From patchwork Sun Apr 6 23:26:40 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41382 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 1151B27BC4A; Mon, 7 Apr 2025 00:28:47 +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=-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 AAE5527BC49 for ; Mon, 7 Apr 2025 00:28:45 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u1ZPk-0000BL-LD; Sun, 06 Apr 2025 19:28:32 -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 1u1ZPH-0008Ub-6M for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:04 -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 1u1ZPG-00034t-Rt for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:02 -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=PkodX/EahN0PCcvOLrxxFwQi87meOCzt63DZP1NmI7o=; b=Mm2g8/7q/kpkT5d6xxv0EuCcLkmYeceHCM+pTOpPL9L2ZLPUYy8SiJAi0L1Nyz68yzqfAoSq/8dLTCW7m2cWf2mE2cJS7DlUAZztE61lu+e8mHVtaCED/bhPwcS9fP0ceg1Vwfl8YZZhNW7IyniwVV7hCCWhJKL5G0eAstqJy/K9ucBg3bEAgtY3bOPyBtReAx52yd1UhgCwxiXUeKi1KMEDwaNU/UMjl7qaeWumaCg5DlbL1kTs9VEp/GSmVrJAnf2+i9meMLCAx7Pr4yBgb6IkydQ6yLcOjwhBfBebg7aB9d0UoOWJXbWR+TeQAZPdsVKuW82Nsg9xSzn6LC45lQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u1ZPG-00050E-Kg for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH 1/3] gnu: hdf5: Update to 1.14.6. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Apr 2025 23:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77590 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77590@debbugs.gnu.org Cc: David Elsing Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174398204219080 (code B ref 77590); Sun, 06 Apr 2025 23:28:02 +0000 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:22 +0000 Received: from localhost ([127.0.0.1]:50116 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOS-0004x5-L4 for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:22 -0400 Received: from mout02.posteo.de ([185.67.36.66]:54461) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZOM-0004vi-HX for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 9FE08240101 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:26:59 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982019; bh=m6H3bWVoTlmByrJHGI2I9w2KbrNgyQeWhtq8NJFAvY8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=R9cidCSEv0qKnQ8eA1txhT22fk6NHnwYMWAxp9BiTOxut0J4LVKta8VZmUXZIrlP9 kIFJHIFRpVsWo5uHu72AniNUGHA6rWcpWowo1GfCdJILXxowZM6oiCzfPAqjVcI43w hyp91KFI+IovesDRmNUFmfpLhu7aVrub1ZpV9e02kwiD2+bqIfHxYiXzQubNe+4wi4 Qs9Uvao4YP75k+N3XLSTtV6nkRBR6qJdJEegMc31iFaPza8U8ZCe6KZ6x7nBDrgt5i 02MBY++C0e1lf24oFEzPh7E+5UtR938AekmgtTgqwA5AO7moaQUUQHNeHg8GzUcy91 cRaU8VdZH9bLA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lk4Xb5z6tlh; Mon, 7 Apr 2025 01:26:58 +0200 (CEST) From: David Elsing Date: Sun, 6 Apr 2025 23:26:40 +0000 Message-ID: <6baf0e901a9e8e4e6c784957cf92270e6e085149.1743980993.git.david.elsing@posteo.net> 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 (hdf5): Update to 1.14.6. Do not inherit from hdf5-1.8. [source]: Switch to git-fetch. Add modules field and snippet. [outputs]: Remove field. [arguments]<#:phases>: Use gexps. Add 'hide-gfortran, 'make-gen-deterministic, 'generate-flexbison, 'patch-trace-shebang, 'patch-configure.ac, 'fix-fortran-i686-test, 'generate-headers, and 'remove-subfiling-cppflags phases. Adjust 'patch-configure, 'patch-settings and 'patch-references phases. Remove 'split phase. [license]: Adjust URL. --- gnu/packages/maths.scm | 208 ++++++++++++++++++++++++++++++++++------- 1 file changed, 176 insertions(+), 32 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6910b32dae..e8258b681d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -62,7 +62,7 @@ ;;; Copyright © 2022 Roman Scherer ;;; Copyright © 2023 Jake Leporte ;;; Copyright © 2023 Camilo Q.S. (Distopico) -;;; Copyright © 2023 David Elsing +;;; Copyright © 2023, 2025 David Elsing ;;; Copyright © 2024 Herman Rimm ;;; Copyright © 2024 Foundation Devices, Inc. ;;; Copyright © 2024, 2025 Artyom V. Poptsov @@ -1837,41 +1837,185 @@ (define-public hdf5-1.10 ;; When updating this package, please also update hdf-java. (define-public hdf5 (package - (inherit hdf5-1.8) - (version "1.14.3") + (name "hdf5") + (version "1.14.6") (source (origin - (method url-fetch) - (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" - "hdf5-" (version-major+minor version) - "/hdf5-" version "/src/hdf5-" - version ".tar.bz2") - (string-append "https://support.hdfgroup.org/ftp/HDF5/" - "current" - (apply string-append - (take (string-split version #\.) 2)) - "/src/hdf5-" version ".tar.bz2"))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/HDFGroup/hdf5") + (commit (string-append "hdf5_" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "05zr11y3bivfwrbvzbky1q2gjf6r7n92cvvdnh5jilbmxljg49cl")) - (patches (search-patches "hdf5-config-date.patch")))) + (base32 + "1f7yv0xra465c3qy8c79fzddib653wzj5dsakb0bs02nwp3xm54q")) + (patches (search-patches "hdf5-config-date.patch")) + (modules '((guix build utils))) + (snippet + '(for-each + delete-file + (append + (find-files "." "Makefile\\.in$") + (find-files "java/lib" "\\.jar$") + (list "aclocal.m4" + "bin/compile" + "bin/config.guess" + "bin/config.sub" + "bin/depcomp" + "bin/install-sh" + "bin/ltmain.sh" + "bin/missing" + "bin/test-driver" + "configure" + "HDF5Examples/aclocal.m4" + "HDF5Examples/compile" + "HDF5Examples/configure" + "HDF5Examples/depcomp" + "HDF5Examples/missing" + "HDF5Examples/test-driver" + "hl/src/H5LTanalyze.c" + "hl/src/H5LTparse.c" + "hl/src/H5LTparse.h" + "hl/tools/gif2h5/testfiles/ex_image2.h5" + "hl/tools/gif2h5/testfiles/h52giftst.h5" + "m4/ax_prog_doxygen.m4" + "m4/libtool.m4" + "m4/lt~obsolete.m4" + "m4/ltoptions.m4" + "m4/ltsugar.m4" + "m4/ltversion.m4" + "src/H5config.h.in" + "src/H5Edefin.h" + "src/H5Einit.h" + "src/H5Epubgen.h" + "src/H5Eterm.h" + "src/H5overflow.h" + "src/H5version.h")))))) + (build-system gnu-build-system) + (inputs + (list zlib)) + (native-inputs + (list autoconf-2.71 + autoconf-archive + automake + bison + flex + gfortran + libtool + ;; Needed to generate some headers and for tests + perl + which)) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.8) - ((#:phases phases #~%standard-phases) - #~(modify-phases #$phases - (add-after 'configure 'skip-version-test - (lambda _ - ;; Skip test_check_version since the 'patch-settings' phase - ;; modifies the test reference. - (substitute* "test/test_check_version.sh.in" - (("TESTING\\(\\).*" all) - (string-append all "\nSKIP; exit 0\n"))))) - (add-after 'patch-configure 'patch-configure-build-settings - (lambda _ - (substitute* "src/H5build_settings.autotools.c.in" - ;; Don't record the build-time kernel version to make the - ;; library file reproducible. - (("@UNAME_INFO@") - "Linux")))))))))) + (list + ;; Some of the users, notably Flann, need the C++ interface. + #:configure-flags + ''("--enable-cxx" + "--enable-fortran" + "--enable-fortran2003" + + ;; Build a thread-safe library. Unfortunately, + ;; 'configure' invites you to either turn off C++, + ;; Fortran, and the high-level interface (HL), or + ;; to pass '--enable-unsupported'. Debian + ;; packagers chose to pass '--enable-unsupported' + ;; and we follow their lead here. + "--enable-threadsafe" + "--with-pthread" + "--enable-unsupported") + ;; Use -fPIC to allow the R bindings to link with the static libraries + #:make-flags ''("CFLAGS=-fPIC" "CXXFLAGS=-fPIC") + #:phases + #~(modify-phases %standard-phases + ;; XXX: src/H5private.h includes and fails to find the + ;; stdlib types when the gfortran header is used. Remove gfortran + ;; from CPLUS_INCLUDE_PATH as a workaround. + (add-after 'set-paths 'hide-gfortran + (lambda _ + (let ((gfortran #$(this-package-native-input "gfortran"))) + (setenv "CPLUS_INCLUDE_PATH" + (string-join + (delete (string-append gfortran "/include/c++") + (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) + ":"))))) + (add-after 'unpack 'make-gen-deterministic + (lambda _ + (substitute* "bin/make_err" + (("keys %major" all) + (string-append "sort " all)) + (("while.*each \\(%section\\).*") + (string-append + "foreach $sect_name (sort keys %section) {\n" + " $sect_desc = $section{$sect_name};\n"))))) + (add-after 'unpack 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src"))) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each patch-shebang + (find-files "bin" (lambda (file stat) + (executable-file? file)))))) + ;; Fixes build on i686, see + ;; https://github.com/HDFGroup/hdf5/commit/0af668f4091f1c35f621d2acdeadd34db6756976 + (add-after 'unpack 'patch-configure.ac + (lambda _ + (substitute* "configure.ac" + (("AC_DEFINE.*HAVE_FLOAT128.*" orig) + (string-append orig "\nAC_CHECK_SIZEOF([__float128])\n"))))) + ;; This is a known issue on i686, see + ;; https://github.com/HDFGroup/hdf5/issues/4926 + (add-after 'unpack 'fix-fortran-i686-test + (lambda _ + (substitute* "fortran/test/tH5R.F90" + (((string-append + "CALL h5rget_obj_name_f\\(C_LOC\\(ref_ptr\\(2\\)\\)," + " \"\", error, name_len=buf_size \\)")) + (string-append + "CALL h5rget_obj_name_f(C_LOC(ref_ptr(2))," + " \"xxxxxxxxxxxxxx\", error, name_len=buf_size)"))))) + (add-before 'configure 'patch-configure + (lambda _ + (substitute* "configure" + (("/bin/mv") "mv")))) + (add-after 'configure 'patch-settings + (lambda _ + ;; libhdf5.settings contains the full path of the compilers + ;; used, and its contents are included in libhdf5.so. We + ;; truncate the hashes to avoid unnecessary store references to + ;; those compilers: + (substitute* '("src/H5build_settings.c" + "src/libhdf5.settings") + (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash) + (string-append prefix (string-take hash 10) "...")) + ;; Don't record the build-time kernel version to make the + ;; settings file reproducible. + (("Uname information:[^\"\n\\\\]*") + "Uname information: Linux")))) + (add-after 'configure 'generate-headers + (lambda _ + (invoke "perl" "bin/make_err" "src/H5err.txt") + (invoke "perl" "bin/make_vers" "src/H5vers.txt") + (invoke "perl" "bin/make_overflow" "src/H5overflow.txt"))) + ;; Remove include flag to directory in source tree + (add-after 'configure 'remove-subfiling-cppflags + (lambda _ + (substitute* '("src/H5build_settings.c" + "src/libhdf5.settings" + "bin/h5cc" + "c++/src/h5c++") + (("-I.*/src/H5FDsubfiling") "")))) + (add-after 'install 'patch-references + (lambda _ + (let ((bin (string-append #$output "/bin")) + (zlib #$(this-package-input "zlib"))) + (substitute* (find-files bin "h5p?cc") + (("-lz" lib) + (string-append "-L" zlib "/lib " lib))))))))) + (home-page "https://www.hdfgroup.org") + (synopsis "Management suite for extremely large and complex data") + (description "HDF5 is a suite that makes possible the management of +extremely large and complex data collections.") + (license (license:x11-style + "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html")))) ;; Keep this in sync with the current hdf5 package. (define-public hdf-java From patchwork Sun Apr 6 23:26:41 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41381 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 2304027BC4B; Mon, 7 Apr 2025 00:28:33 +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=-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 831A527BC49 for ; Mon, 7 Apr 2025 00:28:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u1ZPg-000080-1k; Sun, 06 Apr 2025 19:28:29 -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 1u1ZPH-0008Ua-1f for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:04 -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 1u1ZPG-00034m-8l for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:02 -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=wBx5/WqGnZf//FLDHoBvk2IKUwvpet/BmVDyz7b+ldo=; b=vVFHqJfrURMzCwxD4v327pWcj3srYPWiuajDc3bU7Sl84FwTYDz0uj2/QzaUecO6ucxOUdtog4XJKsmDi64tEEoRbjQJ74Ow+w6EOA5Hj3dBBIPhogxluTWTN9Z4EFPqHSR0vRDUz6p4N11XQ5VyXQjdC6NWU7YLei+Y8hoVxlenOkedXbN5Tj3YSS4BiPix1dRtK0ygeWa3Y14w66zaBxKHge0DYMi0N0nG0RtrxXofFMVFU+Qi50s0vwbFFmc9aFnMlbgWdjxAnZ2NDCzz5P8O4i5xQKP1hPSupe/cahBZ3PMmk9C4zfiBt36IkkyIJsghURkiciB/Xwp6UuydcA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u1ZPG-000505-2G for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH 2/3] gnu: Add hdf5-examples. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Apr 2025 23:28:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77590 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77590@debbugs.gnu.org Cc: David Elsing Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174398203019028 (code B ref 77590); Sun, 06 Apr 2025 23:28:01 +0000 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:10 +0000 Received: from localhost ([127.0.0.1]:50114 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOQ-0004wo-81 for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:10 -0400 Received: from mout01.posteo.de ([185.67.36.65]:41079) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZON-0004w8-Tx for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:08 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 91AF2240027 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:27:01 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982021; bh=nCgZpNIjZYCbIK+u2qHUP6M4Fz9ILIvVx4SakpO48V8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=BcEpeA+oqwDjtsvzkousoP/ZqARlIM1LCPAGk/lO2ilKhQgGRL5qxTez4u4C+FMij YRLB6umdVWgWRzpz2mnpw4TB+yHknDWiSKPRVfjedQuleleTgOQa8Y3ScIh23l6PeA l3EUP0Lh0d7eKXGUlDRfQB8T19YjA5q+DSuRxXE/oe7xfzVcji+xbFe4U5eZYi4LRz peAmDW9YSK0pBAXc3KnAKGJjhbqIP5tQ+dgdYLiXhjG7URhrxz2kGVU12Z71zuzLiy A1vcZhD1XaB/XArbZ0SCInjIMRYAcAeGKAQetMsy4s7wvboIbyuN1jRragTCU8xXtb 1J5LxIEM7GcpA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lm5HV5z6tlh; Mon, 7 Apr 2025 01:27:00 +0200 (CEST) From: David Elsing Date: Sun, 6 Apr 2025 23:26:41 +0000 Message-ID: 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 (hdf5-examples): New variable. --- gnu/packages/maths.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e8258b681d..15e4ae6c86 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2017,6 +2017,20 @@ (define-public hdf5 (license (license:x11-style "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html")))) +;; This package builds and tests the examples, but has empty output. +(define-public hdf5-examples + (package/inherit hdf5 + (name "hdf5-examples") + (arguments + (substitute-keyword-arguments (package-arguments hdf5) + ((#:phases _ #f) + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "HDF5Examples"))))))) + (inputs (list hdf5 zlib)) + (native-inputs (list autoconf-2.71 automake gfortran)))) + ;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package From patchwork Sun Apr 6 23:26:42 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41383 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 5B23A27BC4B; Mon, 7 Apr 2025 00:28:48 +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 A4ACF27BC49 for ; Mon, 7 Apr 2025 00:28:47 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u1ZPl-0000EZ-Rg; Sun, 06 Apr 2025 19:28:33 -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 1u1ZPH-0008Uc-Kx for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:04 -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 1u1ZPH-000353-C6 for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:03 -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=/u0i8uaotw0BjQ5r3ns0pq5FZfTGB5KWkfgqUCBxq5I=; b=mdxuLRH7Yeg3QGve3P73gOjqSz4MjL1UB7p84Mf66CraE54HA4g32SvOk8oMLbI++O8CuteoYk6flvA766m1pEoOgttgCgMMI5VnH0LxAJmSS1BrRmqIZdHo3f6Ljt50uuuXMnBldg3wz0gaT8XdrFQYYiknYz37nN0Rg8ct6TqGD2e4LF5k3HLbR90ddubBWaeeLhyx9+rHhx4s/vUq2xHAL/fWdkcq+GNox4Jr100Wz4eWbjnuMYQ8SXatPBcQEoKWlheP1O29/q+C+YgRihblJjgY5N0J7n4GF96/IXmsAjkm/ivkQCCXd9sLzhXO21N8OSer0fQGoOVxnExEOg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u1ZPH-00050O-5n for guix-patches@gnu.org; Sun, 06 Apr 2025 19:28:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH 3/3] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 06 Apr 2025 23:28:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77590 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77590@debbugs.gnu.org Cc: David Elsing Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174398204319088 (code B ref 77590); Sun, 06 Apr 2025 23:28:03 +0000 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:23 +0000 Received: from localhost ([127.0.0.1]:50118 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOc-0004xl-Hv for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:23 -0400 Received: from mout01.posteo.de ([185.67.36.65]:36241) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZOP-0004wB-00 for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id A3A64240027 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:27:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982022; bh=O+FFWU1AyPT98cyPgtQdEmcP+b4+wBOQaUQR9VSXpqM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=I888tmwHPm3ZkVeO94T20UT18cRQp+/sMR4MBW3tyaGC4/c+RFB7fSnyPh3tnlKZp Bl0tcUu8PgpWLP1/HDlf0XWGPuZElc7hjQpDfN/7n3FTcvfBMILqQVcJ2244uFYl/M H6jKcf0JsDPJIxfUNKsxvqRP0byAvXmVKTp5HjiX/UxVsx0170q8tG35optoFTrKaQ s+NVz7fGTSz77dAIo7oNmoYy099lheusQp2Dynisg16JUgPEYzcP3BOSYOudMy+toh V6uXDgtvuKMaZjgYrYpS5XJPUEW0Wa5Djkd8t13UB4ohbDM6kuaegtDesGhxhxJlE8 IigKcjaLi56sQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lp2Hdvz6tlh; Mon, 7 Apr 2025 01:27:02 +0200 (CEST) From: David Elsing Date: Sun, 6 Apr 2025 23:26:42 +0000 Message-ID: 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 (hdf-java): Update to 1.14.6. [name]: Rename to hdf5-java. [version]: Use the same as hdf5. [source]: Use the same as hdf5. [arguments]: Adjust 'unbundle phase. Add 'patch-trace-shebang and 'generate-flexbison phases. [native-inputs]: Use modify-inputs. [inputs]: Remove hdf4 and hdf5. [synopsis, description]: Remove mention of HDF4. [license]: Use the same as hdf5. --- gnu/packages/maths.scm | 75 +++++++++++++++++------------------------- 1 file changed, 30 insertions(+), 45 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 15e4ae6c86..251d1d8481 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2031,27 +2031,11 @@ (define-public hdf5-examples (inputs (list hdf5 zlib)) (native-inputs (list autoconf-2.71 automake gfortran)))) -;; Keep this in sync with the current hdf5 package. -(define-public hdf-java +(define-public hdf5-java (package - (name "hdf-java") - (version "1.14.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/HDFGroup/hdf5") - (commit (string-append "hdf5-" - (string-map - (lambda (c) (if (char=? c #\.) #\_ c)) - version))))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0lw9f62zxyjiv7vx9nvnashjj39i44j8d626i7b788zkxw58csvs")) - (modules '((guix build utils))) - (snippet ; Make sure we don't use the bundled sources and binaries. - '(for-each delete-file - (find-files "java/lib" "\\.jar$"))))) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) (build-system gnu-build-system) (arguments (list @@ -2074,8 +2058,7 @@ (define-public hdf-java (hamcrest (search-input-file inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) - (substitute* (append (find-files "java" "Makefile.am") - (find-files "java" "Makefile.in")) + (substitute* (find-files "java" "Makefile.am") (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar") simple) (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar") @@ -2085,10 +2068,10 @@ (define-public hdf-java (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar") hamcrest)) (substitute* '("java/test/junit.sh.in" - "java/examples/datatypes/JavaDatatypeExample.sh.in" - "java/examples/datasets/JavaDatasetExample.sh.in" - "java/examples/intro/JavaIntroExample.sh.in" - "java/examples/groups/JavaGroupExample.sh.in") + "HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in" + "HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in" + "HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in" + "HDF5Examples/JAVA/TUTR/runExample.sh.in") (("^LIST_JAR_TESTFILES=\"" m) (string-append m hamcrest "\n" junit "\n" @@ -2108,30 +2091,32 @@ (define-public hdf-java (("/usr/bin/uname") (search-input-file inputs "/bin/uname"))) (substitute* (find-files "java/test/testfiles/" ".*\\.txt$") - (("JUnit version 4.11") - "JUnit version 4.12-SNAPSHOT")))))))) + (("JUnit version 4.13.2") + "JUnit version 4.12-SNAPSHOT"))))) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each patch-shebang + (find-files "bin" (lambda (file stat) + (executable-file? file)))))) + (add-after 'unpack 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src")))))) (native-inputs - (list `(,icedtea "jdk") - ;; For tests: - java-hamcrest-core - java-junit - java-slf4j-simple)) + (modify-inputs (package-native-inputs hdf5) + (prepend `(,icedtea "jdk")) + (prepend java-hamcrest-core) + (prepend java-junit) + (prepend java-slf4j-simple) + (delete "gfortran"))) (inputs - (list hdf4 - hdf5 - java-slf4j-api + (list java-slf4j-api libjpeg-turbo zlib)) (home-page "https://www.hdfgroup.org") - (synopsis "Java interface for the HDF4 and HDF5 libraries") - (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use -the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are -implemented in C.") - - ;; BSD-style license: - (license (license:x11-style - "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ -/current/src/unpacked/COPYING.html")))) + (synopsis "Java interface for the HDF5 library") + (description "The Java HDF5 Interface (JHI5) uses the Java Native +Interface to wrap the HDF5 library, which is implemented in C.") + (license (package-license hdf5)))) (define-public hdf-eos2 (package