ,pkg-config) + ("rxcpp" ,rxcpp))) ;; Non-portable SSE instructions are used so building fails on platfor= ms ;; other than x86_64. (supported-systems '("x86_64-linux")) =2D-=20 2.17.0 --=-=-=-- --==-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlsNvlcACgkQ5qXuPBlG eg1rZw//bm2jCNudExPJf4j72lym63blW+GCX7HapP/AyaNxqYjTi3JEtrHulYWv y45nTFFLJb9NtQ1BJTIrTxYTDn8/9GEqseSrrQ6ucqpdcCsxrACKOA95HNv/tSAd Kr4zOouBXsJtYt+VpCsdKl4vhKeTZREZIjpdvbTmuujY+v2GKgJ/UWYr0mwZK8Ly 70SrA5IRpzMbqb4Frx5ccpKGLERBakt7Cgjc2xLeDIpmRFJw82i6rv7+4NgWO6QT stEyCd5d30fZ+X4Ew/DxphBIHlgEtBO6IcFsN+eKQMYKLTVV1vo/QF0YCyUrr+Co U61Z9g4KRB4sarMGOMOg60lwPdLGl8MR6SFA3yPKuoTabaWgC5/y9nu0/vw66Ike gujm9dxftRMZ8jZzLUbICt0KS3NN5W3ZxwVxeZFGs4pGfGGALU06uB9aSmSSYCQR VeEy0/QNpi1dwbtPTOFcwEkuZ8sFGKznC3WqobEsTsSR/LpWavtpojE8zOd09Jly DCgaSWo1mVjQY62I4UTiGNaBLGddkwWpK0b55XAnlFY9Hs4fX5uzpGCTOUd/saaI f6XClyn96PybbO2INSm6ym6cpYKbokvZUErYzvA8FBhwG1+x4Vz6c+EgtBMA6lMy TBttoZZpjDf84ge3KZpNk5cdy8i++zNOfiQ5QpejRDRWe0G8/Zs= =gd9t -----END PGP SIGNATURE----- --==-=-=-- From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 29 May 2018 21:33:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Kei Kebreau Cc: ludo@gnu.org, 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.15276295776536 (code B ref 31479); Tue, 29 May 2018 21:33:01 +0000 Received: (at 31479) by debbugs.gnu.org; 29 May 2018 21:32:57 +0000 Received: from localhost ([127.0.0.1]:54372 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fNmEj-0001hL-54 for submit@debbugs.gnu.org; Tue, 29 May 2018 17:32:57 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:53490) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fNmEh-0001hD-0C for 31479@debbugs.gnu.org; Tue, 29 May 2018 17:32:55 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 0CC45115C3FA; Tue, 29 May 2018 23:32:54 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received:received; s=mdc; t=1527629568; x= 1529443969; bh=CVfNitFuAXf3PzRZMs/UeQ73eo8p7eJwinzN90hibSs=; b=l RWJYWjHzPy5XkL5/PyTB0TbT72UbPxSAxzYFEO+RBtgFeQ/c8yIy3L6isgfysQvz uo62KPnBsKdkx7G8eHEr0tU4qWKQ2RWDXvD+VcJ7iB8cTKETur0IlPf4boQKt+SY UbiMYq7IzyRGl/zGvJTzOSPmmPNe5fPG0mEDREfwjI= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id hUchcDjSe9e6; Tue, 29 May 2018 23:32:48 +0200 (CEST) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1 with cipher ECDHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS; Tue, 29 May 2018 23:32:48 +0200 (CEST) Received: from SW-IT-P-CAS3.mdc-berlin.net (141.80.113.58) by HTCATWO.mdc-berlin.net (141.80.180.190) with Microsoft SMTP Server (TLS) id 14.3.399.0; Tue, 29 May 2018 23:32:48 +0200 Received: from localhost (141.80.113.51) by SW-IT-P-CAS3.mdc-berlin.net (141.80.113.58) with Microsoft SMTP Server id 14.3.399.0; Tue, 29 May 2018 23:32:47 +0200 References: <20180516231033.1680-1-kkebreau@posteo.net> <87a7spcte2.fsf@mdc-berlin.de> <87po1hnba0.fsf@posteo.net> <87h8mqkwq0.fsf@posteo.net> User-agent: mu4e 1.0; emacs 25.3.1 From: Ricardo Wurmus In-Reply-To: <87h8mqkwq0.fsf@posteo.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 29 May 2018 23:32:37 +0200 Message-ID: <878t82qhai.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.51] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.2.1013-23876.003 X-TM-AS-Result: No-4.131300-8.000000-10 X-TMASE-MatchedRID: u1zqiMeMcrpLtdw1KWxtuBxQCXaqsX3JC/ExpXrHizz0NSuQztbtQ8+S Ma11oH/Qc2Ei+4N86I9VkLMRx+TUi5cFdomgH0lnFEUknJ/kEl7x9AXm5DmylPoLR4+zsDTt9xS 3mVzWUuBGS1XF2lG3Yj0+2+hV6d09QgM8KLjdgCNZd4HOeP64uA8ugExzulHaHHxhNdHPNJ+FAp XHnp2/q8e8sD1AGZpHQdLXQfJrMF9xFc4VeZoOmA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.131300-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.2.1013-23876.003 X-Spam-Score: 0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Kei Kebreau writes: > The shogun patch below builds successfully for me! If no corrections > need to be made, I'll push this patch series to master! Beautiful! This looks good to me. Thank you for making the extra effort even though you just wanted to update Octave! -- Ricardo From unknown Sun Jun 22 00:09:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#31479] [PATCH 3/3] gnu: Update shogun to 6.1.3. Resent-From: Kei Kebreau Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 29 May 2018 22:36:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 31479 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ricardo Wurmus Cc: ludo@gnu.org, jonathan.brielmaier@web.de, 31479@debbugs.gnu.org Received: via spool by 31479-submit@debbugs.gnu.org id=B31479.152763330719678 (code B ref 31479); Tue, 29 May 2018 22:36:01 +0000 Received: (at 31479) by debbugs.gnu.org; 29 May 2018 22:35:07 +0000 Received: from localhost ([127.0.0.1]:54397 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fNnCt-00057K-Bq for submit@debbugs.gnu.org; Tue, 29 May 2018 18:35:07 -0400 Received: from mout01.posteo.de ([185.67.36.65]:53768) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fNnCq-00056g-Co for 31479@debbugs.gnu.org; Tue, 29 May 2018 18:35:05 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 23DDB21134 for <31479@debbugs.gnu.org>; Wed, 30 May 2018 00:34:57 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1527633298; bh=U4DKjfOKLRw3+Q/iBKUxULbjeKr2b9h/h3REWgGYy/A=; h=From:To:Cc:Subject:Date:From; b=acyXmnVZNh0HF1qwB3eNcHWZ7wjx4uvzAy8765DwhA3R9t+9V9GDHwSKBPhGk6eSE Gx4zsmeo+Cv6G9PJLtL8G6uYj9jm/DnFFBUqXmQcK3uWO5Dpe8LxsqfqJRz2NLn8db 0AlFlxj8/yglGVDEYLPghkursIoLAo1zjvXTo74F0CHOi+OGfOgs2BX2cF83xqcnLs TzIPqsxqrrKh5/6Kz5AGyzE/L/r5R1Q1yEGGBlH1zQzeulH4ljuoNpT0yAmegFGaVY NUvvDnCXg9WvYxUst3FkmCyKTXQiIba3oFbxNtCgpmLR1FejuT38CyBwkvmZdzynz7 GwiIZUHCpOvsg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 40wT7N1Cyvz9rxK; Wed, 30 May 2018 00:34:56 +0200 (CEST) From: Kei Kebreau References: <20180516231033.1680-1-kkebreau@posteo.net> <87a7spcte2.fsf@mdc-berlin.de> <87po1hnba0.fsf@posteo.net> <87h8mqkwq0.fsf@posteo.net> <878t82qhai.fsf@mdc-berlin.de> Date: Tue, 29 May 2018 18:34:54 -0400 In-Reply-To: <878t82qhai.fsf@mdc-berlin.de> (Ricardo Wurmus's message of "Tue, 29 May 2018 23:32:37 +0200") Message-ID: <87d0xeks4x.fsf@posteo.net> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.3 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha256; protocol="application/pgp-signature" X-Spam-Score: -2.3 (--) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) --=-=-= Content-Type: text/plain Ricardo Wurmus writes: > Kei Kebreau writes: >> The shogun patch below builds successfully for me! If no corrections >> need to be made, I'll push this patch series to master! > > Beautiful! This looks good to me. > > Thank you for making the extra effort even though you just wanted to > update Octave! Packaging things like this makes for a great puzzle, and I love puzzles. Pushed to master! Thanks to everyone involved in the review! --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEg7ZwOtzKO2lLzi2m5qXuPBlGeg0FAlsN1Y4ACgkQ5qXuPBlG eg3L7xAAszaV7MY10bENzYWccoqdRiscIAdp+iELRuyEZaN/GSnEnfGMXYlaZDp5 eL7e7u0K727Ntm8fevfMoER68X20dgWo4LcckVz5S56kb8G4AY2K6Njk78Ar3h5Q qp4MNNaSjMt/9V+7+0BUFpY8oKLpnJrOJI0yF8aGKBZMV+6cVMqs2Yg8Mxh7UvWs uW3RrJr03vdUkFr8/jlF17ryhAS/4KylSFFW3mFcrukfnctotpSrVoBzDhHKcaJi ylXAtkLlA2BExbNrAreVQ4A1ZhBOmwGcEsSBgvGuyAwphtOXvfjK6j9e5aum+J3k 7aPXrshuq5DIMvnnZvsVXudgd/kFVuHjQZOfHo80A4nyuirMhYD05CB5uRy8Of7r LfAL402kouuhwH8s85l8iokyCHMaNru85oVTRP4aK/FhoQ3knFLdkYyYplUgFr0C lDAFb7r0WiDwUtBaGoPAhqcZpDc3kHYH1iYuFWzfcqWNRX2+F1Iv5i3xdaM8pZmH P/hp7nQs7jDUB07cWEFNog+sNiZtxsrBa7q4deht9NmPGudAR35svbhHTIegt/Kt eqV/kpkaLjV2b4aUtcp+cgB0YGZEduVEJ6plYHuGUkL3bvCT0/ezMijeU67RnJ1Z 0tmteqd+AJ2oEdCMSnQXxY93zAjITERdBkDRb+0iWi+O0rrVxAI= =ptLd -----END PGP SIGNATURE----- --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Thu May 31 11:41:55 2018 Received: (at control) by debbugs.gnu.org; 31 May 2018 15:41:55 +0000 Received: from localhost ([127.0.0.1]:56169 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fOPi7-00085S-JW for submit@debbugs.gnu.org; Thu, 31 May 2018 11:41:55 -0400 Received: from eggs.gnu.org ([208.118.235.92]:43568) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fOPi6-00085G-JB for control@debbugs.gnu.org; Thu, 31 May 2018 11:41:54 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fOPhv-0002tn-VD for control@debbugs.gnu.org; Thu, 31 May 2018 11:41:48 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:50677) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fOPhv-0002th-RZ for control@debbugs.gnu.org; Thu, 31 May 2018 11:41:43 -0400 Received: from [193.50.110.154] (port=58218 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fOPhv-0002gx-7x for control@debbugs.gnu.org; Thu, 31 May 2018 11:41:43 -0400 Date: Thu, 31 May 2018 17:41:41 +0200 Message-Id: <876033omru.fsf@gnu.org> To: control@debbugs.gnu.org From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: control message for bug #31479 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) tags 31479 fixed close 31479