From patchwork Thu Mar 27 19:49:43 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40887 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 536FA27BBE9; Thu, 27 Mar 2025 19:51:22 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 39D4C27BBE2 for ; Thu, 27 Mar 2025 19:51:19 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1txtFt-0008LO-1r; Thu, 27 Mar 2025 15:51:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1txtFm-0008GZ-Tx for guix-patches@gnu.org; Thu, 27 Mar 2025 15:51:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1txtFm-0006Yh-HY for guix-patches@gnu.org; Thu, 27 Mar 2025 15:51:02 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=nncTbuWuC4OAjLPJ0YZ4oQ/DiOogshle4wP7sIZF3lY=; b=hGOldlvw+W85Uu37nW5Zg26rwc97w52usLyddjpi57mSckKMNXGoExF3J4whqAhJP85OAxsZErQo5CVYEHcO02KRiYZwKbsvNc3nzYX4/1bz6xumZOolt654yBlbVziASTnZuyHUcLWVL9NexXwJKc674oc0LylyRPlpdqfvLqX3585aurBhEnHjr+THJYcQN87vcwD8dePiNBpvJTc1NJvZeZsn9zyjyxvGlHspHOBc+D/aVwLEB0Ae1bYEp9oGFRi9kGiSJfrm2K/6z1neB9F8jHIzXFKyxFXLjPztKPtz2m7uTztmvc+9z0NkHTd6O6BHNtg/mTafXRDp+yQPYA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1txtFm-0007hN-3G for guix-patches@gnu.org; Thu, 27 Mar 2025 15:51:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77321] [PATCH 1/2] gnu: Remove shogun. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 27 Mar 2025 19:51:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77321 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77321@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge , sharlatanus@gmail.com, bavier@posteo.net Received: via spool by 77321-submit@debbugs.gnu.org id=B77321.174310500429154 (code B ref 77321); Thu, 27 Mar 2025 19:51:02 +0000 Received: (at 77321) by debbugs.gnu.org; 27 Mar 2025 19:50:04 +0000 Received: from localhost ([127.0.0.1]:51461 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1txtEp-0007Zw-2e for submit@debbugs.gnu.org; Thu, 27 Mar 2025 15:50:03 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44330) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1txtEl-0007ZE-65 for 77321@debbugs.gnu.org; Thu, 27 Mar 2025 15:50:00 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id CF73A30A; Thu, 27 Mar 2025 20:49:51 +0100 (CET) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id t5QeuygXBVKX; Thu, 27 Mar 2025 20:49:50 +0100 (CET) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 5D49C2A6; Thu, 27 Mar 2025 20:49:48 +0100 (CET) From: Andreas Enge Date: Thu, 27 Mar 2025 20:49:43 +0100 Message-ID: <60c3440208b902d919486dbedc3c6306b4390556.1743104583.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: CF73A30A X-Spamd-Result: default: False [-2.60 / 15.00]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-3.00)[-1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; MIME_TRACE(0.00)[0:+]; RCVD_COUNT_TWO(0.00)[2]; RCVD_TLS_ALL(0.00)[]; FROM_EQ_ENVFROM(0.00)[]; RCPT_COUNT_FIVE(0.00)[5]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; FREEMAIL_CC(0.00)[elephly.net,posteo.net,gmail.com,enge.fr]; TO_DN_SOME(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: -- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/machine-learning.scm (shogun): Delete variable. The package depends on atlas, which does not build any more. The ftp server that is supposed to contain the source code has become private and does not accept anonymous connections. The package has not been updated since 2018. It has no dependent packages. Change-Id: Ia2e1ef51180397a056410fd8d33ce2827623aaa0 --- gnu/packages/machine-learning.scm | 148 ------------------------------ 1 file changed, 148 deletions(-) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 4ea05a7752..818e208a37 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -1422,154 +1422,6 @@ (define-public python-spacy model packaging, deployment and workflow management.") (license license:expat))) -(define-public shogun - (package - (name "shogun") - (version "6.1.3") - (source - (origin - (method url-fetch) - (uri (string-append - "ftp://shogun-toolbox.org/shogun/releases/" - (version-major+minor version) - "/sources/shogun-" version ".tar.bz2")) - (sha256 - (base32 - "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp")) - (modules '((guix build utils) - (ice-9 rdelim))) - (snippet - '(begin - ;; Remove non-free sources and files referencing them - (for-each delete-file - (find-files "src/shogun/classifier/svm/" - "SVMLight\\.(cpp|h)")) - (for-each delete-file - (find-files "examples/undocumented/libshogun/" - (string-append - "(classifier_.*svmlight.*|" - "evaluation_cross_validation_locked_comparison).cpp"))) - ;; Remove non-free functions. - (define (delete-ifdefs file) - (with-atomic-file-replacement file - (lambda (in out) - (let loop ((line (read-line in 'concat)) - (skipping? #f)) - (if (eof-object? line) - #t - (let ((skip-next? - (or (and skipping? - (not (string-prefix? - "#endif //USE_SVMLIGHT" line))) - (string-prefix? - "#ifdef USE_SVMLIGHT" line)))) - (when (or (not skipping?) - (and skipping? (not skip-next?))) - (display line out)) - (loop (read-line in 'concat) skip-next?))))))) - (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)"))) - #t)))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ;no check target - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'delete-broken-symlinks - (lambda _ - (for-each delete-file '("applications/arts/data" - "applications/asp/data" - "applications/easysvm/data" - "applications/msplicer/data" - "applications/ocr/data" - "examples/meta/data" - "examples/undocumented/data")) - #t)) - (add-after 'unpack 'change-R-target-path - (lambda* (#:key outputs #:allow-other-keys) - (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/CMakeLists.txt" - (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}") - "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"))) - (substitute* '("src/interfaces/octave/swig_typemaps.i" - "src/interfaces/octave/sg_print_functions.cpp") - ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave. - (("octave/config\\.h") "octave/octave-config.h") - (("octave/oct-obj.h") "octave/ovl.h")) - #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 - "-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-cli) - ("swig" ,swig) - ("eigen" ,eigen) - ("hdf5" ,hdf5) - ("atlas" ,atlas) - ("arpack" ,arpack-ng) - ("openblas" ,openblas) - ("glpk" ,glpk) - ("libxml2" ,libxml2) - ("lzo" ,lzo) - ("zlib" ,zlib))) - (native-inputs - (list pkg-config rxcpp)) - ;; Non-portable SSE instructions are used so building fails on platforms - ;; other than x86_64. - (supported-systems '("x86_64-linux")) - (home-page "https://shogun-toolbox.org/") - (synopsis "Machine learning toolbox") - (description - "The Shogun Machine learning toolbox provides a wide range of unified and -efficient Machine Learning (ML) methods. The toolbox seamlessly -combines multiple data representations, algorithm classes, and general purpose -tools. This enables both rapid prototyping of data pipelines and extensibility -in terms of new algorithms.") - (license license:gpl3+))) - (define-public onnx (package (name "onnx")