From patchwork Sat Mar 29 09:21:25 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40955 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 5B8C527BBE9; Sat, 29 Mar 2025 09:32:53 +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 0118F27BBE2 for ; Sat, 29 Mar 2025 09:32:52 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySYb-0003O0-3P; Sat, 29 Mar 2025 05:32:49 -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 1tySVv-0002SN-UC for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:05 -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 1tySVv-0006ni-Il for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:03 -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=bq2eHfqgOZtE04V0iZ2WHMuPsrXcOE8Bsd+z7QvwF54=; b=aV/khErI9XXsSb7XJNHfLLuVY4FnzVgNGKHyYnDsLICNUej52wzS7Cnw64+mVTP6ddnVG/xHkMOf0luyUyPW0LuOGVlb6OfnAVF5JgSO24tz1zWUffhqOkHvgljpXP/Pq3+0SzUW1WQZYFURWBUgqRBznj7F7hkXYN6bVpi2TKYb563zkBYh/ZgaZzlio5BIN5rhzDKA2dYWpVb04mNgF5hGmXwoHJfrdB21Bnbnq4P7YQr7uCf2A4fxZvW25Nwu9YBlqSWO1r4G+yDKD9SIY5o8v5Sj8RSwIRTDYLFhqyKN1CgdZ600PNfUzFtYo1RqUcJ9quWRGECq0C3GPwkkqQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVu-0004tn-V3; Sat, 29 Mar 2025 05:30:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 1/8] gnu: Remove h5check. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324055818688 (code B ref 77287); Sat, 29 Mar 2025 09:30:02 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:18 +0000 Received: from localhost ([127.0.0.1]:56850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVC-0004rK-18 for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:18 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:58516) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySUy-0004pe-BA for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:04 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 52B7DB2; Sat, 29 Mar 2025 10:28:58 +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 UEnLpGjad3r8; Sat, 29 Mar 2025 10:28:57 +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 384102E6; Sat, 29 Mar 2025 10:28:56 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:25 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 52B7DB2 X-Spamd-Result: default: False [-6.51 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.91)[-0.971]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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/maths.scm (h5check): Delete variable. Change-Id: Ia7ced02059734cf8a5a2db39bbe0f1b38f67df12 --- gnu/packages/maths.scm | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3de5b7b8ae..0d56dd4410 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2144,26 +2144,6 @@ (define-public hdf5-blosc Blosc-compressed datasets.") (license license:expat))) -(define-public h5check - (package - (name "h5check") - (version "2.0.1") - (source - (origin - (method url-fetch) - (uri (string-append "https://www.hdfgroup.org/ftp/HDF5/tools/" - "h5check/src/h5check-" version ".tar.gz")) - (sha256 - (base32 - "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) - (build-system gnu-build-system) - (inputs (list hdf5-1.8)) ;h5cc for tests - (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") - (synopsis "HDF5 format checker") - (description "@code{h5check} is a validation tool for verifying that an -HDF5 file is encoded according to the HDF File Format Specification.") - (license (license:x11-style "file://COPYING")))) - (define-public itex2mml (package (name "itex2mml") From patchwork Sat Mar 29 09:21:26 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40951 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 3B9B927BBEA; Sat, 29 Mar 2025 09:32:04 +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=ham 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 9788327BBE2 for ; Sat, 29 Mar 2025 09:32:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySXD-0002ge-Up; Sat, 29 Mar 2025 05:31:23 -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 1tySVw-0002SS-9P for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:05 -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 1tySVv-0006pX-UN for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:03 -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=Sl5j7BQONQ6Mfrqpl95TqjwJAGuJnXWo59HTTUf4cpXdf8HvDU4qHf1cCVfYZKqO9nU3vwFtS9ldXz0XotZmWl2hcLA5Mk3iE6Sh7zDTLxW6w8/xQkuH5j25BVg6Uk2y5M5+FYO8YeA9GswFLM32qSdO2lHJn+CGMjKOx8c6r/Tkri/Ym3EHgKTG5HeXxWm9rlxIGpw9OoBHZ5GtdgTxA5yrOkkSf+pL5Ylgogt5ghxEM8nrNX4IptMMMQuMnLs0Lqr6IAz18c7nJKY3H8xG/1ZVkiJCwXCRVXXBe7ZLiiXHn44+wlOMhlWm8xc5ppIfJrJQm0zVI8jSU0ZanVMnlQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVv-0004tw-Lf for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 2/8] gnu: Remove shogun. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324055918695 (code B ref 77287); Sat, 29 Mar 2025 09:30:03 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:19 +0000 Received: from localhost ([127.0.0.1]:56852 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVC-0004rN-Cg for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:18 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44896) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV0-0004pm-NC for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:07 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id AEB4F2BB; Sat, 29 Mar 2025 10:29:00 +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 cR4F0OiPrlgs; Sat, 29 Mar 2025 10:28:59 +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 856282F8; Sat, 29 Mar 2025 10:28:58 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:26 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: AEB4F2BB X-Spamd-Result: default: False [-6.35 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.75)[-0.918]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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") From patchwork Sat Mar 29 09:21:27 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40949 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 3540427BBE9; Sat, 29 Mar 2025 09:31:54 +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 39E7927BBE2 for ; Sat, 29 Mar 2025 09:31:51 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySXD-0002gO-BX; Sat, 29 Mar 2025 05:31:23 -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 1tySVx-0002SX-Hp for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:07 -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 1tySVw-0006x2-RW for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:05 -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=MjMtvumsd+kCjoQajqoxG6q29N3qa4URVP80AyA4EH4=; b=RvImiLYYh8S6D8EloxcpNIlDnRTJDwfQQ1kFXRuKA6E+I99cfipZK0qE/Mg0w/KrLnC4FtDyZIvCBTicMBd4EluJ7tNNJDpKrv8XsG1E67gIEesV1cRmhE/4Y+v3je/3TPaEWD65JmAYb8OWL6Z5c5jCEivGdEWtzHevcR0stGcfMNN9jUVQzsdbEtuF/xA/SPZX7W8gcWN4lSCeBmads+dNXgFTyyJNE5p7l8QmX7X+SLTacDVTGSI/wjXkKEAvznw2rX28XBmLwm87pSgEax/7XKwJLv3DGSH4ns8QSel0YMDg1REt/soUW+BqoeALwxv8FDp8aGJs1+sM8h3c2Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVw-0004uB-JJ; Sat, 29 Mar 2025 05:30:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 3/8] gnu: Remove atlas. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324055918702 (code B ref 77287); Sat, 29 Mar 2025 09:30:04 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:19 +0000 Received: from localhost ([127.0.0.1]:56854 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVC-0004rU-W8 for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:19 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44910) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV2-0004q6-Un for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:09 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id F3A9A3AC; Sat, 29 Mar 2025 10:29:02 +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 VlOwMcQ6L79B; Sat, 29 Mar 2025 10:29:02 +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 B0DD835B; Sat, 29 Mar 2025 10:29:00 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:27 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: F3A9A3AC X-Spamd-Result: default: False [-6.28 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.68)[-0.893]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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/maths.scm (atlas): Delete variable. The package does not build anymore. Its last release dates from 2016. After the removal of shogun there are no other dependent packages. Change-Id: Ibe988d33451b63ef7680b6c0a19cff6430a42a68 --- gnu/packages/maths.scm | 129 ----------------------------------------- 1 file changed, 129 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0d56dd4410..017abecc00 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6995,135 +6995,6 @@ (define-public suitesparse ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK (license (list license:gpl2+ license:lgpl2.1+)))) -(define-public atlas - (package - (name "atlas") - (version "3.10.3") - (source (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/math-atlas/Stable/" - version "/atlas" version ".tar.bz2")) - (patches (search-patches "atlas-gfortran-compat.patch")) - (sha256 - (base32 - "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216")))) - (build-system gnu-build-system) - (home-page "https://math-atlas.sourceforge.net/") - (inputs `(("gfortran" ,gfortran) - ("lapack-tar" ,(package-source lapack)))) - (outputs '("out" "doc")) - ;; For the moment we drop support for MIPS at it fails to compile. See - ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html - (supported-systems (delete "mips64el-linux" %supported-systems)) - (arguments - `(#:parallel-build? #f - #:parallel-tests? #f - - ;; ATLAS tunes itself for the machine it is built on, as explained at - ;; . - ;; For this reason, we want users to build it locally instead of using - ;; substitutes. - #:substitutable? #f - - #:modules ((srfi srfi-26) - (guix build gnu-build-system) - (guix build utils)) - #:configure-flags - `(;; Generate position independent code suitable for dynamic libraries - ;; and use WALL timer to get more accurate timing. - "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" - ;; Set word width. - "-b" - ,,(if (string-match "64" (%current-system)) - "64" - "32") - ;; Disable parallel build as it gives errors: atlas_pthread.h is - ;; needed to compile C files before it is generated. - "-Ss" "pmake" "make -j 1" - ;; Probe is failing for MIPS. We therefore define the system - ;; architecture explicitly by setting (-A) MACHINETYPE = 49 - ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. - ,,@(if (string-prefix? "mips" (%current-system)) - (list "-A" "49" "-V" "1") - (list)) - ;; Generate shared libraries. - "--shared" - ;; Build a full LAPACK library. - ,(string-append "--with-netlib-lapack-tarfile=" - (assoc-ref %build-inputs "lapack-tar"))) - #:phases - (modify-phases %standard-phases - (add-after 'install 'install-doc - (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((doc (string-append (assoc-ref outputs "doc") - "/share/doc/atlas"))) - (mkdir-p doc) - (for-each (cut install-file <> doc) - (find-files "../ATLAS/doc" ".*")) - #t))) - (add-after 'check 'check-pt - (lambda _ (invoke "make" "ptcheck"))) - ;; Fix files required to run configure. - (add-before 'configure 'fix-/bin/sh - (lambda _ - ;; Use `sh', not `/bin/sh'. - (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") - (("/bin/sh") - "sh")) - #t)) - ;; Fix /bin/sh in generated make files. - (add-after 'configure 'fix-/bin/sh-in-generated-files - (lambda _ - (substitute* (find-files "." "^[Mm]ake\\.inc.*") - (("/bin/sh") - "sh")) - #t)) - ;; ATLAS configure program does not accepts the default flags - ;; passed by the 'gnu-build-system'. - (replace 'configure - (lambda* (#:key native-inputs inputs outputs - (configure-flags '()) - #:allow-other-keys #:rest args) - (let* ((prefix (assoc-ref outputs "out")) - (bash (or (and=> (assoc-ref - (or native-inputs inputs) "bash") - (cut string-append <> "/bin/bash")) - "/bin/sh")) - (flags `(,(string-append "--prefix=" prefix) - ,@configure-flags)) - (abs-srcdir (getcwd)) - (srcdir (string-append "../" (basename abs-srcdir)))) - (format #t "source directory: ~s (relative from build: ~s)~%" - abs-srcdir srcdir) - (mkdir "../build") - (chdir "../build") - (format #t "build directory: ~s~%" (getcwd)) - (format #t "configure flags: ~s~%" flags) - (apply invoke bash - (string-append srcdir "/configure") - flags))))))) - (synopsis "Automatically Tuned Linear Algebra Software") - (description - "ATLAS is an automatically tuned linear algebra software library -providing C and Fortran77 interfaces to a portably efficient BLAS -implementation, as well as a few routines from LAPACK. - -Optimization occurs at build time. For this reason, the library is built on -the machine where it is installed, without resorting to pre-built substitutes. - -Before building the library, CPU throttling should be disabled. This can be -done in the BIOS, or, on GNU/Linux, with the following command: - -@example -# cpupower --governor performance -@end example - -Failure to do so will result in a library with poor performance.") - ;; The test suite is notoriously lengthy and routinely exceeds the default - ;; timeout of 21600 seconds on the not unbeefy berlin build nodes. - (properties '((timeout . 86400))) ; 1 day - (license license:bsd-3))) - (define-public cglm (package (name "cglm") From patchwork Sat Mar 29 09:21:28 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40952 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 0373827BBEA; Sat, 29 Mar 2025 09:32:23 +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=ham 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 ABFBA27BBE2 for ; Sat, 29 Mar 2025 09:32:22 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySXM-0002hc-OA; Sat, 29 Mar 2025 05:31:38 -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 1tySW0-0002Sp-Em for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:17 -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 1tySVy-000703-DW for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:08 -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=/YsFNn7tuOEnYE+HPNJK0TID2WafC0IUUIHbyyWdQ2s=; b=gM+BUyTWwUc+4gyTJGBIlMZwwPzgW92lzpDhP8bbODKsJs4uhuP+0s33PZ0Df9xbHgO84YvxchJpPZs8gFOhP9FyIpZdTXrAWvEKbL/PO/u7FvSbkdI598WS4G3sbgeVeoyzVGkjH5MBzayhYggpenYCbWW/7TI6pHZywskynNjQP8JRVvN1ZTe8yZDxDPQ5qIXWWfk/k8JBQteY6Ooy/A5jjX9g25smdSh7Nq7GdZhOozmgYKLkSQxig3IH5J4xlwEAUamBQv+xwT5hz/o56FnYlOBG6TAidFytEwP9fD8jzf1ahw6z+LQXsxaS70ymV6Masr6jiA9NvK2A+duh/Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVy-0004uU-4v for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 4/8] gnu: Remove variant-tools. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324057818740 (code B ref 77287); Sat, 29 Mar 2025 09:30:06 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:38 +0000 Received: from localhost ([127.0.0.1]:56858 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVW-0004sB-3y for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:38 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44914) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV4-0004qJ-UI for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:11 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 0AD942F8; Sat, 29 Mar 2025 10:29:05 +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 r5Fe8NUORS7X; Sat, 29 Mar 2025 10:29:04 +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 E4A79172; Sat, 29 Mar 2025 10:29:02 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:28 +0100 Message-ID: <7e352f0d38c546703ababed978329d754df2eeaf.1743240092.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 0AD942F8 X-Spamd-Result: default: False [-6.43 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.83)[-0.943]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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/bioinformatics.scm (variant-tools): Delete variable. The package does not compile any more and has no dependent packages. The last release dates from 2020; there is an additional commit in 2022; the git repository has been archived in 2023. Change-Id: Idb5df024121c5085f764f179d31ac67cff3fc5c7 --- gnu/packages/bioinformatics.scm | 37 --------------------------------- 1 file changed, 37 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0825fbb6ef..e8b585e495 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15248,43 +15248,6 @@ (define-public multiqc common bioinformatics tools.") (license license:gpl3+))) -(define-public variant-tools - (package - (name "variant-tools") - (version "3.1.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/vatlab/varianttools") - ;; There is no tag corresponding to version 3.1.2 - (commit "813ae4a90d25b69abc8a40f4f70441fe09015249"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g")))) - (build-system python-build-system) - (inputs - (list boost - c-blosc - gsl - hdf5 - hdf5-blosc - python-cython - zlib)) - (propagated-inputs - (list python-numpy python-pycurl python-pyzmq python-scipy - python-tables)) - (home-page "https://vatlab.github.io/vat-docs/") - (synopsis "Analyze genetic variants from Next-Gen sequencing studies") - (description - "Variant tools is a tool for the manipulation, annotation, -selection, simulation, and analysis of variants in the context of next-gen -sequencing analysis. Unlike some other tools used for next-gen sequencing -analysis, variant tools is project based and provides a whole set of tools to -manipulate and analyze genetic variants.") - (license license:gpl3+))) - (define-public r-chromvarmotifs (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") (revision "1")) From patchwork Sat Mar 29 09:21:29 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40950 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 5E09C27BBE2; Sat, 29 Mar 2025 09:31:54 +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 CA48F27BBEA for ; Sat, 29 Mar 2025 09:31:53 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySXM-0002hd-OF; Sat, 29 Mar 2025 05:31:38 -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 1tySW0-0002So-CQ for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:17 -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 1tySVx-0006zv-Tu for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:06 -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=kSNKYHOtLyNLZ+M7fr4NYhnMjfuZoyknCrVGJcQTz3o=; b=KY2G7rsyGhV9abgHdgDb6ZCjzmVlFcQ8Iu/fO08PVZmCqRoSsOTuq1aaAMigPp1LjizVDL4SICQla8JT+nxx1Ejz6oikiDQiNNnDkm7AZxC0drPrIXFWTZwruQ64lQsGEtZ/cgD2Qp9F2aNvWeiXiVPix08sTzqsIfNHPtrVpPlgBVVYHFM2EwSmh6G6E3+8eiOMw9vnNH8lMhWUAD8H9HA01dUc5+OZip2PahEDkn2N3r6S6l/Zn79nqGcncddSxeMAXzHrp0y+gy4yrGzvMjtOf84dkDfzFcv9A5F6SSpfd3KFGDKKWd5ckz8yD7WGsSKcOv6tk5V5/WTDclZNvA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVx-0004uN-GI for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 5/8] gnu: Remove mia. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324057718732 (code B ref 77287); Sat, 29 Mar 2025 09:30:05 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:37 +0000 Received: from localhost ([127.0.0.1]:56856 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVV-0004s3-2s for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:37 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44928) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV7-0004qV-AT for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:13 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 6009C1AD; Sat, 29 Mar 2025 10:29:07 +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 wxE8-JQSsHxg; Sat, 29 Mar 2025 10:29:06 +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 4E611172; Sat, 29 Mar 2025 10:29:05 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:29 +0100 Message-ID: <83fd17f4f5f2111aaf51f62c9f32568653d7441b.1743240092.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 6009C1AD X-Spamd-Result: default: False [-6.45 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.85)[-0.950]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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 The package has no dependent packages. It does not build any more since May 2023, and has not seen a newer release since the currently packaged release from 2020. * gnu/packages/image-processing.scm (mia): Delete variable. Change-Id: I62556d2690903b6171b5ff752094310fb989fc03 --- gnu/packages/image-processing.scm | 56 ------------------------------- 1 file changed, 56 deletions(-) diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index c4eb028877..4ddb01f450 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -206,62 +206,6 @@ (define-public dcmtk "A union of the Apache 2.0 licence and various non-copyleft licences similar to the Modified BSD licence.")))) -(define-public mia - (package - (name "mia") - (version "2.4.7") - (source (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/mia/mia/" - (version-major+minor version) - "/mia-" version ".tar.xz")) - (sha256 - (base32 - "0qpcd3n26q52dpyibm11f5l6cgscdr54p2jish39gc3p1f5h3ws1")) - (patches (search-patches "mia-fix-boost-headers.patch" - "mia-vtk9.patch" - "mia-vtk92.patch" - "mia-vtk-version.patch")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list "-DMIA_CREATE_NIPYPE_INTERFACES=OFF" - "-DCMAKE_CXX_FLAGS=-fpermissive"))) - (inputs - (list boost - dcmtk - doxygen - eigen - fftw - fftwf - gsl - gts - hdf5 - itpp - libjpeg-turbo - libpng - libtiff - libxml2 - libxml++ - maxflow - niftilib - nlopt - openexr-2 - python-lxml - vtk)) - (native-inputs - (list pkg-config - python-wrapper)) - (home-page "https://mia.sourceforge.net") - (synopsis "Toolkit for gray scale medical image analysis") - (description "MIA provides a combination of command line tools, plug-ins, -and libraries that make it possible run image processing tasks interactively -in a command shell and to prototype using the shell's scripting language. It -is built around a plug-in structure that makes it easy to add functionality -without compromising the original code base and it makes use of a wide variety -of external libraries that provide additional functionality.") - (license license:gpl3+))) - (define-public opencolorio (package (name "opencolorio") From patchwork Sat Mar 29 09:21:30 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40956 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 ACEF127BBEA; Sat, 29 Mar 2025 09:33:03 +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=ham 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 13D1927BBE2 for ; Sat, 29 Mar 2025 09:33:03 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySYd-0003Vr-30; Sat, 29 Mar 2025 05:32:51 -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 1tySW0-0002Sq-Uf for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:14 -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 1tySW0-00070M-HT for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:08 -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=dQp3qMC7UHXJA9sLL81H8rfT1GTNgT6+bUjimyVPYaU=; b=L6fEMBpJTOtRwkYIxxf66jKcTD24nlpolNhVYXjijzjAoknrDsizEXHD0IfPl8XgPQL7gpJHDPCNB1dagE9S/TBctbJZaIuljom34D5ma/3QJ43srI3eHNsWXXobOSpMzvDqS83L5uMGCk5e+JiEzen20DrndrvlMznybqs3a286ahmR2rL10lh0/wzuxP5Mf+nT90Apyu2nzsBfy+cDumMcBn5bBgKQLjDH9LCedKuPMTBW68dZAhxfeWYIrQ8bh0G9lqk+8DQAcJiuAk+hTNqnkSwiBayXCBaDrhoA50FCTPvW2RSK3Fi5dJEHC2uSs1Xojj5xbmILg+rm3sUItA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySW0-0004uv-Bv for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:08 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 6/8] gnu: Remove itk-snap. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324058018763 (code B ref 77287); Sat, 29 Mar 2025 09:30:08 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:40 +0000 Received: from localhost ([127.0.0.1]:56864 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVX-0004sU-F0 for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:39 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60028) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySVA-0004qj-0w for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:16 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id C03022BB; Sat, 29 Mar 2025 10:29:09 +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 2Fsd1uT6NB-V; Sat, 29 Mar 2025 10:29:09 +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 669F935B; Sat, 29 Mar 2025 10:29:07 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:30 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: C03022BB X-Spamd-Result: default: False [-6.32 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.72)[-0.905]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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 TODO: So far this is only for testing purposes. * gnu/packages/image-processing.scm (itk-snap): Delete variable. Change-Id: Iccdc5c60987fec57ee11ca190b43effb19675165 --- gnu/packages/image-processing.scm | 131 ------------------------------ 1 file changed, 131 deletions(-) diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm index 4ddb01f450..a89874fc06 100644 --- a/gnu/packages/image-processing.scm +++ b/gnu/packages/image-processing.scm @@ -1386,137 +1386,6 @@ (define-public insight-toolkit-4.12 ;; error: ISO C++17 does not allow dynamic exception specifications #~(cons* "-DCMAKE_CXX_FLAGS=-std=c++14" #$cf)))))) -(define-public itk-snap - (package - (name "itk-snap") - (version "3.8.0") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://git.code.sf.net/p/itk-snap/src") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "15i5ixpryfrbf3vrrb5rici8fb585f25k0v1ljds16bp1f1msr4q")) - (patches (search-patches "itk-snap-alt-glibc-compat.patch")))) - (build-system cmake-build-system) - (arguments - `(#:configure-flags - (list "-DSNAP_VERSION_GIT_SHA1=release" - "-DSNAP_VERSION_GIT_BRANCH=release" - "-DSNAP_VERSION_GIT_TIMESTAMP=0" - "-DSNAP_PACKAGE_QT_PLUGINS=OFF" - "-DCMAKE_POSITION_INDEPENDENT_CODE=ON") - #:phases - (modify-phases %standard-phases - ;; During the installation phase all libraries provided by all - ;; dependencies will be copied to the lib directory. That's insane, - ;; so we disable this. - (add-after 'unpack 'do-not-copy-dependencies - (lambda _ - (substitute* "CMakeLists.txt" - (("install_qt5_executable\ -\\(\\$\\{SNAP_MAIN_INSTALL_DIR\\}/\\$\\{SNAP_EXE\\}\\)") - "")))) - (add-after 'unpack 'disable-gui-tests - (lambda _ - ;; The GUI tests just time out. - (substitute* "CMakeLists.txt" - ((" (Workspace|DiffSpace|ProbeIntensity|RegionCompetition\ -|RandomForest|RandomForestBailOut)") - "")))) - (add-after 'unpack 'make-reproducible - (lambda _ - (substitute* "CMakeLists.txt" - (("TODAY\\(SNAP_VERSION_COMPILE_DATE\\)") - "SET(SNAP_VERSION_COMPILE_DATE \"(removed for reproducibility)\")")))) - (add-after 'unpack 'prepare-submodules - (lambda* (#:key inputs #:allow-other-keys) - (rmdir "Submodules/c3d") - (copy-recursively (assoc-ref inputs "c3d-src") - "Submodules/c3d") - (substitute* '("Submodules/c3d/adapters/BiasFieldCorrectionN4.cxx" - "Submodules/c3d/adapters/ApplyMetric.cxx") - (("vcl_") "std::")) - (rmdir "Submodules/greedy") - (symlink (assoc-ref inputs "greedy-src") - "Submodules/greedy"))) - (add-after 'unpack 'fix-includes - (lambda _ - (substitute* "GUI/Model/RegistrationModel.cxx" - (("") - "")))) - (add-before 'check 'prepare-tests - (lambda _ - ;; Needed by at least one test. - (setenv "HOME" "/tmp"))) - (add-after 'install 'wrap-executable - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/itksnap") - `("QT_PLUGIN_PATH" ":" prefix - ,(map (lambda (label) - (string-append (assoc-ref inputs label) - "/lib/qt5/plugins")) - '("qtbase" "qtdeclarative-5")))))))))) - (inputs - (list bash-minimal - curl - fftw - fftwf - glu - hdf5 - mesa-opencl - ;; This package does not build with either insight-toolkit 5.0.0 - ;; and not with 4.13. It really needs to be 4.12. - insight-toolkit-4.12 - vtk-7 - qtbase-5 - qtdeclarative-5 - vxl-1 - zlib)) - (native-inputs - `(("googletest" ,googletest) - ("qttools-5" ,qttools-5) - ("pkg-config" ,pkg-config) - ("c3d-src" - ,(let* ((commit "f521358db26e00002c911cc47bf463b043942ad3") - (revision "1") - (version (git-version "0" revision commit))) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pyushkevich/c3d") - (commit commit))) - (file-name (git-file-name "c3d" version)) - (sha256 - (base32 - "0kyv3rxrxwr8c3sa9zv01lsnhk95b27gx1s870k3yi8qp52h7bx3"))))) - ;; We are using an arbitrary commit from 2017 because the latest - ;; version breaks the build... - ("greedy-src" - ,(let* ((commit "97e340f7e8e66597599144947775e6039e79a0d3") - (revision "1") - (version (git-version "0" revision commit))) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pyushkevich/greedy") - (commit commit))) - (file-name (git-file-name "greedy" version)) - (sha256 - (base32 - "0k5bc9za4jrc8z9dj08z1rkcp5xf0gnd1d2jmi1w9ny4vxh2q2ab"))))))) - (home-page "https://sourceforge.net/p/itk-snap/") - (synopsis "Medical image segmentation") - (description "ITK-SNAP is a tool for segmenting anatomical structures in -medical images. It provides an automatic active contour segmentation -pipeline, along with supporting a manual segmentation toolbox. ITK-SNAP has a -full-featured UI aimed at clinical researchers.") - ;; This includes the submodules greedy and c3d. - (license license:gpl3+))) - (define-public metapixel ;; Follow stable branch. 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Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, laurent.gatto@gmail.com, rekado@elephly.net, sharlatanus@gmail.com, zimon.toutoune@gmail.com, guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge , Andreas Enge , Eric Bavier , Laurent Gatto , Ricardo Wurmus , Sharlatan Hellseher , Simon Tournier X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Laurent Gatto , Ricardo Wurmus , Sharlatan Hellseher , Simon Tournier Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324057918757 (code B ref 77287); Sat, 29 Mar 2025 09:30:07 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:39 +0000 Received: from localhost ([127.0.0.1]:56862 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVW-0004sQ-VZ for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:39 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44914) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV6-0004qJ-12 for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id BA0B6172; Sat, 29 Mar 2025 10:29:11 +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 6UWuLa0Svpzy; Sat, 29 Mar 2025 10:29:11 +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 B1A7DB2; Sat, 29 Mar 2025 10:29:09 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:31 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: BA0B6172 X-Spamd-Result: default: False [-6.45 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.85)[-0.951]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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 This replaces all inputs hdf5@1.10 by hdf5@1.14 unless explicitly specified otherwise. * gnu/packages/maths.scm (hdf5-1.14): Rename to... (hdf5): ...this, which was previously defined as hdf5-1.10. (hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names. (hdf-java)[inputs]: Keep hdf5-1.10. * gnu/packages/bioinformatics.scm (fast5, ncbi-vdb), gnu/packages/cran.scm (r-h5), gnu/packages/image.scm (vigra)[inputs]: Keep hdf5-1.10. Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485 --- gnu/packages/bioinformatics.scm | 4 ++-- gnu/packages/cran.scm | 2 +- gnu/packages/image.scm | 2 +- gnu/packages/maths.scm | 16 ++++++---------- 4 files changed, 10 insertions(+), 14 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8b585e495..8fd7789028 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7941,7 +7941,7 @@ (define-public fast5 (add-after 'unpack 'chdir (lambda _ (chdir "python")))))) - (inputs (list hdf5)) + (inputs (list hdf5-1.10)) (propagated-inputs (list python-dateutil)) (native-inputs @@ -11349,7 +11349,7 @@ (define-public ncbi-vdb (install-file "libs/kfg/default.kfg" target) (install-file "libs/kfg/certs.kfg" target))))))) (inputs - (list file hdf5 java-ngs libxml2 ngs-sdk )) + (list file hdf5-1.10 java-ngs libxml2 ngs-sdk )) (native-inputs (list perl)) ;; NCBI-VDB requires SSE capability. (supported-systems '("i686-linux" "x86_64-linux")) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 8522eb07a5..4e96d70849 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14934,7 +14934,7 @@ (define-public r-h5 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) (build-system r-build-system) (inputs - (list zlib hdf5)) + (list zlib hdf5-1.10)) (native-inputs (list r-knitr r-testthat which)) (propagated-inputs diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 89e7ef83e6..83b694b409 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -1389,7 +1389,7 @@ (define-public vigra `(("boost" ,boost) ("fftw" ,fftw) ("fftwf" ,fftwf) - ("hdf5" ,hdf5) + ("hdf5" ,hdf5-1.10) ("ilmbase" ,ilmbase) ; propagated by openexr, but needed explicitly ; to create a configure-flag ("libjpeg" ,libjpeg-turbo) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 017abecc00..f851937a7c 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1834,7 +1834,7 @@ (define-public hdf5-1.10 (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00")) (patches (search-patches "hdf5-config-date.patch")))))) -(define-public hdf5-1.14 +(define-public hdf5 (package (inherit hdf5-1.8) (version "1.14.3") @@ -1872,10 +1872,6 @@ (define-public hdf5-1.14 (("@UNAME_INFO@") "Linux")))))))))) -(define-public hdf5 - ;; Default version of HDF5. - hdf5-1.10) - ;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package @@ -1963,7 +1959,7 @@ (define-public hdf-java java-slf4j-simple)) (inputs (list hdf4 - hdf5 + hdf5-1.10 java-slf4j-api libjpeg-turbo zlib)) @@ -2041,7 +2037,7 @@ (define-public hdf-eos5 (list autoconf automake gfortran libtool)) (build-system gnu-build-system) (inputs - (list hdf5-1.14 zlib gctp)) + (list hdf5 zlib gctp)) (arguments (list #:configure-flags ''("--enable-install-include" "--enable-shared" @@ -2076,13 +2072,13 @@ (define-public hdf-eos5 (license (license:non-copyleft home-page)))) (define-public hdf5-parallel-openmpi - (package/inherit hdf5-1.14 ;use the latest + (package/inherit hdf5 (name "hdf5-parallel-openmpi") (inputs `(("mpi" ,openmpi) ,@(package-inputs hdf5))) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.14) + (substitute-keyword-arguments (package-arguments hdf5) ((#:configure-flags flags) #~(cons "--enable-parallel" (delete "--enable-cxx" @@ -10481,7 +10477,7 @@ (define-public scilab curl fftw gettext-minimal - hdf5-1.14 + hdf5 libarchive libx11 libxml2 From patchwork Sat Mar 29 09:21:32 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40953 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 4DA8627BBEA; Sat, 29 Mar 2025 09:32:37 +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=ham 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 0E4D627BBE2 for ; Sat, 29 Mar 2025 09:32:37 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySYJ-000331-LL; Sat, 29 Mar 2025 05:32:31 -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 1tySW2-0002Su-0N for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:17 -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 1tySW1-00070U-MB for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:09 -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=dFgx1C8cUF0ZNR41wXEICtVW6vsCiwkDsnBAHp2EwKY=; b=kMUkyxwXyn1MdPNCK2/fW3SJgijYL8Aykzu7XW/ZrLH4W+tjLNyjWPIRArs0zh5ccZhyAv0URyAo9MXuKC/tl9s3dXgbo5383kR11vlobSveOyywfeHZmR4A1RP0BujUywiqhjbo/lFV6mPmWsjRuzJQ/kWg/zyWiqmxhUHeHpcN4+mq5HxbMbnpYi/BMAuyvhURaHqG7ScnKkBq4cCcIg6KOylMYHy8qkeSl3PnXEbu4jl9xiCShQMitwe7NGKPv7v7xmdZjvMRUZkOaHx274GdIqbQfhgzNryJk/mZbJzoIUzKKQQBu7+hk/tL8pV9/4VB2lz8RCnrRv1WWpl1aw==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVz-0004uf-3F; Sat, 29 Mar 2025 05:30:07 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 8/8] gnu: hdf-java: Update to 1.14.3. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324057818747 (code B ref 77287); Sat, 29 Mar 2025 09:30:06 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:38 +0000 Received: from localhost ([127.0.0.1]:56860 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVW-0004sI-J5 for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:38 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44914) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV7-0004qJ-VI for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:14 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id B483B2F8; Sat, 29 Mar 2025 10:29:13 +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 wgXoKODOK5LE; Sat, 29 Mar 2025 10:29:13 +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 E5A52B2; Sat, 29 Mar 2025 10:29:11 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:32 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: B483B2F8 X-Spamd-Result: default: False [-6.47 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.87)[-0.956]; 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]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(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/maths.scm (hdf-java): Update to 1.14.3. [inputs]: Remove hdf5-1.10; add hdf5. Change-Id: I43db316c3a83f5ddac14b0c670430811dcac6bdc --- gnu/packages/maths.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f851937a7c..c9a00c4b94 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1876,7 +1876,7 @@ (define-public hdf5 (define-public hdf-java (package (name "hdf-java") - (version "1.10.9") + (version "1.14.3") (source (origin (method git-fetch) @@ -1888,7 +1888,7 @@ (define-public hdf-java version))))) (file-name (git-file-name name version)) (sha256 - (base32 "1sjdcnafvzsy99vqhybkps8rnwmxb6fsvmkw89wb2mrrp4vi5z9v")) + (base32 "0lw9f62zxyjiv7vx9nvnashjj39i44j8d626i7b788zkxw58csvs")) (modules '((guix build utils))) (snippet ; Make sure we don't use the bundled sources and binaries. '(for-each delete-file @@ -1959,7 +1959,7 @@ (define-public hdf-java java-slf4j-simple)) (inputs (list hdf4 - hdf5-1.10 + hdf5 java-slf4j-api libjpeg-turbo zlib))