From patchwork Wed Apr 30 16:27:03 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42190 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 0601527BC49; Wed, 30 Apr 2025 17:29:54 +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=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 F284827BC4A for ; Wed, 30 Apr 2025 17:29:51 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAAJQ-00076l-Es; Wed, 30 Apr 2025 12:29:32 -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 1uAAJ0-0006xu-0q for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:06 -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 1uAAIx-0007Xo-He for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:05 -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=UteqYAOJZ8WPUso5C2zUBLHFEaMEnSly2wRgtmSrm1M=; b=PUH40DxpU0XxK8QYcxNBaXw8k+EVBmGCafdlcPQnOBkHSgy/PUjmYgUhww4OSln9cNe7TcIBETUtg6+sCEPu39z9VTTF39YVa7YmzFl0NQ/UjTygVc0fc1gT4kuhcgoNyo/ORgde8aj8XZAJhz2Klb6Gz4QinIp7g0FX1DYYpDeKPq6F2hg82C5m1t9ZOJWkp2DG4xmXs0tO4/+w8CNJQLRr0gjsR/Ns6pzvgviEJg3NFU6cmXKlcC0ysmHv3rTDj+Jm7tKejxG+0iWwt/7XxWseqljvhNt8k9NTPu8tHN++esWKssz+09thUv3mIAo3jm21IW3guci6VpWUuy4Gdg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAAIx-0008IQ-Cm for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v6 1/7] gnu: hdf5: Update to 1.14.6. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Apr 2025 16:29:03 +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 , Andreas Enge Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174603049831762 (code B ref 77590); Wed, 30 Apr 2025 16:29:03 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:18 +0000 Received: from localhost ([127.0.0.1]:44230 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAI5-0008Fy-FO for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:17 -0400 Received: from mout02.posteo.de ([185.67.36.66]:35997) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAHx-0008EN-2u for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:03 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 7C996240101 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:27:54 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030474; bh=3hC+yV6w1HTPEdhSfSLD/Uwb+YbDkP590bDaURoTAW4=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=eNmdsE06DDBNA5xXheUQmb+FhWVmrZrEIGsO3af+isz6o7cFwVEBGbAk5LCpQWLyH MaND22/M1dzgHM9jrmVCp7KGzCP+y2qPcrYeWFfJvT0i63Kz3hcdLKQ7zmWPcRsKZS ZwLCnKMRvpSYwjWVB0BuHD5ZOoVnt7fjgQSngq52w40qrDv9mU4/ljzY4OSRzzowf5 fm0e/j4jxkEGoH+ZY8KjnzWhKUpITdVV9tugHvgyDWp9Av7N8csjvyBC17YLSYS6hI /NVKO8rdfOl+1DTT3JJLaUfcvZm5PHdjF6OBvIBxzSV8/sG62N2oazZuTt5LwpJX/R Fz4M3rQyShF4w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjK55dG9z6txm; Wed, 30 Apr 2025 18:27:53 +0200 (CEST) From: David Elsing Date: Wed, 30 Apr 2025 16:27:03 +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): Update to 1.14.6. Do not inherit from hdf5-1.8. [name, version]: New field. [source]: Switch to git-fetch. Add modules and snippet fields. Use different patch file. [build-system]: New field. Use CMake. [inputs]: New field. [native-inputs]: New field. Add bison, flex and which. [arguments]: Do not inherit from hdf5-1.8. <#:configure-flags>: New field. <#:phases>: New field. Use gexps. Remove 'patch-configure, 'patch-settings, 'patch-references, 'split, 'skip-version-test and 'patch-configure-build-settings phases. Add 'make-gen-deterministic, 'generate-flexbison, 'patch-trace-shebang, 'fix-fortran-i686-test and 'generate-headers phases. [home-page, synopsis, description]: New fields. [license]: New field. Adjust URL. (hdf5-parallel-openmpi)[inputs]: Use modify-inputs and drop labels. [arguments]<#:configure-flags> Use flags for CMake. <#:phases>: Delete 'patch-tests phase. * gnu/packages/patches/hdf5-config-dependencies.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. Signed-off-by: Andreas Enge --- gnu/local.mk | 1 + gnu/packages/maths.scm | 193 +++++++++++++----- .../patches/hdf5-config-dependencies.patch | 31 +++ 3 files changed, 171 insertions(+), 54 deletions(-) create mode 100644 gnu/packages/patches/hdf5-config-dependencies.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3efe47fe17..f6f95bbf10 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1575,6 +1575,7 @@ dist_patch_DATA = \ %D%/packages/patches/hdf4-reproducibility.patch \ %D%/packages/patches/hdf4-shared-fortran.patch \ %D%/packages/patches/hdf5-config-date.patch \ + %D%/packages/patches/hdf5-config-dependencies.patch \ %D%/packages/patches/hdf-eos2-build-shared.patch \ %D%/packages/patches/hdf-eos2-remove-gctp.patch \ %D%/packages/patches/hdf-eos2-fortrantests.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0b653f4daf..dfc5456797 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 @@ -139,6 +139,7 @@ (define-module (gnu packages maths) #:use-module (gnu packages gettext) #:use-module (gnu packages gcc) #:use-module (gnu packages gd) + #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages glib) #:use-module (gnu packages gperf) @@ -1836,44 +1837,141 @@ (define-public hdf5-1.10 (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00")) (patches (search-patches "hdf5-config-date.patch")))))) -;; 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")) + (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")))) + (patches (search-patches "hdf5-config-dependencies.patch")))) + (build-system cmake-build-system) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.8) - ((#:phases phases #~%standard-phases) - #~(modify-phases #$phases - (add-after 'configure 'skip-version-test - (lambda _ - ;; Skip test_check_version since the 'patch-settings' phase - ;; modifies the test reference. - (substitute* "test/test_check_version.sh.in" - (("TESTING\\(\\).*" all) - (string-append all "\nSKIP; exit 0\n"))))) - (add-after 'patch-configure 'patch-configure-build-settings - (lambda _ - (substitute* "src/H5build_settings.autotools.c.in" - ;; Don't record the build-time kernel version to make the - ;; library file reproducible. - (("@UNAME_INFO@") - "Linux")))))))))) + (list + ;; Some of the users, notably Flann, need the C++ interface. + #:configure-flags + #~(list + (string-append "-DHDF5_INSTALL_CMAKE_DIR=" #$output "/lib/cmake") + "-DHDF5_BUILD_CPP_LIB=ON" + "-DHDF5_BUILD_FORTRAN=ON" + ;; Build a thread-safe library. Unfortunately, CMakeLists.txt + ;; invites you to either turn off C++, Fortran, and the high-level + ;; interface (HL), or to enable 'ALLOW_UNSUPPORTED'. Debian + ;; packagers chose to pass '--enable-unsupported' to the 'configure' + ;; script and we follow their lead here. + "-DHDF5_ENABLE_THREADSAFE=ON" + "-DALLOW_UNSUPPORTED=ON" + "-DHDF5_BUILD_DOC=ON") + #: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)))))) + ;; 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-after 'unpack '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")))))) + (inputs (list libaec zlib)) + (native-inputs + (list bison + doxygen + flex + gfortran + graphviz + ;; Needed to generate some headers and for tests + perl + which)) + (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 @@ -2077,32 +2175,19 @@ (define-public hdf-eos5 (define-public hdf5-parallel-openmpi (package/inherit hdf5 (name "hdf5-parallel-openmpi") - (inputs - `(("mpi" ,openmpi) - ,@(package-inputs hdf5))) + (inputs (modify-inputs (package-inputs hdf5) + (prepend openmpi))) (arguments (substitute-keyword-arguments (package-arguments hdf5) - ((#:configure-flags flags) - #~(cons "--enable-parallel" - (delete "--enable-cxx" - (delete "--enable-threadsafe" #$flags)))) + ((#:configure-flags _ #f) + ''("-DHDF5_ENABLE_THREADSAFE=OFF" + "-DHDF5_ENABLE_PARALLEL=ON" + "-DHDF5_BUILD_CPP_LIB=OFF" + "-DHDF5_BUILD_DOC=ON")) ((#:phases phases) #~(modify-phases #$phases (add-after 'build 'mpi-setup - #$%openmpi-setup) - (add-before 'check 'patch-tests - (lambda _ - ;; OpenMPI's mpirun will exit with non-zero status if it - ;; detects an "abnormal termination", i.e. any process not - ;; calling MPI_Finalize(). Since the test is explicitly - ;; avoiding MPI_Finalize so as not to have at_exit and thus - ;; H5C_flush_cache from being called, mpirun will always - ;; complain, so turn this test off. - (substitute* "testpar/Makefile" - (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) - (string-append front back "\n"))) - (substitute* "tools/test/h5diff/testph5diff.sh" - (("/bin/sh") (which "sh"))))))))) + #$%openmpi-setup))))) (synopsis "Management suite for data with parallel IO support"))) (define-public hdf5-blosc diff --git a/gnu/packages/patches/hdf5-config-dependencies.patch b/gnu/packages/patches/hdf5-config-dependencies.patch new file mode 100644 index 0000000000..cf448dac44 --- /dev/null +++ b/gnu/packages/patches/hdf5-config-dependencies.patch @@ -0,0 +1,31 @@ +The installed CMake configuration is missing targets for zlib and +libaec. Taken from +https://github.com/microsoft/vcpkg/blob/e36fe7110deac47a3aff8eda3dcc7cfb894a2ebf/ports/hdf5/hdf5_config.patch + +diff --git a/config/cmake/hdf5-config.cmake.in b/config/cmake/hdf5-config.cmake.in +index 1a3fb7bbf2..79081ce040 100644 +--- a/config/cmake/hdf5-config.cmake.in ++++ b/config/cmake/hdf5-config.cmake.in +@@ -120,12 +114,22 @@ set (${HDF5_PACKAGE_NAME}_VERSION_MINOR @HDF5_VERSION_MINOR@) + # Don't include targets if this file is being picked up by another + # project which has already built hdf5 as a subproject + #----------------------------------------------------------------------------- ++include(CMakeFindDependencyMacro) + if (NOT TARGET "@HDF5_PACKAGE@") + if (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS) + include (@PACKAGE_SHARE_INSTALL_DIR@/@ZLIB_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) ++ elseif (${HDF5_PACKAGE_NAME}_ENABLE_Z_LIB_SUPPORT) ++ find_dependency(ZLIB) + endif () + if (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT AND ${HDF5_PACKAGE_NAME}_PACKAGE_EXTLIBS) + include (@PACKAGE_SHARE_INSTALL_DIR@/@LIBAEC_PACKAGE_NAME@@HDF_PACKAGE_EXT@-targets.cmake) ++ elseif (${HDF5_PACKAGE_NAME}_ENABLE_SZIP_SUPPORT) ++ if (${HDF5_PACKAGE_NAME}_BUILD_STATIC_LIBS) ++ set(libaec_USE_STATIC_LIBS ON) ++ else() ++ set(libaec_USE_STATIC_LIBS OFF) ++ endif() ++ find_dependency(libaec) + endif () + include (@PACKAGE_SHARE_INSTALL_DIR@/@HDF5_PACKAGE@@HDF_PACKAGE_EXT@-targets.cmake) + endif () From patchwork Wed Apr 30 16:27:04 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42185 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 CF7AE27BC4B; Wed, 30 Apr 2025 17:29:17 +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 3ED9627BC49 for ; Wed, 30 Apr 2025 17:29:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAAJ5-0006zf-Nn; Wed, 30 Apr 2025 12:29:11 -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 1uAAIz-0006xm-TB for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:06 -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 1uAAIw-0007Xe-VP for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:03 -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=7q9R52PFBZlDv5aEfL2TijfjyChjXG0mIXuQ/iOf47M=; b=YuaH84tfC+ytTP38C8BHVx+DiRlzByBlV45Xtqre95LOI367y/CyA8ZA1O17kSmSQgej3uLQkP3Lyaq6SOAVpNlbFsnVx9ltaKPF1luFyFHkmYv5LnQ9aqqOzGMNwLPIDPvFRiQHHYRcraS72e8PvJL022yrt3NFPrI8LvUHKAsiwV8hUD5zf6yGAMdWGlGqaaw+tc0P4+Kdyh7Hwsbxs1Y/k/sVZkgHK843S9xeypRFq2eEnZFjtsdgtIK7+fYR0Pq28n3EVMLAjdgxpbV6XmYRlg8/u+hZP1xf7CZTRRtk7frimu4VN/x8HWP8eqUik8OPr0DHGo9DYtKZ1QGt9g==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAAIw-0008IB-Bz for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v6 2/7] 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: Wed, 30 Apr 2025 16:29:02 +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 , Andreas Enge Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174603048931736 (code B ref 77590); Wed, 30 Apr 2025 16:29:02 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:09 +0000 Received: from localhost ([127.0.0.1]:44226 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAI1-0008FT-B6 for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:08 -0400 Received: from mout02.posteo.de ([185.67.36.66]:38379) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAHx-0008EP-3I for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:03 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 26AF6240101 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:27:55 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030475; bh=aPuHF1aX2UFuJNS/cprKC+1dONkAR57YAEe1EWZQPJk=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=r54nBjyFCXAz0Do4i4Cv6WVR1fct0TAMD1KLHrcIrlZ29/+hxHsQp4FAoHKzKjQjc 8Q/WQ7haM5uXNNtbrV4OOTnxslJyjyxdnEtFaY4B01G7k+1AwtvO0UwYNqbPiOH9yp DUTXlVr2Sr8EkrZgNlGyso5V2EpiWEvUJX9laaRzMFuVBiHa9k2Xhxg6MdIgLYNH/S VsSVcQ8uFCufXwQQeaeTsuIV4+HZaETwr8BmKavIKAongo7B5FJzkcwr+OS0xxA+ue d5PU2+qIe2owgQ/X9fSNSsy4k1lmUlfnPwmU/hENwCAgRwdZFCkQZ2IwL/Or8FyS2+ nqVzNqilbetjA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjK6499Kz6txf; Wed, 30 Apr 2025 18:27:54 +0200 (CEST) From: David Elsing Date: Wed, 30 Apr 2025 16:27:04 +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): Define as deprecated alias for... (hdf5-java): ...this new variable. Update to 1.14.6. [name]: Rename to hdf5-java. [version]: Use the same as hdf5. [source]: Use the same as hdf5. [build-system]: Change to cmake-build-system. [arguments]: Adjust #:configure-flags. Add (guix build ant-build-system) to #:modules and #:imported-modules. Adjust 'unbundle phase. Add 'patch-trace-shebang, 'generate-flexbison, 'generate-headers and 'strip-jar-timestamps phases. [native-inputs]: Use modify-inputs. Add java-slf4j-nop and zip. [inputs]: Remove hdf4 and hdf5. [synopsis, description]: Remove mention of HDF4. [license]: Use the same as hdf5. Change-Id: Idfceec17b9a8c432ab85e2fcc87de6bb5bd5a422 Signed-off-by: Andreas Enge --- gnu/packages/maths.scm | 119 +++++++++++++++++++++++------------------ 1 file changed, 66 insertions(+), 53 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index dfc5456797..e42b00d6ad 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1973,33 +1973,24 @@ (define-public hdf5 (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 +(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$"))))) - (build-system gnu-build-system) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) + (build-system cmake-build-system) (arguments (list #:configure-flags - #~(list "--enable-java" - "--disable-tools") + #~(list "-DHDF5_BUILD_JAVA=ON" + "-DHDF5_BUILD_TOOLS=OFF") + #:modules + '((guix build cmake-build-system) + ((guix build ant-build-system) #:prefix ant:) + (guix build utils)) + #:imported-modules + `((guix build ant-build-system) + ,@%cmake-build-system-modules) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'unbundle @@ -2010,27 +2001,35 @@ (define-public hdf-java (api (search-input-file inputs "/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar")) + (nop + (search-input-file + inputs "/lib/m2/org/slf4j/slf4j-nop/1.7.25/slf4j-nop-1.7.25.jar")) (junit (search-input-file inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar")) (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")) - (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar") - simple) - (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar") - api) - (("\\$\\(top_srcdir\\)/java/lib/junit.jar") + (substitute* "CMakeLists.txt" + (("(set *\\(HDF5_JAVA_LOGGING_JAR ).*" _ orig) + (string-append orig api ")\n")) + (("(set *\\(HDF5_JAVA_LOGGING_NOP_JAR ).*" _ orig) + (string-append orig nop ")\n")) + (("(set *\\(HDF5_JAVA_LOGGING_SIMPLE_JAR ).*" _ orig) + (string-append orig simple ")\n"))) + ;; Do not install copies of external libraries + (substitute* "java/CMakeLists.txt" + ((".*HDF5_JAVA_LOGGING.*_JAR.*") "")) + (substitute* "java/test/CMakeLists.txt" + (("\\$\\{HDF5_JAVA_LIB_DIR\\}/junit\\.jar") junit) - (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar") + (("\\$\\{HDF5_JAVA_LIB_DIR\\}/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" @@ -2050,30 +2049,44 @@ (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"))) + (add-after 'unpack '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"))) + (add-after 'install 'strip-jar-timestamps + (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) (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-nop) + (prepend java-slf4j-simple) + (prepend (@ (gnu packages compression) zip)) + (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.") + (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)))) - ;; BSD-style license: - (license (license:x11-style - "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ -/current/src/unpacked/COPYING.html")))) +(define-public hdf-java + (deprecated-package "hdf-java" hdf5-java)) (define-public hdf-eos2 (package From patchwork Wed Apr 30 16:27:05 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42187 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 D342627BC49; Wed, 30 Apr 2025 17:29:35 +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=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 0DF2027BC4A for ; Wed, 30 Apr 2025 17:29:34 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAAJE-00072U-DG; Wed, 30 Apr 2025 12:29:23 -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 1uAAIz-0006xq-Uz for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:07 -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 1uAAIx-0007Xk-1t for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:05 -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=OnAiMcbhg9HV2GL7s8E64xarzTGTeJ4wLP3Zjth6ov0=; b=TNEGo8WEK8DnF8LsSvvkEyiTcMnu5gt/81X/ah5TvW0aZ4g6qtJNZdwxfHjvfom2Hl+IdTHn2OQITr67oUu5DeSn7dzyW1mzKEqF+Xn+K4JoLrN3dXuQk0Y4L9Rvl/3cs5WXuREZfB4VwoukPmWc0wmRnm8gOu3vgeHuQ05DWtjtQZkN+DrMVp2fA21h8HNhPyFtfBhDBQAZGDQDO0pWLocbE0RCTcl4RDFpxdfcYJyBVm/IiEooC4p7uOvt05FsJ1gvUT1mfgZHmmtp4AH/y0xOxD70pclFqqg1EnZ0FiMfOKmnELqp3sXxWTxvEsUX4Uo9vOWTrdTpo5KeWb400A==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAAIw-0008II-Sq for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v6 3/7] gnu: netcdf: Build with libaec. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Apr 2025 16:29:02 +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 , Andreas Enge Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174603048931745 (code B ref 77590); Wed, 30 Apr 2025 16:29:02 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:09 +0000 Received: from localhost ([127.0.0.1]:44228 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAI4-0008Fu-VN for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:09 -0400 Received: from mout01.posteo.de ([185.67.36.65]:52605) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAHx-0008ES-Sf for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:03 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id E5FAB240027 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:27:55 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030475; bh=Bg6TdEYJbw/BuD5fAWV0djTc/Wwalpj1vJJTBX1NKp8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=IzhRbyAFry617Qq8qY+y+mNVnPE0r2p/AgnJhJ7Gcu7uKOqP+qgnT+DKCZoWlX4RJ wbrX85W6ouwesIiKDPpBqDlnmzuolGiQ7pglQOrElRMzAVtJDoM3Kfcp4aTe4EbeAg H2bGtTVx0rGm0ctTEufKwxb4Mn3el6DyP5sYzF43RCdjKbk7xio7ajQ3cYIWgARZXT FLNdLmONugV1AOWHJcpj7mlr0J4RMtsOsVkH9/k0ZLjnhIef/LxKhiioR4WpFAjofv FrLJ5Np7ERUwbuM7U/5B6KO51uLdxuwXzwhR9ZcRp0VMc+X0MXPGn1RxS9Bu+K+uOq rQkpOR36YAblw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjK72F2Bz6tw5; Wed, 30 Apr 2025 18:27:55 +0200 (CEST) From: David Elsing Date: Wed, 30 Apr 2025 16:27:05 +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 (netcdf)[inputs]: Add libaec. Change-Id: Ia6a0b742b7e590930c308434b59988e374ccff85 Signed-off-by: Andreas Enge --- gnu/packages/maths.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e42b00d6ad..74ed903462 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2363,11 +2363,12 @@ (define-public netcdf (patches (search-patches "netcdf-date-time.patch")))) (build-system gnu-build-system) (native-inputs - (list m4 doxygen graphviz)) + (list doxygen graphviz m4)) (inputs (list curl hdf4-alt hdf5 + libaec libjpeg-turbo libxml2 unzip From patchwork Wed Apr 30 16:27:06 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42184 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 F0D8227BC4D; Wed, 30 Apr 2025 17:29:16 +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 6E0E727BC4B for ; Wed, 30 Apr 2025 17:29:16 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAAJ8-0006zw-8x; Wed, 30 Apr 2025 12:29:14 -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 1uAAJ0-0006xv-1I for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:07 -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 1uAAIz-0007Xu-LG for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:05 -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=Irq6gs9tUGRpX+DAicQZEULDsLFvc4HfPUm/ss4OYz0=; b=hWd30G1eiEKd1UUtL0DWq0cCo5btTijzXxhFv/cCGf0ogcYUBIo0hP1Wf4aBv3AXhGZvhMyyAem3bP6LVn5SGk8X9KrnRH5QA4eZsASY9KnjXzmYuXMCABtPcj2H2zcp8TW8yFrAgZSkRjBcQLgy0KYXYfAtXJk+xw4PDKbembbCP/CaRI5xBq/HE7E66bzD/Ikmyi2B5fjCyoFmhL8BHXdKUtSJb8KRjbWDHKs6ycXj4n6h8HjVFXxrCQqfDXSkvZXlJ5B6fbiVETb8yHUfzFrhdl0kbMl1M61CqardBXnWL/lYCjI8gx67McbrfAhpNIg3b3546q+EW3m86KpRKA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAAIz-0008Iu-ER for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:05 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v6 4/7] gnu: netcdf-fortran: Add missing inputs. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Apr 2025 16:29:05 +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 , Andreas Enge Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174603050031791 (code B ref 77590); Wed, 30 Apr 2025 16:29:05 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:20 +0000 Received: from localhost ([127.0.0.1]:44238 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAIF-0008Gg-G3 for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:19 -0400 Received: from mout02.posteo.de ([185.67.36.66]:49535) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAHy-0008EX-GA for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:05 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id AD022240101 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:27:56 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030476; bh=lMX6ELMVKdx87osZ5ulqy5hqo8JAmjv0/4EHjvu0oEw=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=mf/bz0Zrq0XqziOj86qpszNRMiPo1fywwdSc+3Go6ao+E6zHXbvoZ4L/vxb7X1bzz PFvFiIUnTJyFmlaxZySCtZmsgvKPiPxIjAplAgNhudgo1F/mgekEkWgZGAWp6fdzfS 9OXG8NqEw8VVhnIUBhLqau31NXCEi/RooGQU0+jymwzH3hS1vnl1FKHlIlYGh0FrK/ Pixi0CK/Mk0D2zKteFfVYufXwIPr5UcKuzXQnROiTI/d2jfF/46kty2SM/eL73nWDd gFs2Lgj/h2yGCYIff5WWkRGPQ4cDMRKfhjWFDB5vJnb4T081v0i8gq+/gfXl5JuvZX nRjCYfbavuoSA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjK80Ktzz6txc; Wed, 30 Apr 2025 18:27:56 +0200 (CEST) From: David Elsing Date: Wed, 30 Apr 2025 16:27:06 +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 (netcdf-fortran)[inputs]: Add libaec and hdf5. Signed-off-by: Andreas Enge --- gnu/packages/maths.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 74ed903462..c6272f79fa 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2457,7 +2457,7 @@ (define-public netcdf-fortran "FFLAGS=-fallow-argument-mismatch") #:parallel-tests? #f)) (inputs - (list netcdf)) + (list libaec hdf5 netcdf)) (native-inputs (list gfortran)) (synopsis "Fortran interface for the netCDF library") From patchwork Wed Apr 30 16:27:07 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42186 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 7912127BC4D; Wed, 30 Apr 2025 17:29:34 +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 0CD7627BC49 for ; Wed, 30 Apr 2025 17:29:34 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAAJ5-0006zD-NU; Wed, 30 Apr 2025 12:29:11 -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 1uAAIz-0006xs-Vr for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:06 -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 1uAAIz-0007Xs-3C for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:05 -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=GDFvY4sX1gAkAXaU93J9bSvM770NooDoKjCmOEl1gfk=; b=Kc9nwqgQMCXJhULgZkcHJWiDbfrtDATwra/91Qxq0FsjF/80LjBVQA5od0zebnTFYYj9AgPk0jFhMwC+7ozOMyyAftQdLLf7EBpui5d3mwKrl9t4EmzvAZ3UQKskwKL9hYKfNnBNZw1NEeAs3rLXvFZkHKF6NgfUZZLtVPFwa14djQLSCannwhO7mXkj7fLWQSIZWE1s/wsG7tn26L7qeUHABUJzWBLxN5ysPaWJDe1RwypOi+h2NpdaMBr5Qk5wOjY7/KdQEWfmindjEqbP2su35AQQ9VKrcQoXdsJZWKKHiGvY0/tMccJtLdP5oadt/ZTLooZQdA+L0i0oF3iTLg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1uAAIy-0008Im-Tq for guix-patches@gnu.org; Wed, 30 Apr 2025 12:29:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v6 5/7] gnu: satdump: Fix RUNPATH for a plugin. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Apr 2025 16:29:04 +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 , Andreas Enge Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174603049931783 (code B ref 77590); Wed, 30 Apr 2025 16:29:04 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:19 +0000 Received: from localhost ([127.0.0.1]:44236 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAIE-0008GY-V6 for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:19 -0400 Received: from mout01.posteo.de ([185.67.36.65]:55143) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAHz-0008EZ-6e for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:05 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 3C07C240027 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:27:57 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030477; bh=8h3HVYNCvfq64liXjxqGqWWxwFbjlEErLTutMCSGG64=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=CeXjAe/Jl2jCg9Ji4IuUtzG0Ywb8Dyv0XvR9+sDYAvn8nW0jROa1+R9JUT6iBjNlB IlOLjvLsSyWiB3hwVzLoS2Q9W/38gDel3RIuDV82odHl5cJNMuv/29iZj77FALTe9J u2s/5A0sYQju0VhEgYctyLmL5Ax1iK76l7PYCIX54nlgjQUqqRTSsDgJ775sl5tliM hx1xjupz7w1dkYhWdTXpvzd41X8VmzG5LF2nto4+ni7u+GYR2cPcIUfKT4imCCLn3+ fVSY2XJjKmDAUuEGXIcY7wGth3ajAqID7LOyQWh0gHRKW/FpJ5OdxmAPWEziPtOLca iIVVEoDTTopWg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjK85c7yz6txm; Wed, 30 Apr 2025 18:27:56 +0200 (CEST) From: David Elsing Date: Wed, 30 Apr 2025 16:27:07 +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/radio.scm (satdump)[arguments]: Add 'fix-runpath phase. Signed-off-by: Andreas Enge --- gnu/packages/radio.scm | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 78888dcee5..54b1f0c373 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -3349,7 +3349,22 @@ (define-public satdump volk (list zstd "lib"))) (arguments - (list #:tests? #f)) ; No test suite + (list + #:tests? #f ; No test suite + #:phases + #~(modify-phases %standard-phases + ;; The RUNPATH of this shared library is missing the + ;; .../lib/satdump/plugins directory, which fails the + ;; 'validate-runpath' phase. + (add-after 'unpack 'fix-runpath + (lambda _ + (substitute* "plugins/official_products_support/CMakeLists.txt" + (("add_library\\(official_products_loader_support.*" orig) + (string-append + orig "\n" "set_target_properties(" + "official_products_loader_support" + " PROPERTIES INSTALL_RPATH \"" + #$output "/lib:" #$output "/lib/satdump/plugins\")\n")))))))) (home-page "https://www.satdump.org/") (synopsis "Satellite data processing software") (description "SatDump is a generic satellite data processing software. 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Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Apr 2025 16:29:03 +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=B77590.174603049831769 (code B ref 77590); Wed, 30 Apr 2025 16:29:03 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:18 +0000 Received: from localhost ([127.0.0.1]:44232 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAIE-0008GF-2J for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:18 -0400 Received: from mout01.posteo.de ([185.67.36.65]:57083) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAHz-0008Ea-Ln for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:04 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id DFA8C240027 for <77590@debbugs.gnu.org>; 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charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 42189 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 B82D327BC4A; Wed, 30 Apr 2025 17:29:42 +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=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 9029727BC49 for ; Wed, 30 Apr 2025 17:29:41 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1uAAJ7-0006zu-8t; Wed, 30 Apr 2025 12:29:14 -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 1uAAJ0-0006xt-0Z for guix-patches@gnu.org; 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Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 30 Apr 2025 16:29:04 +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=B77590.174603049831776 (code B ref 77590); Wed, 30 Apr 2025 16:29:04 +0000 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:28:18 +0000 Received: from localhost ([127.0.0.1]:44234 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAAIE-0008GO-Gv for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:18 -0400 Received: from mout02.posteo.de ([185.67.36.66]:59097) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAAI0-0008Ec-Dv for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:28:05 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 91400240101 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:27:58 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030478; bh=sjDGCxzCSqcEvRqJdbyd54ZBwcd8kwfI3416l4dOF1s=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=plV9jI7YiEccjQ7EpVzsyDWIOiaRDELgOXpnJIoDgux/cctGEknQ3MB6iFBlXEzKs vuTxuJw1FsLSCls2SlCPZxemMWIDI9YHg2OCfTpk4aCxzFHRAnqcB/HX+BhkOw/TNp f26iMcbu6jIjwrCWpgZwUDtQAvUycMOZnmVMCHts0zPd+2ycF2FbbLJbLWGL5u2uwK lYv/q6854IcT+vByP+6pFzkEG+SadZfbalaC0qYZ79NvbbYrw+MLI4iAK1EhcEf7HW rXWvKa9M8NmwYkHlFWD09fC9kIT480ViOHqGi0TdaB4iEWrwRCXUSrDzlgE8N9CV6r arrf+XEj6YDAw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjKB1KhDz6txf; Wed, 30 Apr 2025 18:27:58 +0200 (CEST) From: David Elsing Date: Wed, 30 Apr 2025 16:27:09 +0000 Message-ID: <7a6e4763d29d8895006b3f611b731df16d10851f.1746029810.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/geo.scm (cdo)[inputs]: Add libaec. --- gnu/packages/geo.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index e9fb9c68ff..777e4bc00e 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -276,7 +276,7 @@ (define-public cdo ;; Some tests can fail on machines with many threads. #:parallel-tests? #f)) (inputs - (list curl eccodes fftw hdf5 libxml2 netcdf proj udunits)) + (list curl eccodes fftw hdf5 libaec libxml2 netcdf proj udunits)) (native-inputs (list pkg-config python-wrapper)) (home-page "https://code.mpimet.mpg.de/projects/cdo")