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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f2c2b0f80asm11563896d6.45.2025.04.18.08.14.42 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 18 Apr 2025 08:14:42 -0700 (PDT) From: Greg Hogan Date: Fri, 18 Apr 2025 15:14:09 +0000 Message-ID: <0199e4a26c0ac3f0c07c9e80963f4562f49544e3.1744988258.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 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 (%suitesparse-package-versions): New variable. (suitesparse-version): Update to 7.10.2. (suitesparse-source)[origin]: Update deletion list. (suitesparse-amd, suitesparse-btf, suitesparse-camd, suitesparse-colamd, suitesparse-ccolamd, suitesparse-cholmod, suitesparse-cxsparse, suitesparse-klu, suitesparse-ldl, suitesparse-rbio, suitesparse-monUse goose, suitesparse-spex, suitesparse-spqr, suitesparse-umfpack) [version]: Use %suitesparse-package-versions. (suitesparse-cholmod)[arguments]<#:phases>('install-license-files): Update paths. (suitesparse-klu)[arguments]<#:phases>('build-doc): Update paths. (suitesparse-spex)[native-inputs]: Add texlive-fncychap. (suitesparse-spqr)[native-inputs]: Add texlive-etoolbox. * gnu/packages/patches/gklib-suitesparse.patch: Update version and path. Change-Id: I14a9bfeddb37330c88a2e94b0992c2f1afbc5310 --- gnu/packages/maths.scm | 64 ++++++++++++-------- gnu/packages/patches/gklib-suitesparse.patch | 6 +- 2 files changed, 42 insertions(+), 28 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 4be9e71320..4cfcd5ba9e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6060,9 +6060,25 @@ (define-public openspecfun ;; public domain software. (license (list license:expat license:public-domain)))) +(define %suitesparse-package-versions + '(("AMD" . "3.3.3") + ("BTF" . "2.3.2") + ("CAMD" . "3.3.3") + ("CCOLAMD" . "3.3.4") + ("CHOLMOD" . "5.3.2") + ("COLAMD" . "3.3.4") + ("CXSparse" . "4.4.1") + ("KLU" . "2.3.5") + ("LDL" . "3.3.2") + ("SuiteSparse_Mongoose" . "3.3.4") + ("RBio" . "4.3.4") + ("SPEX" . "3.2.3") + ("SPQR" . "4.3.4") + ("UMFPACK" . "6.3.5"))) + ;; Source for the modular SuiteSparse packages. When updating, also update the ;; (different) versions of the subpackages. -(define suitesparse-version "7.2.0") +(define suitesparse-version "7.10.2") (define suitesparse-source (origin (method git-fetch) @@ -6072,10 +6088,12 @@ (define suitesparse-source (file-name (git-file-name "suitesparse" suitesparse-version)) (sha256 (base32 - "1draljn8i46862drc6008cnb2zjpklf74j8c34jirjazzpf53kaa")) + "1ndwx2cp5zxrikq4xdrzjrxk1b5ps7lyi6qw34m8jpfpa0ba01ln")) (modules '((guix build utils))) (snippet #~(begin + ;; Empty except for a .gitignore. + (delete-file-recursively "build") ;; Delete autogenerated and bundled files (for-each delete-file (find-files "." "\\.pdf$")) ;; ssget @@ -6086,19 +6104,13 @@ (define suitesparse-source (delete-file-recursively "CHOLMOD/SuiteSparse_metis") ; GraphBLAS (delete-file "GraphBLAS/README.md") - (delete-file "GraphBLAS/Config/GB_config.h") (delete-file "GraphBLAS/Config/GB_prejit.c") (delete-file-recursively "GraphBLAS/cpu_features") - (delete-file "GraphBLAS/CUDA/GB_cuda_common_jitFactory.hpp") - (delete-file "GraphBLAS/JITpackage/GB_JITpackage.c") (delete-file-recursively "GraphBLAS/lz4/lz4.c") (delete-file-recursively "GraphBLAS/lz4/lz4.h") (delete-file-recursively "GraphBLAS/lz4/lz4hc.c") (delete-file-recursively "GraphBLAS/lz4/lz4hc.h") - (delete-file "GraphBLAS/GraphBLAS/Config/GB_config.h") (delete-file "GraphBLAS/Tcov/PreJIT/GB_prejit.c") - (delete-file-recursively "GraphBLAS/Source/FactoryKernels") - (delete-file "GraphBLAS/Source/GB_AxB__include1.h") (delete-file "GraphBLAS/xxHash/xxhash.h") (delete-file-recursively "GraphBLAS/zstd/zstd_subset") ;; KLU @@ -6144,7 +6156,7 @@ (define-public suitesparse-config (define-public suitesparse-amd (package (name "suitesparse-amd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "AMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6192,7 +6204,7 @@ (define-public suitesparse-amd (define-public suitesparse-btf (package (name "suitesparse-btf") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "BTF")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6225,7 +6237,7 @@ (define-public suitesparse-btf (define-public suitesparse-camd (package (name "suitesparse-camd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "CAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6270,7 +6282,7 @@ (define-public suitesparse-camd (define-public suitesparse-colamd (package (name "suitesparse-colamd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "COLAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6303,7 +6315,7 @@ (define-public suitesparse-colamd (define-public suitesparse-ccolamd (package (name "suitesparse-ccolamd") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "CCOLAMD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6386,7 +6398,7 @@ (define-public metis-suitesparse (define-public suitesparse-cholmod (package (name "suitesparse-cholmod") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "CHOLMOD")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6448,7 +6460,7 @@ (define-public suitesparse-cholmod (let ((out (string-append #$output "/share/doc/" #$name "-" #$version))) (install-file "../CHOLMOD/Doc/License.txt" out) - (install-file "../CHOLMOD/Core/lesser.txt" out) + (install-file "../CHOLMOD/Check/lesser.txt" out) (install-file "../CHOLMOD/MatrixOps/gpl.txt" out))))))) (inputs (list gklib-suitesparse @@ -6471,7 +6483,7 @@ (define-public suitesparse-cholmod (define-public suitesparse-cxsparse (package (name "suitesparse-cxsparse") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "CXSparse")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6505,7 +6517,7 @@ (define-public suitesparse-cxsparse (define-public suitesparse-klu (package (name "suitesparse-klu") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "KLU")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6537,7 +6549,7 @@ (define-public suitesparse-klu (lambda _ (substitute* "../KLU/Doc/Makefile" (("\\.\\./\\.\\./BTF/Include/btf.h") - (string-append #$suitesparse-btf "/include/btf.h"))) + (string-append #$suitesparse-btf "/include/suitesparse/btf.h"))) (with-directory-excursion "../KLU/Doc" (invoke "make")))) (add-after 'install 'install-doc @@ -6569,7 +6581,7 @@ (define-public suitesparse-klu (define-public suitesparse-ldl (package (name "suitesparse-ldl") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "LDL")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6622,7 +6634,7 @@ (define-public suitesparse-ldl (define-public suitesparse-rbio (package (name "suitesparse-rbio") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "RBio")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6660,7 +6672,7 @@ (define-public suitesparse-rbio (define-public suitesparse-mongoose (package (name "suitesparse-mongoose") - (version "3.2.0") + (version (assoc-ref %suitesparse-package-versions "SuiteSparse_Mongoose")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6735,7 +6747,7 @@ (define-public suitesparse-mongoose (define-public suitesparse-spex (package (name "suitesparse-spex") - (version "2.2.0") + (version (assoc-ref %suitesparse-package-versions "SPEX")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6778,6 +6790,7 @@ (define-public suitesparse-spex texlive-soul texlive-multirow texlive-algorithms + texlive-fncychap texlive-float texlive-algorithmicx texlive-cprotect @@ -6801,7 +6814,7 @@ (define-public suitesparse-spex (define-public suitesparse-spqr (package (name "suitesparse-spqr") - (version "4.2.0") + (version (assoc-ref %suitesparse-package-versions "SPQR")) (source suitesparse-source) (build-system cmake-build-system) (arguments @@ -6851,7 +6864,8 @@ (define-public suitesparse-spqr (propagated-inputs (list suitesparse-cholmod)) (native-inputs (list (texlive-updmap.cfg - (list texlive-epsf)))) + (list texlive-epsf + texlive-etoolbox)))) (home-page "https://people.engr.tamu.edu/davis/suitesparse.html") (synopsis "Sparse QR factorization method") (description "The SPQR (SuiteSparseQR) package provides sparse QR @@ -6862,7 +6876,7 @@ (define-public suitesparse-spqr (define-public suitesparse-umfpack (package (name "suitesparse-umfpack") - (version "6.2.0") + (version (assoc-ref %suitesparse-package-versions "UMFPACK")) (source suitesparse-source) (build-system cmake-build-system) (arguments diff --git a/gnu/packages/patches/gklib-suitesparse.patch b/gnu/packages/patches/gklib-suitesparse.patch index 8b6c708b6a..d207f080b1 100644 --- a/gnu/packages/patches/gklib-suitesparse.patch +++ b/gnu/packages/patches/gklib-suitesparse.patch @@ -1,5 +1,5 @@ This patch contains the relevant changes to GKlib made in SuiteSparse -(CHOLMOD) for the version 7.2.0 +(CHOLMOD) for the version 7.10.2 (https://github.com/DrTimothyAldenDavis/SuiteSparse/commit/8a7641cdb4809533c681417e94f98058c07c5da2). The disabling of signal handling when MATLAB_MEX_FILE is defined is omitted. @@ -10,7 +10,7 @@ diff -ur a/CMakeLists.txt b/CMakeLists.txt option(BUILD_SHARED_LIBS "Build shared libraries (.dll/.so) instead of static ones (.lib/.a)" OFF) -+find_package ( SuiteSparse_config 7.1.0 REQUIRED ) ++find_package ( SuiteSparse_config 7.10.2 REQUIRED ) + get_filename_component(abs "." ABSOLUTE) set(GKLIB_PATH ${abs}) @@ -25,7 +25,7 @@ diff -ur a/GKlib.h b/GKlib.h +/* -------------------------------------------------------------------------- */ +/* Added for incorporation into SuiteSparse. + Tim Davis, Oct 31, 2022, Texas A&M University. */ -+#include "SuiteSparse_config.h" ++#include "suitesparse/SuiteSparse_config.h" +#define malloc SuiteSparse_config_malloc +#define calloc SuiteSparse_config_calloc +#define realloc SuiteSparse_config_realloc From patchwork Fri Apr 18 15:14:10 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Greg Hogan X-Patchwork-Id: 41770 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 4DF5227BC4A; Fri, 18 Apr 2025 16:16:57 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-6.4 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,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 843DE27BC49 for ; Fri, 18 Apr 2025 16:16:56 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u5nSM-0005vG-8a; Fri, 18 Apr 2025 11:16:43 -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 1u5nRm-0005qM-Dg for guix-patches@gnu.org; Fri, 18 Apr 2025 11:16:08 -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 1u5nRm-0005wx-3A for guix-patches@gnu.org; Fri, 18 Apr 2025 11:16:06 -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=j48hDdxDEJk1ah0EPJXxOtAXU2VoTCbr49Jf+bt65LI=; b=DWFIWW2Vi1VasVCeIi4i7cQHFpqcWToNTEoHn33IchL4OqzbfLvI5DshUY97SzvtPxRTmNm5hFo7h7hMf2PtzCr4lY3Qq98Ri138Cxu3bGOP6a3EhF/6BB4lg1VfwDD5CgoRwaPg31Xf7RzFPALDKYcfRr6P9YmHx0PZd3XpxguRW2lxA7+cbP97kVi5oA+AINsZpEV40Un65bniKyjmpqigLhuDDimjcu9Oo3s77yKwMkHNDcuYRs5GGgx9ZhQku0W9C+4cN8OJLos28zDff0qXmxh/MF4StjIPMT8Iy+/OyrjXv2+yARYX62FDQBaFItJC+VP/ML1Kwb5WkWcSow==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u5nRl-0001vG-QT for guix-patches@gnu.org; Fri, 18 Apr 2025 11:16:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77902] [PATCH science-team 2/2] gnu: igraph: Update to 0.10.15. 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[52.70.167.183]) by smtp.gmail.com with ESMTPSA id 6a1803df08f44-6f2c2b0f80asm11563896d6.45.2025.04.18.08.14.43 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 18 Apr 2025 08:14:43 -0700 (PDT) From: Greg Hogan Date: Fri, 18 Apr 2025 15:14:10 +0000 Message-ID: <4765db19bd76943e2303a04eae2f77f2a43b445b.1744988258.git.code@greghogan.com> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 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/graph.scm (igraph): Update to 0.10.15. [source]: Remove patches. [inputs]: Replace suitesparse-cxsparse with suitesparse. * gnu/packages/patches/igraph-fix-varargs-integer-size.patch: Delete. * gnu/local.mk (dist_patch_DATA): Update accordingly. Change-Id: Iffbfdc83b347f9abf82891f5b97954903d3df3dd --- gnu/local.mk | 1 - gnu/packages/graph.scm | 7 ++-- .../igraph-fix-varargs-integer-size.patch | 39 ------------------- 3 files changed, 3 insertions(+), 44 deletions(-) delete mode 100644 gnu/packages/patches/igraph-fix-varargs-integer-size.patch diff --git a/gnu/local.mk b/gnu/local.mk index 62cfe230bb..2828d8913f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1610,7 +1610,6 @@ dist_patch_DATA = \ %D%/packages/patches/id3lib-CVE-2007-4460.patch \ %D%/packages/patches/id3lib-UTF16-writing-bug.patch \ %D%/packages/patches/idris-test-ffi008.patch \ - %D%/packages/patches/igraph-fix-varargs-integer-size.patch \ %D%/packages/patches/ilmbase-fix-tests.patch \ %D%/packages/patches/indent-CVE-2024-0911.patch \ %D%/packages/patches/inferno-fix-crash.patch \ diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index 467a7f661b..af4943c281 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -106,7 +106,7 @@ (define-public plfit (define-public igraph (package (name "igraph") - (version "0.10.7") + (version "0.10.15") (source (origin (method git-fetch) @@ -114,7 +114,6 @@ (define-public igraph (url "https://github.com/igraph/igraph") (commit version))) (file-name (git-file-name name version)) - (patches (search-patches "igraph-fix-varargs-integer-size.patch")) (modules '((guix build utils) (ice-9 ftw) (srfi srfi-26))) @@ -136,7 +135,7 @@ (define-public igraph (("add_sub.*vendor.*") "")))) (sha256 (base32 - "025f9c2jsawniqkig4l5z3v9aw3ipazmnlsf80b653mns5bvj1yn")))) + "0z9jqvl65j4z6brrjlfyykba2bs10az6dx6m8g41snlfnx21a82d")))) (build-system cmake-build-system) (arguments (list @@ -201,7 +200,7 @@ (define-public igraph ;lapack openblas plfit - suitesparse-cxsparse)) + suitesparse)) ;; libxml2 is in the 'Requires.private' of igraph.pc. (propagated-inputs (list libxml2)) (home-page "https://igraph.org") diff --git a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch b/gnu/packages/patches/igraph-fix-varargs-integer-size.patch deleted file mode 100644 index 2d7ffd7e68..0000000000 --- a/gnu/packages/patches/igraph-fix-varargs-integer-size.patch +++ /dev/null @@ -1,39 +0,0 @@ -If the size of int is different from IGRAPH_INTEGER_SIZE, the integer size -passed to these vararg arguments is different from the assumed one, -leading to undefined behavior. -Submitted upstream: https://github.com/igraph/igraph/pull/2423 - - -diff -ur a/examples/simple/igraph_union.c b/examples/simple/igraph_union.c ---- a/examples/simple/igraph_union.c -+++ b/examples/simple/igraph_union.c -@@ -103,7 +103,7 @@ - igraph_vector_ptr_init(&glist, 10); - for (i = 0; i < igraph_vector_ptr_size(&glist); i++) { - VECTOR(glist)[i] = calloc(1, sizeof(igraph_t)); -- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1); -+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1); - igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_DIRECTED); - igraph_vector_int_destroy(&v); - } -@@ -123,7 +123,7 @@ - igraph_vector_ptr_init(&glist, 10); - for (i = 0; i < igraph_vector_ptr_size(&glist); i++) { - VECTOR(glist)[i] = calloc(1, sizeof(igraph_t)); -- igraph_vector_int_init_int_end(&v, -1, i, i + 1, 1, 0, -1); -+ igraph_vector_int_init_int_end(&v, -1, (int) i, (int) i + 1, 1, 0, -1); - igraph_create(VECTOR(glist)[i], &v, 0, IGRAPH_UNDIRECTED); - igraph_vector_int_destroy(&v); - } -diff -ur a/src/core/matrix.pmt b/src/core/matrix.pmt ---- a/src/core/matrix.pmt -+++ b/src/core/matrix.pmt -@@ -1863,7 +1863,7 @@ - #ifdef FPRINTFUNC_ALIGNED - FPRINTFUNC_ALIGNED(file, VECTOR(column_width)[j], MATRIX(*m, i, j)); - #else -- fprintf(file, format, VECTOR(column_width)[j], MATRIX(*m, i, j)); -+ fprintf(file, format, (int) VECTOR(column_width)[j], MATRIX(*m, i, j)); - #endif - } - fprintf(file, "\n");