From patchwork Mon Apr 14 17:09:24 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41674 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 6C5BE27BC4B; Mon, 14 Apr 2025 18:11:35 +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=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 11FF427BC49 for ; Mon, 14 Apr 2025 18:11:34 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u4NKs-0001OV-HC; Mon, 14 Apr 2025 13:11:06 -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 1u4NKo-0001Nv-FP for guix-patches@gnu.org; Mon, 14 Apr 2025 13:11:02 -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 1u4NKo-000485-1l for guix-patches@gnu.org; Mon, 14 Apr 2025 13:11:02 -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=xNZUbpQKxtzcG3kECcvsS6P46Jo4V9NENppdMU4YLSk=; b=T0DjQBUKPWiIODLuCZ+IzgwYo+N+KFIPEYOyTkTbZKqgGGs9ZNgOEQMfYwy38sWKah9Cr59uqudPLuOhvfICqrrcxl4sNBKQ6q0+k5yUJwjvKFtkVMumTCORrTq4kr1Yz8ED8iu1SZgnNm9j4pMGcuRAPBjgHP1CYLfKK8P///qDx996t3uNpIwIs5xkITOVuQ8ll730gWTYogNoUz+3M4cEJTqjiwUNaaERPonZ6Ldt5vgmmEwO/oAdZaarjAKZC6IZ1L4w4kShvjfRzX6nULKxF3yPtT0JFvQil1w7shd1MZ1O9cS/B1JEM5Mbz30Zqx0yYF2IAbKuFub6m4em+Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u4NKn-0007KD-Nq for guix-patches@gnu.org; Mon, 14 Apr 2025 13:11:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v4 1/5] gnu: hdf5: Update to 1.14.6. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Apr 2025 17:11:01 +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=B77590.174465062028084 (code B ref 77590); Mon, 14 Apr 2025 17:11:01 +0000 Received: (at 77590) by debbugs.gnu.org; 14 Apr 2025 17:10:20 +0000 Received: from localhost ([127.0.0.1]:48749 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4NK0-0007IX-VM for submit@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:20 -0400 Received: from mout02.posteo.de ([185.67.36.66]:38275) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4NJw-0007CH-J7 for 77590@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:10 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 0F782240101 for <77590@debbugs.gnu.org>; Mon, 14 Apr 2025 19:10:01 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744650602; bh=X1Q/1u4Dga1GHVYS2F9a5rVbDLIvSp0q7LR9GBf5QCo=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=VP4t4EA1S/VcJ+/j9MNSxAkUzgsq+NBbEMJrD/xzCM1f4onEOpqFiadluG+FmwVYf f9tieRrDdD7JweNZEyEWCwDKvYBJfu3TXyw+l6eJjWpv8ZJsEeMh5GfrAgUv86cdon 4O53y2T4rFeGl1GrQQQNek04QjT38aanf6N4K1zU/+A9jkZV501gc7PnHGwXc9BLQh 3zpozpl5+by0MwyGLJdTH7rs3C4vr7kzEVctGBmg/rnYLB4C5eQPj+ERJngDTq6PPu hnrZV6QC3T6NFlkCbQ/1PDRH+cGQdcZlat4RhMqjI/4lj6LmIAWD2nr20G49ugYnqn IhmZsBgZVMHrw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zbv152wrTz6v0V; Mon, 14 Apr 2025 19:10:01 +0200 (CEST) From: David Elsing Date: Mon, 14 Apr 2025 17:09:24 +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. * gnu/packages/patches/hdf5-config-dependencies.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- 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 8ff2af1474..714798768f 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1572,6 +1572,7 @@ 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 11a86216aa..ddea48a046 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 @@ -137,6 +137,7 @@ (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) @@ -1834,44 +1835,141 @@ (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 @@ -2075,32 +2173,19 @@ (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 Mon Apr 14 17:09:25 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41675 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 B5BBC27BC4A; Mon, 14 Apr 2025 18:11:39 +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 21B1527BC49 for ; Mon, 14 Apr 2025 18:11:37 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u4NKt-0001PG-Ph; Mon, 14 Apr 2025 13:11:07 -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 1u4NKo-0001Nw-Pn for guix-patches@gnu.org; Mon, 14 Apr 2025 13:11:03 -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 1u4NKo-00048G-Fw for guix-patches@gnu.org; Mon, 14 Apr 2025 13:11:02 -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=fJltyJxtyrx12HPjxeyHekpqDsh6IMmGkvZikYYjqVI=; b=b6AyM/AkcFvRsY8JVni19szGKEjzBGzKCuYBiRwMJxPF9GW06ti71Zi0JYxIckkbceFfgbELKdPAyUclL7Pw+hEXQ+Yt5usA0yu2sgxcLf1mgaZeT+A+bqKGWQdLT9sim54AXmXoQeuYr9xDMs/b6ACgJfxUOE5/v1lKN3Akjs+8lgRiNGK/UjJAVN47UeHtbzrB1ZT7+cGeC8g1NOByJr+3oThVR7UPxYOVaV8I3iTzuFcd7NVt1QJxlkCHCHL7/jzDjf0tY3wnJQn2YnHq8zIQpOnDgF92IeFPCzSre3vrDT1G8Ydgxwncsw3A9XR1tE+T7ztwA620xjVVAW9tqA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u4NKo-0007KL-8m for guix-patches@gnu.org; Mon, 14 Apr 2025 13:11:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v4 2/5] 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: Mon, 14 Apr 2025 17:11:02 +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=B77590.174465064628133 (code B ref 77590); Mon, 14 Apr 2025 17:11:02 +0000 Received: (at 77590) by debbugs.gnu.org; 14 Apr 2025 17:10:46 +0000 Received: from localhost ([127.0.0.1]:48753 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4NKX-0007Jg-LP for submit@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:46 -0400 Received: from mout02.posteo.de ([185.67.36.66]:43317) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4NJy-0007Cl-4A for 77590@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:11 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 40599240103 for <77590@debbugs.gnu.org>; Mon, 14 Apr 2025 19:10:04 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744650604; bh=92sIBQ/+uZifLvlGIY4rebisyxwqDHI3zmxXOhgNg4Y=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=bm1vtALPfUedaCK2t4bbn9LT24GpaKyz2UlcFH4eFu4edDDdp8pBVNkN/+PglNTTt xy/NVY3cCAtZN7akGOXKfJoeVHOTppnyxm2i5eNiHK9vBK4JihUQN4A9K4CtT2Ksg2 jjIK8XW6ncDoVddiMffr4rcJ1oz5lwNfAAXxFu/Gz9jYwLqPBmiHmU4BP106fiGz3P Pkx1sFhQ7bdIb8YbN1FrcWfTC2DAkoMZvE1aZx0Bg8KD0xQEVk8clVNFQfNDhbPjiO eBTKRBrZWkF4uGD1XYwaZmGi8lPfABaSSC/VpdVvVTjGzOfc+sg5IG3bBVfzE+8yqt lDTcqU+yt0TFw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zbv173Whpz6v0V; Mon, 14 Apr 2025 19:10:03 +0200 (CEST) From: David Elsing Date: Mon, 14 Apr 2025 17:09:25 +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. [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. --- gnu/packages/maths.scm | 118 ++++++++++++++++++++++------------------- 1 file changed, 64 insertions(+), 54 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ddea48a046..1d7e81815d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1971,33 +1971,24 @@ (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 @@ -2008,27 +1999,35 @@ (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" @@ -2048,30 +2047,41 @@ (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.") - - ;; 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 From patchwork Mon Apr 14 17:09:26 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41676 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 3763127BC4B; Mon, 14 Apr 2025 18:12:50 +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 AD13B27BC49 for ; Mon, 14 Apr 2025 18:12:49 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u4NML-0001of-Sl; Mon, 14 Apr 2025 13:12:38 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u4NLm-0001j9-Jt for guix-patches@gnu.org; Mon, 14 Apr 2025 13:12:04 -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 1u4NLm-0004FJ-8m for guix-patches@gnu.org; Mon, 14 Apr 2025 13:12:02 -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=jCoaI8AAGsId4bbvV3QoMaf9Ajb7dOPaSg1L3o+zGes=; b=ORK5apm43EDM0epjpfJIONXVcZ++ZXI0pAeYA5w4fSAfrJgXN8b17x6NkwRmCoA/tmW8gIoxBXbznLcZcoIzc9UxlEecCPiK4K+xf8U/oOadmnhfohd2VJ1WHi1Y9T86jE62glbAKrfX+wjyM55Q9nX4A+l6tghdAs+VeC7QRbog30Q73Wp8RKqwClRA2dyjPHgjrt69/UFX7CPMIGg915wj7j8izVrf5eJWQhPFfl4Z31r61yTdFniIdt5TjCZd0OOslJZZT8MMw3GmgjptSLvecGadeOmMnAiD7w1ozQS6F0eRI1aFXnWybOe4uO7G1e26ho9sWWatsRy9DPzrFg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u4NLl-0007Mw-UU for guix-patches@gnu.org; Mon, 14 Apr 2025 13:12:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v4 3/5] gnu: netcdf: Fix test. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Apr 2025 17:12:01 +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=B77590.174465068128236 (code B ref 77590); Mon, 14 Apr 2025 17:12:01 +0000 Received: (at 77590) by debbugs.gnu.org; 14 Apr 2025 17:11:21 +0000 Received: from localhost ([127.0.0.1]:48760 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4NL6-0007LL-SN for submit@debbugs.gnu.org; Mon, 14 Apr 2025 13:11:21 -0400 Received: from mout02.posteo.de ([185.67.36.66]:44283) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4NJz-0007E7-Is for 77590@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:11 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 9F5C1240103 for <77590@debbugs.gnu.org>; Mon, 14 Apr 2025 19:10:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744650605; bh=v0EGNDDwyxmzPcai1vGewlm5/sRgaX0+KuzuAuSrQNE=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=lwHeQMT6l4RJZnJdhj4UFoXQokOUMZKga9/MmcOwifG860WFkZxumeMKL1JPNn2kz t8KBfdSKLQj52D29Vf25HL8jonXMrirI8cbghbmxlN8h9ayBLVFhFIyWyNwWX3msh4 cmz9yUnvwKGORfFNT5holRMlfg/y5hP8/nYbDx1i0wPczcf9yP97kFBzf8caLXFWM8 jT1ZGwf+GDdExet8F62AT7Nu+qYihpjdF1Cj66OT5hmWTkhIlUKZq9cz547ppRw1AH nDA2KXb8jf7ldhx6AR6pKVB7DRvmzLL5N+tXZdHHYfeoP5u4dWChWeGzdwdY/66P16 D/PnEm2qOtiKg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zbv191mMjz6txT; Mon, 14 Apr 2025 19:10:05 +0200 (CEST) From: David Elsing Date: Mon, 14 Apr 2025 17:09:26 +0000 Message-ID: <411373c696cf2a12c16011fa518cd1d0c1676a5d.1744649508.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 (netcdf) [native-inputs]: Add libaec. --- gnu/packages/maths.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1d7e81815d..ee27eb2ddc 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2379,7 +2379,10 @@ (define-public netcdf (patches (search-patches "netcdf-date-time.patch")))) (build-system gnu-build-system) (native-inputs - (list m4 doxygen graphviz)) + (list doxygen + graphviz + libaec + m4)) (inputs (list curl hdf4-alt From patchwork Mon Apr 14 17:09:27 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41678 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 D480227BC4B; Mon, 14 Apr 2025 18:13:09 +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 99DC727BC49 for ; Mon, 14 Apr 2025 18:13:09 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u4NMM-0001ol-5u; Mon, 14 Apr 2025 13:12:38 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u4NLo-0001jM-9Y 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: Mon, 14 Apr 2025 17:12:02 +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=B77590.174465068128243 (code B ref 77590); Mon, 14 Apr 2025 17:12:02 +0000 Received: (at 77590) by debbugs.gnu.org; 14 Apr 2025 17:11:21 +0000 Received: from localhost ([127.0.0.1]:48762 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4NL7-0007LO-8H for submit@debbugs.gnu.org; Mon, 14 Apr 2025 13:11:21 -0400 Received: from mout02.posteo.de ([185.67.36.66]:48895) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4NK0-0007FX-KZ for 77590@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:13 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id C6E47240101 for <77590@debbugs.gnu.org>; Mon, 14 Apr 2025 19:10:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744650606; bh=0MPoSMp0ummeDyFZHncweQtrRA6negG6ZUTw036PnMM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=l5OcoqslRqXlqt/RdvijEXG1Jf3WXyxMkSQ8viNrtyqnc5b6L5oJw8/vfZ5dBujov lGRLPCVg4tUyi4ln0dvDte6SbivXJpxJuJEE6xgUkAtb/MxgEiaqVfz05QuWTa1mDe YgqrkWb6UTeHV+Q0XBgckbSHzRq5eo8eTzJvK5VDCGcC/QJ3k+6ZfEwQveax8kYC3Z agGd9KyhDWGNxCm8wBcN9VuPKvladZ4T3Z2+3hYrP2CkBmR/setwqPAm5MauLPd1ID LzznkRU3qCy9IS91RlEmaQrAO+ySCFSvquhF60puwkdW1NOKp3StTrI095CNUQxp92 5TNEfMoQIUMiw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zbv1B16Kpz6twp; Mon, 14 Apr 2025 19:10:06 +0200 (CEST) From: David Elsing Date: Mon, 14 Apr 2025 17:09:27 +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. --- 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 ee27eb2ddc..59f227afa0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2475,7 +2475,7 @@ (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 Mon Apr 14 17:09:28 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41677 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 2899F27BC49; Mon, 14 Apr 2025 18:12:54 +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 CF9F027BC4A for ; Mon, 14 Apr 2025 18:12:53 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u4NMJ-0001oK-Pc; Mon, 14 Apr 2025 13:12:36 -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 1u4NLn-0001jD-GA for guix-patches@gnu.org; Mon, 14 Apr 2025 13:12:04 -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 1u4NLn-0004FV-5h for guix-patches@gnu.org; Mon, 14 Apr 2025 13:12:03 -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=D1mn9foO/lqd+CvESGtgNwid7D7waczvKB5IzWp0bL4=; b=HapV79LKzpAcNqsYoStGnHK/JIW2hgnjEDMWfjjy0KEVxdA2IDIj1paRPFuneMJn7MUzh2wOY7natocuxCunIt4DFZQRTWJ2X/bNPB++S0azcWyVTq7Oh7yl4tGJCiDP7RkEN8JVMA2awZXcZAmpOAN7CcNQxCoY/UrD8n1m5BB9lNgy3g1cNKul2nBIOuK0ztYU4f/xZ12qiEeCxW8XRGcebEl5aSQ22CetJC2lUHrSiW1wJBl8wzWTKuYXTfGaOolK9yhU+LcvAT57Reqn6LMujPmOHLK6QQifVkuw98dbDbeEajfGdEqTJMQjNn9kWOKVniuoxOZpU3rw8RjgFQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u4NLm-0007NC-T0 for guix-patches@gnu.org; Mon, 14 Apr 2025 13:12:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v4 5/5] gnu: satdump: Fix RUNPATH for a plugin. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 14 Apr 2025 17:12:02 +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=B77590.174465068228253 (code B ref 77590); Mon, 14 Apr 2025 17:12:02 +0000 Received: (at 77590) by debbugs.gnu.org; 14 Apr 2025 17:11:22 +0000 Received: from localhost ([127.0.0.1]:48765 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4NL7-0007LU-JG for submit@debbugs.gnu.org; Mon, 14 Apr 2025 13:11:21 -0400 Received: from mout01.posteo.de ([185.67.36.65]:56721) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4NK1-0007Gf-K0 for 77590@debbugs.gnu.org; Mon, 14 Apr 2025 13:10:14 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id C46F1240027 for <77590@debbugs.gnu.org>; Mon, 14 Apr 2025 19:10:07 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744650607; bh=MxqYuQAjapVo4BMz7J1D/KzOg55SZCS8epxcoSgTwIc=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=RbkTz2ENTPivZL14+YUIyybf16rQ22w0t5ylRWhTnf37dICIEoBXK8+4cfRyx7gTp 5+o7k3tbExYMDwPgrXzTvGbqHaSKGfrObOAMTQs+ER3rKT6Nr5ZbXhIBc1oUfyAgL0 wl2DBLl15zgGxaFd1yEQ4hOr+2lYifnGw+ljHFn9JlBCmkV8H7tqGK8n14f888oV+E wwBILFTQIEqf+lNL2Q/H/RkVFD8gdBvIikoF1iSwO4EkYnj4vxh3PqEx0SKwFO/Iqx y3hItNNWWl8D8ZKlAc2r0/FSs+UbsCBw3Lsgk557D3cE9nP3klgxtrZ8RjzyMZXL6f VTwyZplt//cyw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Zbv1C2sZFz6twp; Mon, 14 Apr 2025 19:10:07 +0200 (CEST) From: David Elsing Date: Mon, 14 Apr 2025 17:09:28 +0000 Message-ID: <45f0b4aed43653e4a1bec382b536fc29ba070ab5.1744649508.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/radio.scm (satdump)[arguments]: Add 'fix-runpath phase. --- 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 3724988ce4..24ae6ec821 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -3245,7 +3245,22 @@ (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.