From patchwork Tue Apr 29 13:07:52 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 42140 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 E5CF027BC49; Tue, 29 Apr 2025 14:15:14 +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 BA71D27BC49 for ; Tue, 29 Apr 2025 14:15:13 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u9knl-0000AW-Sl; Tue, 29 Apr 2025 09:15:09 -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 1u9kni-00009u-80 for guix-patches@gnu.org; Tue, 29 Apr 2025 09:15:07 -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 1u9kng-0003t3-S6 for guix-patches@gnu.org; Tue, 29 Apr 2025 09:15:05 -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=h9OjskrZnoiz0tsVWLr4dt55VEEYcO0uKb0Ys8oIBK0=; b=j0sdFlDP0kUdtDoXgeNHxVZBTB3CYw8LsQe7K3DMzBp47b92Jk1QARCFrhGZvEmQBZmONkn4YiVnAqj+aHcy+eI169+1RIjYviuxdFPENVQn4Wee1S3iptMKkznnlQ9rUcD6URxt4Jjyv7V9geQzzkOoVpAlgJVnYZWvExKg0ByuXfSee4/bnKkBXOdgZ2lydKH3VaKuOrMFYvUKidpM+w62ivE85XnSYxx0zBylB68VtF1kqiwUdpK0gfRZ7mUF1ll9FUbvZB5WGmP1lyLaBEkZW68gtoznoZYFnsBaZDR1hwb95m1Yh64cbsYD7vOXgKpN9iybzDQw/ABkjFeWrQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u9knd-0005eO-TN; Tue, 29 Apr 2025 09:15:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v5 1/5] gnu: hdf5: Update to 1.14.6. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 29 Apr 2025 13:15:01 +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 , Andreas Enge , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174593244721328 (code B ref 77590); Tue, 29 Apr 2025 13:15:01 +0000 Received: (at 77590) by debbugs.gnu.org; 29 Apr 2025 13:14:07 +0000 Received: from localhost ([127.0.0.1]:53406 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9kmd-0005WG-SL for submit@debbugs.gnu.org; Tue, 29 Apr 2025 09:14:06 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:46428) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9kmH-0005Rk-31 for 77590@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:47 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id D28576F7; Tue, 29 Apr 2025 15:13:29 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id SDajZNF1LPjt; Tue, 29 Apr 2025 15:13:26 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id B29DA206; Tue, 29 Apr 2025 15:13:24 +0200 (CEST) From: Andreas Enge Date: Tue, 29 Apr 2025 15:07:52 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: D28576F7 X-Spamd-Result: default: False [7.90 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_SPAM(3.00)[1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; MIME_GOOD(-0.10)[text/plain]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_MATCH_ENVRCPT_SOME(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; ARC_NA(0.00)[] X-Spamd-Bar: +++++++ X-Rspamd-Action: add header X-Rspamd-Server: hera X-Spam: Yes 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 From: David Elsing * 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. 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 cc57222a91..78b3a03b07 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1574,6 +1574,7 @@ 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 bb2b401dd2..a2dd515dc4 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 Tue Apr 29 13:07:53 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 42138 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 B480327BC4D; Tue, 29 Apr 2025 14:14:35 +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 EACC627BC49 for ; Tue, 29 Apr 2025 14:14:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u9kn1-0008Lb-1J; Tue, 29 Apr 2025 09:14:23 -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 1u9kmi-0008H6-Pl for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1u9kmi-0003VP-Cm for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:04 -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=p8WIKw4sUx1CkDc/CLDbkGeU3EVHo9B87/lWzjo00M0=; b=r/ufIr3SBre7kgl6SDPk7HWeaa/hHyVtIPeRA/Q2fzKq/f8VVYn56y0PI2iQhiwKgljDW9FlRGRav7FFHxpgxx1NYkXsn37s+lgewCma3pkat+5qnvlpED2BMd40NmAp1FsfeNhOgMYIcZJNHjCx9eJcrPJyAFDIjZ4GziRwmZRnPP4BxRRxe+DOX1BCBIaioes4tuyQgp1fuUJRHtV1vxij9qSBLNHaP93Tth9kr5XXdCipaL5Skcapyp9MJNrzHflik+JfS5CK210PSUqygWx3vEjTO57kUpdbWV0dpCLs8DYqlJhhjnNt/S7K04IgQdXa5/3Rlm+pKWleXb6bzQ==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u9kmi-0005XA-1L; Tue, 29 Apr 2025 09:14:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v5 2/5] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 29 Apr 2025 13:14:03 +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 , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174593243921218 (code B ref 77590); Tue, 29 Apr 2025 13:14:03 +0000 Received: (at 77590) by debbugs.gnu.org; 29 Apr 2025 13:13:59 +0000 Received: from localhost ([127.0.0.1]:53404 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9kmc-0005W5-Sm for submit@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:59 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:46438) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9kmH-0005Rq-Vj for 77590@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:42 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id D950FC43; Tue, 29 Apr 2025 15:13:30 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 1zKM2p40LGgv; Tue, 29 Apr 2025 15:13:28 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id BE48C193; Tue, 29 Apr 2025 15:13:26 +0200 (CEST) From: Andreas Enge Date: Tue, 29 Apr 2025 15:07:53 +0200 Message-ID: <1cea46daabf08bd5333d5d01e3973ceaa1d5eab4.1745932076.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: D950FC43 X-Spamd-Result: default: False [-2.60 / 15.00]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-3.00)[-1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: -- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches From: David Elsing * 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 a2dd515dc4..bb0facc55a 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 Tue Apr 29 13:07:54 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 42137 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 E2D8827BC4B; Tue, 29 Apr 2025 14:14:32 +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 AC02A27BC49 for ; Tue, 29 Apr 2025 14:14:32 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u9kmz-0008KF-91; Tue, 29 Apr 2025 09:14:22 -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 1u9kmi-0008Gy-4e for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:04 -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 1u9kmh-0003Uz-RG for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:03 -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=+BTXO6N13d+OU/urbAejLIbN4zW1FTy2B9+TJURNSBo=; b=p2fl/p+C7sRi0DWm4vipoMXMhOPo/2zRwCMw9nnmhU8hrVLyJzOUfaX0qpumGNmWc8wv3vAGVWA/WgHiUhjP3SW6it2HbVxSaoP788LPTb14PXG3H5rG036W8R7l8bFcCQQte6V0EpCNBaV9O82zwpdLurBgWl5dS2fdPsB1zO0jbWM/QLSMazTTPlfqNb/Ep/gV2c5/fG0cu85xmuWtrIeA3pKVIUe+DKtYdXyRZmM2Xf/Yi+cd5gkQKO0M+H2pmIGFIN6ZiyeAPkS4GsLWlyAVCIEW/2VhE+xXiEavQEGPUVSilDkgYJceZXkhXYzQYGUDYLZn7dVOhnLUMrG8bg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u9kmg-0005Wh-Dk; Tue, 29 Apr 2025 09:14:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v5 3/5] gnu: netcdf: Fix test. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 29 Apr 2025 13:14:02 +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 , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174593242721101 (code B ref 77590); Tue, 29 Apr 2025 13:14:02 +0000 Received: (at 77590) by debbugs.gnu.org; 29 Apr 2025 13:13:47 +0000 Received: from localhost ([127.0.0.1]:53397 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9kmR-0005UA-63 for submit@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:47 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:46466) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9kmI-0005S1-Pk for 77590@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:41 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id B20FF206; Tue, 29 Apr 2025 15:13:31 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id X4FH1iGNQm8q; Tue, 29 Apr 2025 15:13:31 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id D2ACA5F7; Tue, 29 Apr 2025 15:13:28 +0200 (CEST) From: Andreas Enge Date: Tue, 29 Apr 2025 15:07:54 +0200 Message-ID: <634c49f90e875607080d1b4e967869410c451ac8.1745932076.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: B20FF206 X-Spamd-Result: default: False [-2.60 / 15.00]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-3.00)[-1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: -- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches From: David Elsing * gnu/packages/maths.scm (netcdf)[native-inputs]: Add libaec. Change-Id: Ia6a0b742b7e590930c308434b59988e374ccff85 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 bb0facc55a..1bfde8fa8d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2363,7 +2363,7 @@ (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 Tue Apr 29 13:07:55 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 42139 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 1243427BC49; Tue, 29 Apr 2025 14:14:36 +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 3EFF027BC4B for ; Tue, 29 Apr 2025 14:14:35 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u9kmy-0008Jv-6t; Tue, 29 Apr 2025 09:14:21 -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 1u9kmi-0008Gx-4f for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:04 -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 1u9kmh-0003Uy-R3 for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:03 -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=Q+JcSI1oeAFzk0UZxPIweORb7+Ab5q1uA7z/9L7+PBg=; b=BunPR5ui4hkQMbaQS0jeyqtTa0UzFAYN6jvUZiT6jnKfTwvCObkZQtwyX8nyJKH6ktS2gK/gWOar4Prt3TIkPEMAN8zhB7qdHtSwNSZusXHLvh1WMLhjyfTmD/8bmpF1xL4CRE/4MbqrKXU3QMAuz8+O+rRwVydyTnWDKliWxbXrzGIPYMulm7eB7eYTH60wMDP6QSMbohSpa1hy244pGHLHXoZS38Em8IZfC0FlvAKdjaDRe16DpY9fjX8gtFrfa+vHhRopqnrMUtQiyKHtsfApZwfuP3Qf8hnPUcKQhNQF4ZfAU2WeUnnsfrxJTHhqAY8oD0JNwhURmN9+wwkMBg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u9kmg-0005Wp-Tq; Tue, 29 Apr 2025 09:14:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v5 4/5] gnu: netcdf-fortran: Add missing inputs. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: andreas@enge.fr, bavier@posteo.net, sharlatanus@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 29 Apr 2025 13:14:02 +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 , Andreas Enge , Eric Bavier , Sharlatan Hellseher X-Debbugs-Original-Xcc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Received: via spool by 77590-submit@debbugs.gnu.org id=B77590.174593242821107 (code B ref 77590); Tue, 29 Apr 2025 13:14:02 +0000 Received: (at 77590) by debbugs.gnu.org; 29 Apr 2025 13:13:48 +0000 Received: from localhost ([127.0.0.1]:53399 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9kmR-0005UI-Mb for submit@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:48 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:46454) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9kmI-0005Rt-Ia for 77590@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:41 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 838C0193; Tue, 29 Apr 2025 15:13:32 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id AxCAycHQTVL6; Tue, 29 Apr 2025 15:13:32 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id B843588A; Tue, 29 Apr 2025 15:13:30 +0200 (CEST) From: Andreas Enge Date: Tue, 29 Apr 2025 15:07:55 +0200 Message-ID: <118deee626a36e86b0f867feabba9d3596367c44.1745932076.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 838C0193 X-Spamd-Result: default: False [-2.60 / 15.00]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-3.00)[-1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: -- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches From: David Elsing * 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 1bfde8fa8d..76b7b290af 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2456,7 +2456,7 @@ (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 Tue Apr 29 13:07:56 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 42136 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 D358A27BC4B; Tue, 29 Apr 2025 14:14:21 +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 85AA527BC49 for ; Tue, 29 Apr 2025 14:14:21 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1u9kmp-0008Hu-LD; Tue, 29 Apr 2025 09:14:13 -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 1u9kmh-0008Gv-U4 for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:04 -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 1u9kmh-0003Us-LI for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:03 -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=6xI5ZKELuiiNZ5qCQqmgnT1B/q8Bf5zknoDHSqmttrw=; b=QyhMvPOWLrhM5cayjZm7MZjBnuKEqxmURkON3ajfLLXeaSZgBVwlrHu8+1rCK1M5sNKuXZB80xbXpcnNUuuZaGT2PVFBKd3+OMZTbidB8GGcREONV878ZW0I+5AzewnzhibzSqy3KtWWbTm9yGW/oVYrjn+SaFPaGYnKblW/JilOWoFs7DsuKfy0wc9dw/ov/H8FK9c/Fmr0yh7P3h4OC1mj4g4Tzk/VTrePJF5ULuPIl0b+tNeawkQmFXk/vXONxhWsAPbHmtu3l2eLPuajZtBIMZiRF2M6ZHOz8ecIgETtXIttkoSGDr5WKetgOd/9ocTbNVJUqWoTJyOqjXkDNg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1u9kmh-0005Ww-EW for guix-patches@gnu.org; Tue, 29 Apr 2025 09:14:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77590] [PATCH v5 5/5] gnu: satdump: Fix RUNPATH for a plugin. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 29 Apr 2025 13:14:03 +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=B77590.174593243821211 (code B ref 77590); Tue, 29 Apr 2025 13:14:03 +0000 Received: (at 77590) by debbugs.gnu.org; 29 Apr 2025 13:13:58 +0000 Received: from localhost ([127.0.0.1]:53402 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9kmc-0005Vx-8s for submit@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:58 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:32934) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9kmL-0005Sk-As for 77590@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:43 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 5F6F21F8; Tue, 29 Apr 2025 15:13:35 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 6fIs0MIgkk_E; Tue, 29 Apr 2025 15:13:34 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 9CF0EC69; Tue, 29 Apr 2025 15:13:32 +0200 (CEST) From: Andreas Enge Date: Tue, 29 Apr 2025 15:07:56 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 5F6F21F8 X-Spamd-Result: default: False [-2.60 / 15.00]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-3.00)[-1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: -- X-Rspamd-Server: hera X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches From: David Elsing * 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.