From unknown Mon Jun 16 23:44:54 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#77590 <77590@debbugs.gnu.org> To: bug#77590 <77590@debbugs.gnu.org> Subject: Status: [PATCH 0/3] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Reply-To: bug#77590 <77590@debbugs.gnu.org> Date: Tue, 17 Jun 2025 06:44:54 +0000 retitle 77590 [PATCH 0/3] Update hdf5 to 1.14.6, fix wrappers and remove ge= nerated source files. reassign 77590 guix-patches submitter 77590 David Elsing severity 77590 normal tag 77590 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Sun Apr 06 19:24:41 2025 Received: (at submit) by debbugs.gnu.org; 6 Apr 2025 23:24:41 +0000 Received: from localhost ([127.0.0.1]:50104 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZM1-0004hU-3w for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:24:41 -0400 Received: from lists.gnu.org ([2001:470:142::17]:51322) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZLz-0004gy-3c for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:24:39 -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 1u1ZLt-00079j-Ee for guix-patches@gnu.org; Sun, 06 Apr 2025 19:24:33 -0400 Received: from mout01.posteo.de ([185.67.36.65]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1u1ZLr-0002PC-16 for guix-patches@gnu.org; Sun, 06 Apr 2025 19:24:33 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 7CC23240027 for ; Mon, 7 Apr 2025 01:24:26 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743981866; bh=BLvVuaRtwTeZepbWfWQSFi5Hv+D6tdo23Y2tqVSUgOA=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=n7WEkgkIoZZlPI2in4kxWDFcgoMHgk9Ic828qOpTT7msMvCUuFODPYmyIZMLOB/X2 gW5/DeFuCXpVTiZJ3KzJ5XJeI6+WuC8rBluSLnGyqcz9v1OY3k73apetziGWQUuLPG Eii7ozGlasjJQZJr28D319EcFKGiI9ZRcTcwMdNKgszGobvd9ITPY4EKCcRl6ml3uB /jEXDHB7G4A/TUK0WkKscyYimCI3bok/bKkV4dnd8HRmrUPNtwSkaEzcH4GLiWI+++ vv65kFD/NJI0qPhyAsq2rEdaRGIJ+Jd3TPUfem3BylA4gbRxoXoffEp6XU1wLsNjoW jHSeIv5TLuNwg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7hp0JlJz9rxB; Mon, 7 Apr 2025 01:24:25 +0200 (CEST) From: David Elsing To: guix-patches@gnu.org Subject: [PATCH 0/3] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Date: Sun, 6 Apr 2025 23:23:10 +0000 Message-ID: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=david.elsing@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H2=-0.01, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) This patch series updates hdf5 to 1.14.6 and applies the improvements from https://issues.guix.gnu.org/64448 only on the hdf5 package, which now does not inherit from hdf5-1.8 anymore. I also changed the package to the Git source, which was already used for hdf-java. Is the commit message fine like this? I mentioned the changes from before, where most things were inherited from hdf5-1.8. The Fortran output is currently only 2.8 MB (compared to 23 MB for the main output), so I removed the additional output, as it was causing problems with linking and the h5fc wrapper. The installation of the examples has been disabled by default upstream (not sure whether intentionally), so instead I made a separate package which builds and checks the examples, but produces no output. For hdf-java, I noticed that the used version does not have support for HDF4 and already uses the Git source of hdf5, so I adjusted the package accordingly and renamed it to hdf5-java. David Elsing (3): gnu: hdf5: Update to 1.14.6. gnu: Add hdf5-examples. gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. gnu/packages/maths.scm | 293 ++++++++++++++++++++++++++++++----------- 1 file changed, 218 insertions(+), 75 deletions(-) -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Apr 06 19:27:10 2025 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:10 +0000 Received: from localhost ([127.0.0.1]:50114 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOQ-0004wo-81 for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:10 -0400 Received: from mout01.posteo.de ([185.67.36.65]:41079) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZON-0004w8-Tx for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:08 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 91AF2240027 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:27:01 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982021; bh=nCgZpNIjZYCbIK+u2qHUP6M4Fz9ILIvVx4SakpO48V8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=BcEpeA+oqwDjtsvzkousoP/ZqARlIM1LCPAGk/lO2ilKhQgGRL5qxTez4u4C+FMij YRLB6umdVWgWRzpz2mnpw4TB+yHknDWiSKPRVfjedQuleleTgOQa8Y3ScIh23l6PeA l3EUP0Lh0d7eKXGUlDRfQB8T19YjA5q+DSuRxXE/oe7xfzVcji+xbFe4U5eZYi4LRz peAmDW9YSK0pBAXc3KnAKGJjhbqIP5tQ+dgdYLiXhjG7URhrxz2kGVU12Z71zuzLiy A1vcZhD1XaB/XArbZ0SCInjIMRYAcAeGKAQetMsy4s7wvboIbyuN1jRragTCU8xXtb 1J5LxIEM7GcpA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lm5HV5z6tlh; Mon, 7 Apr 2025 01:27:00 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH 2/3] gnu: Add hdf5-examples. Date: Sun, 6 Apr 2025 23:26:41 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/maths.scm (hdf5-examples): New variable. --- gnu/packages/maths.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e8258b681d..15e4ae6c86 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2017,6 +2017,20 @@ (define-public hdf5 (license (license:x11-style "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html")))) +;; This package builds and tests the examples, but has empty output. +(define-public hdf5-examples + (package/inherit hdf5 + (name "hdf5-examples") + (arguments + (substitute-keyword-arguments (package-arguments hdf5) + ((#:phases _ #f) + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "HDF5Examples"))))))) + (inputs (list hdf5 zlib)) + (native-inputs (list autoconf-2.71 automake gfortran)))) + ;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Apr 06 19:27:22 2025 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:22 +0000 Received: from localhost ([127.0.0.1]:50116 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOS-0004x5-L4 for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:22 -0400 Received: from mout02.posteo.de ([185.67.36.66]:54461) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZOM-0004vi-HX for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 9FE08240101 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:26:59 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982019; bh=m6H3bWVoTlmByrJHGI2I9w2KbrNgyQeWhtq8NJFAvY8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=R9cidCSEv0qKnQ8eA1txhT22fk6NHnwYMWAxp9BiTOxut0J4LVKta8VZmUXZIrlP9 kIFJHIFRpVsWo5uHu72AniNUGHA6rWcpWowo1GfCdJILXxowZM6oiCzfPAqjVcI43w hyp91KFI+IovesDRmNUFmfpLhu7aVrub1ZpV9e02kwiD2+bqIfHxYiXzQubNe+4wi4 Qs9Uvao4YP75k+N3XLSTtV6nkRBR6qJdJEegMc31iFaPza8U8ZCe6KZ6x7nBDrgt5i 02MBY++C0e1lf24oFEzPh7E+5UtR938AekmgtTgqwA5AO7moaQUUQHNeHg8GzUcy91 cRaU8VdZH9bLA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lk4Xb5z6tlh; Mon, 7 Apr 2025 01:26:58 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH 1/3] gnu: hdf5: Update to 1.14.6. Date: Sun, 6 Apr 2025 23:26:40 +0000 Message-ID: <6baf0e901a9e8e4e6c784957cf92270e6e085149.1743980993.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/maths.scm (hdf5): Update to 1.14.6. Do not inherit from hdf5-1.8. [source]: Switch to git-fetch. Add modules field and snippet. [outputs]: Remove field. [arguments]<#:phases>: Use gexps. Add 'hide-gfortran, 'make-gen-deterministic, 'generate-flexbison, 'patch-trace-shebang, 'patch-configure.ac, 'fix-fortran-i686-test, 'generate-headers, and 'remove-subfiling-cppflags phases. Adjust 'patch-configure, 'patch-settings and 'patch-references phases. Remove 'split phase. [license]: Adjust URL. --- gnu/packages/maths.scm | 208 ++++++++++++++++++++++++++++++++++------- 1 file changed, 176 insertions(+), 32 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6910b32dae..e8258b681d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -62,7 +62,7 @@ ;;; Copyright © 2022 Roman Scherer ;;; Copyright © 2023 Jake Leporte ;;; Copyright © 2023 Camilo Q.S. (Distopico) -;;; Copyright © 2023 David Elsing +;;; Copyright © 2023, 2025 David Elsing ;;; Copyright © 2024 Herman Rimm ;;; Copyright © 2024 Foundation Devices, Inc. ;;; Copyright © 2024, 2025 Artyom V. Poptsov @@ -1837,41 +1837,185 @@ (define-public hdf5-1.10 ;; When updating this package, please also update hdf-java. (define-public hdf5 (package - (inherit hdf5-1.8) - (version "1.14.3") + (name "hdf5") + (version "1.14.6") (source (origin - (method url-fetch) - (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" - "hdf5-" (version-major+minor version) - "/hdf5-" version "/src/hdf5-" - version ".tar.bz2") - (string-append "https://support.hdfgroup.org/ftp/HDF5/" - "current" - (apply string-append - (take (string-split version #\.) 2)) - "/src/hdf5-" version ".tar.bz2"))) + (method git-fetch) + (uri (git-reference + (url "https://github.com/HDFGroup/hdf5") + (commit (string-append "hdf5_" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "05zr11y3bivfwrbvzbky1q2gjf6r7n92cvvdnh5jilbmxljg49cl")) - (patches (search-patches "hdf5-config-date.patch")))) + (base32 + "1f7yv0xra465c3qy8c79fzddib653wzj5dsakb0bs02nwp3xm54q")) + (patches (search-patches "hdf5-config-date.patch")) + (modules '((guix build utils))) + (snippet + '(for-each + delete-file + (append + (find-files "." "Makefile\\.in$") + (find-files "java/lib" "\\.jar$") + (list "aclocal.m4" + "bin/compile" + "bin/config.guess" + "bin/config.sub" + "bin/depcomp" + "bin/install-sh" + "bin/ltmain.sh" + "bin/missing" + "bin/test-driver" + "configure" + "HDF5Examples/aclocal.m4" + "HDF5Examples/compile" + "HDF5Examples/configure" + "HDF5Examples/depcomp" + "HDF5Examples/missing" + "HDF5Examples/test-driver" + "hl/src/H5LTanalyze.c" + "hl/src/H5LTparse.c" + "hl/src/H5LTparse.h" + "hl/tools/gif2h5/testfiles/ex_image2.h5" + "hl/tools/gif2h5/testfiles/h52giftst.h5" + "m4/ax_prog_doxygen.m4" + "m4/libtool.m4" + "m4/lt~obsolete.m4" + "m4/ltoptions.m4" + "m4/ltsugar.m4" + "m4/ltversion.m4" + "src/H5config.h.in" + "src/H5Edefin.h" + "src/H5Einit.h" + "src/H5Epubgen.h" + "src/H5Eterm.h" + "src/H5overflow.h" + "src/H5version.h")))))) + (build-system gnu-build-system) + (inputs + (list zlib)) + (native-inputs + (list autoconf-2.71 + autoconf-archive + automake + bison + flex + gfortran + libtool + ;; Needed to generate some headers and for tests + perl + which)) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.8) - ((#:phases phases #~%standard-phases) - #~(modify-phases #$phases - (add-after 'configure 'skip-version-test - (lambda _ - ;; Skip test_check_version since the 'patch-settings' phase - ;; modifies the test reference. - (substitute* "test/test_check_version.sh.in" - (("TESTING\\(\\).*" all) - (string-append all "\nSKIP; exit 0\n"))))) - (add-after 'patch-configure 'patch-configure-build-settings - (lambda _ - (substitute* "src/H5build_settings.autotools.c.in" - ;; Don't record the build-time kernel version to make the - ;; library file reproducible. - (("@UNAME_INFO@") - "Linux")))))))))) + (list + ;; Some of the users, notably Flann, need the C++ interface. + #:configure-flags + ''("--enable-cxx" + "--enable-fortran" + "--enable-fortran2003" + + ;; Build a thread-safe library. Unfortunately, + ;; 'configure' invites you to either turn off C++, + ;; Fortran, and the high-level interface (HL), or + ;; to pass '--enable-unsupported'. Debian + ;; packagers chose to pass '--enable-unsupported' + ;; and we follow their lead here. + "--enable-threadsafe" + "--with-pthread" + "--enable-unsupported") + ;; Use -fPIC to allow the R bindings to link with the static libraries + #:make-flags ''("CFLAGS=-fPIC" "CXXFLAGS=-fPIC") + #:phases + #~(modify-phases %standard-phases + ;; XXX: src/H5private.h includes and fails to find the + ;; stdlib types when the gfortran header is used. Remove gfortran + ;; from CPLUS_INCLUDE_PATH as a workaround. + (add-after 'set-paths 'hide-gfortran + (lambda _ + (let ((gfortran #$(this-package-native-input "gfortran"))) + (setenv "CPLUS_INCLUDE_PATH" + (string-join + (delete (string-append gfortran "/include/c++") + (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) + ":"))))) + (add-after 'unpack 'make-gen-deterministic + (lambda _ + (substitute* "bin/make_err" + (("keys %major" all) + (string-append "sort " all)) + (("while.*each \\(%section\\).*") + (string-append + "foreach $sect_name (sort keys %section) {\n" + " $sect_desc = $section{$sect_name};\n"))))) + (add-after 'unpack 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src"))) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each patch-shebang + (find-files "bin" (lambda (file stat) + (executable-file? file)))))) + ;; Fixes build on i686, see + ;; https://github.com/HDFGroup/hdf5/commit/0af668f4091f1c35f621d2acdeadd34db6756976 + (add-after 'unpack 'patch-configure.ac + (lambda _ + (substitute* "configure.ac" + (("AC_DEFINE.*HAVE_FLOAT128.*" orig) + (string-append orig "\nAC_CHECK_SIZEOF([__float128])\n"))))) + ;; This is a known issue on i686, see + ;; https://github.com/HDFGroup/hdf5/issues/4926 + (add-after 'unpack 'fix-fortran-i686-test + (lambda _ + (substitute* "fortran/test/tH5R.F90" + (((string-append + "CALL h5rget_obj_name_f\\(C_LOC\\(ref_ptr\\(2\\)\\)," + " \"\", error, name_len=buf_size \\)")) + (string-append + "CALL h5rget_obj_name_f(C_LOC(ref_ptr(2))," + " \"xxxxxxxxxxxxxx\", error, name_len=buf_size)"))))) + (add-before 'configure 'patch-configure + (lambda _ + (substitute* "configure" + (("/bin/mv") "mv")))) + (add-after 'configure 'patch-settings + (lambda _ + ;; libhdf5.settings contains the full path of the compilers + ;; used, and its contents are included in libhdf5.so. We + ;; truncate the hashes to avoid unnecessary store references to + ;; those compilers: + (substitute* '("src/H5build_settings.c" + "src/libhdf5.settings") + (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash) + (string-append prefix (string-take hash 10) "...")) + ;; Don't record the build-time kernel version to make the + ;; settings file reproducible. + (("Uname information:[^\"\n\\\\]*") + "Uname information: Linux")))) + (add-after 'configure 'generate-headers + (lambda _ + (invoke "perl" "bin/make_err" "src/H5err.txt") + (invoke "perl" "bin/make_vers" "src/H5vers.txt") + (invoke "perl" "bin/make_overflow" "src/H5overflow.txt"))) + ;; Remove include flag to directory in source tree + (add-after 'configure 'remove-subfiling-cppflags + (lambda _ + (substitute* '("src/H5build_settings.c" + "src/libhdf5.settings" + "bin/h5cc" + "c++/src/h5c++") + (("-I.*/src/H5FDsubfiling") "")))) + (add-after 'install 'patch-references + (lambda _ + (let ((bin (string-append #$output "/bin")) + (zlib #$(this-package-input "zlib"))) + (substitute* (find-files bin "h5p?cc") + (("-lz" lib) + (string-append "-L" zlib "/lib " lib))))))))) + (home-page "https://www.hdfgroup.org") + (synopsis "Management suite for extremely large and complex data") + (description "HDF5 is a suite that makes possible the management of +extremely large and complex data collections.") + (license (license:x11-style + "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html")))) ;; Keep this in sync with the current hdf5 package. (define-public hdf-java -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Apr 06 19:27:23 2025 Received: (at 77590) by debbugs.gnu.org; 6 Apr 2025 23:27:23 +0000 Received: from localhost ([127.0.0.1]:50118 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZOc-0004xl-Hv for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:23 -0400 Received: from mout01.posteo.de ([185.67.36.65]:36241) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZOP-0004wB-00 for 77590@debbugs.gnu.org; Sun, 06 Apr 2025 19:27:09 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id A3A64240027 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 01:27:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982022; bh=O+FFWU1AyPT98cyPgtQdEmcP+b4+wBOQaUQR9VSXpqM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=I888tmwHPm3ZkVeO94T20UT18cRQp+/sMR4MBW3tyaGC4/c+RFB7fSnyPh3tnlKZp Bl0tcUu8PgpWLP1/HDlf0XWGPuZElc7hjQpDfN/7n3FTcvfBMILqQVcJ2244uFYl/M H6jKcf0JsDPJIxfUNKsxvqRP0byAvXmVKTp5HjiX/UxVsx0170q8tG35optoFTrKaQ s+NVz7fGTSz77dAIo7oNmoYy099lheusQp2Dynisg16JUgPEYzcP3BOSYOudMy+toh V6uXDgtvuKMaZjgYrYpS5XJPUEW0Wa5Djkd8t13UB4ohbDM6kuaegtDesGhxhxJlE8 IigKcjaLi56sQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7lp2Hdvz6tlh; Mon, 7 Apr 2025 01:27:02 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH 3/3] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Date: Sun, 6 Apr 2025 23:26:42 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/maths.scm (hdf-java): Update to 1.14.6. [name]: Rename to hdf5-java. [version]: Use the same as hdf5. [source]: Use the same as hdf5. [arguments]: Adjust 'unbundle phase. Add 'patch-trace-shebang and 'generate-flexbison phases. [native-inputs]: Use modify-inputs. [inputs]: Remove hdf4 and hdf5. [synopsis, description]: Remove mention of HDF4. [license]: Use the same as hdf5. --- gnu/packages/maths.scm | 75 +++++++++++++++++------------------------- 1 file changed, 30 insertions(+), 45 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 15e4ae6c86..251d1d8481 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2031,27 +2031,11 @@ (define-public hdf5-examples (inputs (list hdf5 zlib)) (native-inputs (list autoconf-2.71 automake gfortran)))) -;; Keep this in sync with the current hdf5 package. -(define-public hdf-java +(define-public hdf5-java (package - (name "hdf-java") - (version "1.14.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/HDFGroup/hdf5") - (commit (string-append "hdf5-" - (string-map - (lambda (c) (if (char=? c #\.) #\_ c)) - version))))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0lw9f62zxyjiv7vx9nvnashjj39i44j8d626i7b788zkxw58csvs")) - (modules '((guix build utils))) - (snippet ; Make sure we don't use the bundled sources and binaries. - '(for-each delete-file - (find-files "java/lib" "\\.jar$"))))) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) (build-system gnu-build-system) (arguments (list @@ -2074,8 +2058,7 @@ (define-public hdf-java (hamcrest (search-input-file inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) - (substitute* (append (find-files "java" "Makefile.am") - (find-files "java" "Makefile.in")) + (substitute* (find-files "java" "Makefile.am") (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar") simple) (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar") @@ -2085,10 +2068,10 @@ (define-public hdf-java (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar") hamcrest)) (substitute* '("java/test/junit.sh.in" - "java/examples/datatypes/JavaDatatypeExample.sh.in" - "java/examples/datasets/JavaDatasetExample.sh.in" - "java/examples/intro/JavaIntroExample.sh.in" - "java/examples/groups/JavaGroupExample.sh.in") + "HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in" + "HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in" + "HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in" + "HDF5Examples/JAVA/TUTR/runExample.sh.in") (("^LIST_JAR_TESTFILES=\"" m) (string-append m hamcrest "\n" junit "\n" @@ -2108,30 +2091,32 @@ (define-public hdf-java (("/usr/bin/uname") (search-input-file inputs "/bin/uname"))) (substitute* (find-files "java/test/testfiles/" ".*\\.txt$") - (("JUnit version 4.11") - "JUnit version 4.12-SNAPSHOT")))))))) + (("JUnit version 4.13.2") + "JUnit version 4.12-SNAPSHOT"))))) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each patch-shebang + (find-files "bin" (lambda (file stat) + (executable-file? file)))))) + (add-after 'unpack 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src")))))) (native-inputs - (list `(,icedtea "jdk") - ;; For tests: - java-hamcrest-core - java-junit - java-slf4j-simple)) + (modify-inputs (package-native-inputs hdf5) + (prepend `(,icedtea "jdk")) + (prepend java-hamcrest-core) + (prepend java-junit) + (prepend java-slf4j-simple) + (delete "gfortran"))) (inputs - (list hdf4 - hdf5 - java-slf4j-api + (list java-slf4j-api libjpeg-turbo zlib)) (home-page "https://www.hdfgroup.org") - (synopsis "Java interface for the HDF4 and HDF5 libraries") - (description "Java HDF Interface (JHI) and Java HDF5 Interface (JHI5) use -the Java Native Interface to wrap the HDF4 and HDF5 libraries, which are -implemented in C.") - - ;; BSD-style license: - (license (license:x11-style - "https://support.hdfgroup.org/ftp/HDF5/hdf-java\ -/current/src/unpacked/COPYING.html")))) + (synopsis "Java interface for the HDF5 library") + (description "The Java HDF5 Interface (JHI5) uses the Java Native +Interface to wrap the HDF5 library, which is implemented in C.") + (license (package-license hdf5)))) (define-public hdf-eos2 (package -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 07 10:25:06 2025 Received: (at 77590) by debbugs.gnu.org; 7 Apr 2025 14:25:06 +0000 Received: from localhost ([127.0.0.1]:56090 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1nPN-0007r7-G8 for submit@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:05 -0400 Received: from mout02.posteo.de ([185.67.36.66]:42341) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1nPJ-0007pR-A5 for 77590@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:02 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id D1D4C240101 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 16:24:54 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744035894; bh=lWytgM5Sz6ZjrxvkADVrs55Nl1ym5J7srL8oB+7slh4=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=Qx5LPZqfYMieqhiW0Yt2yRqPmkYVpi6ei+Tca0OOm0w3f7KUfTVZklMEilygWF4ue Gqs4BdXRHl1urv97slZmCE6VRNrbj7/+owG3UFQzzH5zOa+VXxG/2ZwAsDIFaZKlKG 27zbsVrTKlA7bmszqgDPV1Gsv2NtK9Tp3PM6eLr0UJTMRtJLeBxjfIBPxcyvGlseQv yfmCGZM4aot5UubDVM+hAdRaj5geftc/J1ac3ufoKLsQuoss4Ym6+loQ4cpgbkao5e FsS47jQWWSGh/OIlhf/geg/ELDIdgKfhF6R5oB65/zRtt65ZjMkNBrMYfYZcZlY5NN jByEonTllq5xw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWWgp2DqKz9rxB; Mon, 7 Apr 2025 16:24:54 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v2 0/3] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Date: Mon, 7 Apr 2025 14:24:37 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) I forgot to include the updated patch for reproducibility of the hdf5 package and noticed that hdf5-java was also not reproducible, because the current date was included in the jar file. David Elsing (3): gnu: hdf5: Update to 1.14.6. gnu: Add hdf5-examples. gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. gnu/local.mk | 1 + gnu/packages/maths.scm | 304 +++++++++++++----- .../patches/hdf5-reproducibility.patch | 20 ++ 3 files changed, 249 insertions(+), 76 deletions(-) create mode 100644 gnu/packages/patches/hdf5-reproducibility.patch -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 07 10:25:20 2025 Received: (at 77590) by debbugs.gnu.org; 7 Apr 2025 14:25:20 +0000 Received: from localhost ([127.0.0.1]:56096 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1nPT-0007rp-3j for submit@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:20 -0400 Received: from mout02.posteo.de ([185.67.36.66]:59739) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1nPO-0007pu-MP for 77590@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:08 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 6A97A240101 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 16:25:00 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744035900; bh=Ujbb4pkYJRDD6DqsCeVNYTLFcGYwgPRRHfvyrxp7Nzg=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=X4oBI6lyviMVtIQAXEEC3RLz6FHl/SPI79YF2w+ZOXit/7v2C/9HRW5MWTkTvrddQ j+7kxP3PC5gf2ZVoK0Wo589Dw0WuQpDt7gMMCSfwXVnz6tz71QJYvch5VZ11gGGzRI p6PBBU4kBUa/w1xfcIOqBDSSgm8qnWsY+cTW0+Go/QUAhWzrGeqG3dZBguL46LKyIE BRzTpE4nMqR09NCt/9Hbgc3WA8lapJqEW3KraTIrO655fxWOchbLpiSA4EKAPcZ+Sn 9ZSk2QEoGy+XZrDF1F0G/2KaQ+epFIzKRGLRNKoI11lOg/NLlrK6EGwVCFu1i50Vp9 eEWDJa3NBUgHQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWWgw04GYz9rxB; Mon, 7 Apr 2025 16:24:59 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v2 1/3] gnu: hdf5: Update to 1.14.6. Date: Mon, 7 Apr 2025 14:24:38 +0000 Message-ID: <22183d40b459566981fafe58e6e5e6124a28f861.1744035216.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/maths.scm (hdf5): Update to 1.14.6. Do not inherit from hdf5-1.8. [source]: Switch to git-fetch. Add modules field and snippet. Use different patch file. [outputs]: Remove field. [arguments]<#:phases>: Use gexps. Add 'hide-gfortran, 'make-gen-deterministic, 'generate-flexbison, 'patch-trace-shebang, 'patch-configure.ac, 'fix-fortran-i686-test, 'generate-headers, and 'remove-subfiling-cppflags phases. Adjust 'patch-configure, 'patch-settings and 'patch-references phases. Remove 'split phase. [license]: Adjust URL. * gnu/packages/patches/hdf5-reproducibility.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/maths.scm | 209 +++++++++++++++--- .../patches/hdf5-reproducibility.patch | 20 ++ 3 files changed, 197 insertions(+), 33 deletions(-) create mode 100644 gnu/packages/patches/hdf5-reproducibility.patch diff --git a/gnu/local.mk b/gnu/local.mk index acc1a2bfa7..9cf7fb3e24 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-reproducibility.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 6910b32dae..d11fff3bc5 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 @@ -1834,44 +1834,187 @@ (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")) + (patches (search-patches "hdf5-reproducibility.patch")) + (modules '((guix build utils))) + (snippet + '(for-each + delete-file + (append + (find-files "." "Makefile\\.in$") + (find-files "java/lib" "\\.jar$") + (list "aclocal.m4" + "bin/compile" + "bin/config.guess" + "bin/config.sub" + "bin/depcomp" + "bin/install-sh" + "bin/ltmain.sh" + "bin/missing" + "bin/test-driver" + "configure" + "HDF5Examples/aclocal.m4" + "HDF5Examples/compile" + "HDF5Examples/configure" + "HDF5Examples/depcomp" + "HDF5Examples/missing" + "HDF5Examples/test-driver" + "hl/src/H5LTanalyze.c" + "hl/src/H5LTparse.c" + "hl/src/H5LTparse.h" + "hl/tools/gif2h5/testfiles/ex_image2.h5" + "hl/tools/gif2h5/testfiles/h52giftst.h5" + "m4/ax_prog_doxygen.m4" + "m4/libtool.m4" + "m4/lt~obsolete.m4" + "m4/ltoptions.m4" + "m4/ltsugar.m4" + "m4/ltversion.m4" + "src/H5config.h.in" + "src/H5Edefin.h" + "src/H5Einit.h" + "src/H5Epubgen.h" + "src/H5Eterm.h" + "src/H5overflow.h" + "src/H5version.h")))))) + (build-system gnu-build-system) + (inputs + (list zlib)) + (native-inputs + (list autoconf-2.71 + autoconf-archive + automake + bison + flex + gfortran + libtool + ;; Needed to generate some headers and for tests + perl + which)) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.8) - ((#:phases phases #~%standard-phases) - #~(modify-phases #$phases - (add-after 'configure 'skip-version-test - (lambda _ - ;; Skip test_check_version since the 'patch-settings' phase - ;; modifies the test reference. - (substitute* "test/test_check_version.sh.in" - (("TESTING\\(\\).*" all) - (string-append all "\nSKIP; exit 0\n"))))) - (add-after 'patch-configure 'patch-configure-build-settings - (lambda _ - (substitute* "src/H5build_settings.autotools.c.in" - ;; Don't record the build-time kernel version to make the - ;; library file reproducible. - (("@UNAME_INFO@") - "Linux")))))))))) + (list + ;; Some of the users, notably Flann, need the C++ interface. + #:configure-flags + ''("--enable-cxx" + "--enable-fortran" + "--enable-fortran2003" + + ;; Build a thread-safe library. Unfortunately, + ;; 'configure' invites you to either turn off C++, + ;; Fortran, and the high-level interface (HL), or + ;; to pass '--enable-unsupported'. Debian + ;; packagers chose to pass '--enable-unsupported' + ;; and we follow their lead here. + "--enable-threadsafe" + "--with-pthread" + "--enable-unsupported") + ;; Use -fPIC to allow the R bindings to link with the static libraries + #:make-flags ''("CFLAGS=-fPIC" "CXXFLAGS=-fPIC") + #:phases + #~(modify-phases %standard-phases + ;; XXX: src/H5private.h includes and fails to find the + ;; stdlib types when the gfortran header is used. Remove gfortran + ;; from CPLUS_INCLUDE_PATH as a workaround. + (add-after 'set-paths 'hide-gfortran + (lambda _ + (let ((gfortran #$(this-package-native-input "gfortran"))) + (setenv "CPLUS_INCLUDE_PATH" + (string-join + (delete (string-append gfortran "/include/c++") + (string-split (getenv "CPLUS_INCLUDE_PATH") #\:)) + ":"))))) + (add-after 'unpack 'make-gen-deterministic + (lambda _ + (substitute* "bin/make_err" + (("keys %major" all) + (string-append "sort " all)) + (("while.*each \\(%section\\).*") + (string-append + "foreach $sect_name (sort keys %section) {\n" + " $sect_desc = $section{$sect_name};\n"))))) + (add-after 'unpack 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src"))) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each patch-shebang + (find-files "bin" (lambda (file stat) + (executable-file? file)))))) + ;; Fixes build on i686, see + ;; https://github.com/HDFGroup/hdf5/commit/0af668f4091f1c35f621d2acdeadd34db6756976 + (add-after 'unpack 'patch-configure.ac + (lambda _ + (substitute* "configure.ac" + (("AC_DEFINE.*HAVE_FLOAT128.*" orig) + (string-append orig "\nAC_CHECK_SIZEOF([__float128])\n"))))) + ;; This is a known issue on i686, see + ;; https://github.com/HDFGroup/hdf5/issues/4926 + (add-after 'unpack 'fix-fortran-i686-test + (lambda _ + (substitute* "fortran/test/tH5R.F90" + (((string-append + "CALL h5rget_obj_name_f\\(C_LOC\\(ref_ptr\\(2\\)\\)," + " \"\", error, name_len=buf_size \\)")) + (string-append + "CALL h5rget_obj_name_f(C_LOC(ref_ptr(2))," + " \"xxxxxxxxxxxxxx\", error, name_len=buf_size)"))))) + (add-before 'configure 'patch-configure + (lambda _ + (substitute* "configure" + (("/bin/mv") "mv")))) + (add-after 'configure 'patch-settings + (lambda _ + ;; libhdf5.settings contains the full path of the compilers + ;; used, and its contents are included in libhdf5.so. We + ;; truncate the hashes to avoid unnecessary store references to + ;; those compilers: + (substitute* '("src/H5build_settings.c" + "src/libhdf5.settings") + (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash) + (string-append prefix (string-take hash 10) "...")) + ;; Don't record the build-time kernel version to make the + ;; settings file reproducible. + (("Uname information:[^\"\n\\\\]*") + "Uname information: Linux")))) + (add-after 'configure 'generate-headers + (lambda _ + (invoke "perl" "bin/make_err" "src/H5err.txt") + (invoke "perl" "bin/make_vers" "src/H5vers.txt") + (invoke "perl" "bin/make_overflow" "src/H5overflow.txt"))) + ;; Remove include flag to directory in source tree + (add-after 'configure 'remove-subfiling-cppflags + (lambda _ + (substitute* '("src/H5build_settings.c" + "src/libhdf5.settings" + "bin/h5cc" + "c++/src/h5c++") + (("-I.*/src/H5FDsubfiling") "")))) + (add-after 'install 'patch-references + (lambda _ + (let ((bin (string-append #$output "/bin")) + (zlib #$(this-package-input "zlib"))) + (substitute* (find-files bin "h5p?cc") + (("-lz" lib) + (string-append "-L" zlib "/lib " lib))))))))) + (home-page "https://www.hdfgroup.org") + (synopsis "Management suite for extremely large and complex data") + (description "HDF5 is a suite that makes possible the management of +extremely large and complex data collections.") + (license (license:x11-style + "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html")))) ;; Keep this in sync with the current hdf5 package. (define-public hdf-java diff --git a/gnu/packages/patches/hdf5-reproducibility.patch b/gnu/packages/patches/hdf5-reproducibility.patch new file mode 100644 index 0000000000..56c9308c10 --- /dev/null +++ b/gnu/packages/patches/hdf5-reproducibility.patch @@ -0,0 +1,20 @@ +Honor SOURCE_DATE_EPOCH when exporting configuration date. + +--- a/configure.ac ++++ b/configure.ac +@@ -3566,7 +3566,14 @@ + AC_SUBST([H5_VERSION]) + + ## Configuration date +-AC_SUBST([CONFIG_DATE]) CONFIG_DATE="`date`" ++AC_SUBST([CONFIG_DATE]) CONFIG_DATE="`date -u`" ++if test -n "$SOURCE_DATE_EPOCH"; then ++ CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \ ++ || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null` ++ if test -z "$CONFIG_DATE"; then ++ as_fn_error $? "malformed SOURCE_DATE_EPOCH" "$LINENO" 5 ++ fi ++fi + + ## User doing the configuration + AC_SUBST([CONFIG_USER]) CONFIG_USER="`whoami`@`hostname`" -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 07 10:25:21 2025 Received: (at 77590) by debbugs.gnu.org; 7 Apr 2025 14:25:21 +0000 Received: from localhost ([127.0.0.1]:56103 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1nPc-0007y8-MV for submit@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:21 -0400 Received: from mout01.posteo.de ([185.67.36.65]:41539) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1nPR-0007qb-Hw for 77590@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:10 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id D1FA5240028 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 16:25:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744035902; bh=Xmk1PSbJEgZeFSObrQkivCh0Xh3VyV+Xog/ZawSu8Ac=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=pZrn/RUvxIG++Aza7mwmoGCTJRmMyqsR2fpMlcta8tkuFEn2O/DdLZP/svX5+j9im LDiPSy5tykBlWOwWfzY+VeaLUPbsdbRhTskgcLJxQmBMXDoTuDoa8G0lviBEvjuT85 RIlTTN3lh4j0DBaAdPsZstEY2Y1uMo9rEIO3Frtu3KusF/Z4vP3MJo/zgxh/DOJFvV bybCij+T5QOz3LVV7eMq081/mBtznorvNbl0JtuLjBe+zsNjQawH7EZtFwgxkjSdh1 O9B31PwrxU1GvuQTlO3outpr3uiunQHausyJ7qa9AEnW1yPMOM3ELBH9RbFYqe/N2y 4LmhsHmQV48fg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWWgx64Gsz9rxB; Mon, 7 Apr 2025 16:25:01 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v2 2/3] gnu: Add hdf5-examples. Date: Mon, 7 Apr 2025 14:24:39 +0000 Message-ID: <0f14a3f2820462522e3bf967e1c25d4b34578de8.1744035216.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/maths.scm (hdf5-examples): New variable. --- gnu/packages/maths.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d11fff3bc5..6d7466774d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2016,6 +2016,20 @@ (define-public hdf5 (license (license:x11-style "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html")))) +;; This package builds and tests the examples, but has empty output. +(define-public hdf5-examples + (package/inherit hdf5 + (name "hdf5-examples") + (arguments + (substitute-keyword-arguments (package-arguments hdf5) + ((#:phases _ #f) + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "HDF5Examples"))))))) + (inputs (list hdf5 zlib)) + (native-inputs (list autoconf-2.71 automake gfortran)))) + ;; Keep this in sync with the current hdf5 package. (define-public hdf-java (package -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 07 10:25:22 2025 Received: (at 77590) by debbugs.gnu.org; 7 Apr 2025 14:25:22 +0000 Received: from localhost ([127.0.0.1]:56105 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1nPd-0007yJ-LK for submit@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:22 -0400 Received: from mout02.posteo.de ([185.67.36.66]:60399) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1nPT-0007rO-VZ for 77590@debbugs.gnu.org; Mon, 07 Apr 2025 10:25:13 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 9A308240101 for <77590@debbugs.gnu.org>; Mon, 7 Apr 2025 16:25:05 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744035905; bh=szfkX1Fnf8TtARo2EJtsEM4mYkSZC3B4MeiPMfIgHyo=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=csLw6Q11v2tSggc6fmgX5yoWNolHzqOQU96/rU6Pg93/FdkXd2a9XkHtmgST+CZIY p5salb9UklEu2K82BAI3x6sScrwHQmgr3xVSVANvpbCqXCAlP/a5Rc4rzJEILVnQhU 6GfGyXuzDvXv7fOYyUFtQ4rnG6G7Ji3LwPitLua4Xc6p6Y6LYALxbFdtE7S84szALZ vnn+vYXqyrBfpdsJKyEWEnyT1T4Pj0L4brE/FECmnKv1J+Lw9VLZ1hX5Z1B0QyBx1u iU3UvPz+DS+oXrjwuXsQWvPX8hdu1DFKqj9jFMqRFGo14khT+lUHP7WYH1nGS2m5tI vmOp6JgiPo21w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZWWh11cwTz9rxG; Mon, 7 Apr 2025 16:25:05 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v2 3/3] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Date: Mon, 7 Apr 2025 14:24:40 +0000 Message-ID: <86f2e3cc89d54d9e9635b6baa731cb6b4cf537ba.1744035216.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/maths.scm (hdf-java): Update to 1.14.6. [name]: Rename to hdf5-java. [version]: Use the same as hdf5. [source]: Use the same as hdf5. [arguments]: Add (guix build ant-build-system) to #:modules and #:imported-modules. Adjust 'unbundle phase. Add 'patch-trace-shebang, 'generate-flexbison and 'strip-jar-timestamps phases. [native-inputs]: Use modify-inputs. Add zip. [inputs]: Remove hdf4 and hdf5. [synopsis, description]: Remove mention of HDF4. [license]: Use the same as hdf5. --- gnu/packages/maths.scm | 85 ++++++++++++++++++++---------------------- 1 file changed, 40 insertions(+), 45 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6d7466774d..511cd1c94b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2030,33 +2030,24 @@ (define-public hdf5-examples (inputs (list hdf5 zlib)) (native-inputs (list autoconf-2.71 automake gfortran)))) -;; Keep this in sync with the current hdf5 package. -(define-public hdf-java +(define-public hdf5-java (package - (name "hdf-java") - (version "1.14.3") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/HDFGroup/hdf5") - (commit (string-append "hdf5-" - (string-map - (lambda (c) (if (char=? c #\.) #\_ c)) - version))))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0lw9f62zxyjiv7vx9nvnashjj39i44j8d626i7b788zkxw58csvs")) - (modules '((guix build utils))) - (snippet ; Make sure we don't use the bundled sources and binaries. - '(for-each delete-file - (find-files "java/lib" "\\.jar$"))))) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) (build-system gnu-build-system) (arguments (list #:configure-flags #~(list "--enable-java" "--disable-tools") + #:modules + '((guix build gnu-build-system) + ((guix build ant-build-system) #:prefix ant:) + (guix build utils)) + #:imported-modules + `((guix build ant-build-system) + ,@%default-gnu-imported-modules) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'unbundle @@ -2073,8 +2064,7 @@ (define-public hdf-java (hamcrest (search-input-file inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) - (substitute* (append (find-files "java" "Makefile.am") - (find-files "java" "Makefile.in")) + (substitute* (find-files "java" "Makefile.am") (("\\$\\(top_srcdir\\)/java/lib/ext/slf4j-simple-2.0.6.jar") simple) (("\\$\\(top_srcdir\\)/java/lib/slf4j-api-2.0.6.jar") @@ -2084,10 +2074,10 @@ (define-public hdf-java (("\\$\\(top_srcdir\\)/java/lib/hamcrest-core.jar") hamcrest)) (substitute* '("java/test/junit.sh.in" - "java/examples/datatypes/JavaDatatypeExample.sh.in" - "java/examples/datasets/JavaDatasetExample.sh.in" - "java/examples/intro/JavaIntroExample.sh.in" - "java/examples/groups/JavaGroupExample.sh.in") + "HDF5Examples/JAVA/H5D/JavaDatasetExample.sh.in" + "HDF5Examples/JAVA/H5G/JavaGroupExample.sh.in" + "HDF5Examples/JAVA/H5T/JavaDatatypeExample.sh.in" + "HDF5Examples/JAVA/TUTR/runExample.sh.in") (("^LIST_JAR_TESTFILES=\"" m) (string-append m hamcrest "\n" junit "\n" @@ -2107,30 +2097,35 @@ (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 '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-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 -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 09 04:57:27 2025 Received: (at 77590) by debbugs.gnu.org; 9 Apr 2025 08:57:27 +0000 Received: from localhost ([127.0.0.1]:37451 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u2RFP-0000nY-Io for submit@debbugs.gnu.org; Wed, 09 Apr 2025 04:57:27 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:35126) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u2RFN-0000mm-9d for 77590@debbugs.gnu.org; Wed, 09 Apr 2025 04:57:25 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 264C41B2; Wed, 9 Apr 2025 10:57:17 +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 FkwOsGrzPzh5; Wed, 9 Apr 2025 10:57:16 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 06B9A181; Wed, 9 Apr 2025 10:57:14 +0200 (CEST) Date: Wed, 9 Apr 2025 10:57:13 +0200 From: Andreas Enge To: David Elsing Subject: Re: [PATCH v2 1/3] gnu: hdf5: Update to 1.14.6. Message-ID: References: <22183d40b459566981fafe58e6e5e6124a28f861.1744035216.git.david.elsing@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <22183d40b459566981fafe58e6e5e6124a28f861.1744035216.git.david.elsing@posteo.net> X-Rspamd-Server: hera X-Spamd-Bar: +++++ X-Rspamd-Queue-Id: 264C41B2 X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.99%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_FIVE(0.00)[5]; ARC_NA(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; FREEMAIL_CC(0.00)[debbugs.gnu.org,posteo.net,gmail.com,elephly.net] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: rekado@elephly.net, bavier@posteo.net, sharlatanus@gmail.com, 77590@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello David, I only had a very cursory look at your patches; they are not picked up by QA, did you use "git send-email" for submitting them? I do not think the hdf5-examples package makes sense if the examples are not installed as some kind of documentation. What is its goal? We could either drop it altogether. Or include its phases somehow into the main hdf5 package so that its tests constitute an additional check phase. Or also install the examples. I suppose you wrote the reproducibility patch for hdf(5)-java yourself; would it make sense to upstream it? Andreas From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 10 09:22:31 2025 Received: (at 77590) by debbugs.gnu.org; 10 Apr 2025 13:22:32 +0000 Received: from localhost ([127.0.0.1]:44398 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u2rrT-0004Vs-HM for submit@debbugs.gnu.org; Thu, 10 Apr 2025 09:22:31 -0400 Received: from mout01.posteo.de ([185.67.36.65]:46709) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u2rrQ-0004VW-Ex for 77590@debbugs.gnu.org; Thu, 10 Apr 2025 09:22:29 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id D3263240028 for <77590@debbugs.gnu.org>; Thu, 10 Apr 2025 15:22:20 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744291340; bh=pmGvtqX7kmpDsJwNwI/seIZfGuT5PFEWHphyhai0q7w=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: From; b=rkcFgzpKe3w/7v3/WF7ypVRat9aVwMHRpp7GNWYgY/Y7PloRhIuZUKSi2CLCUU2l2 RipNaoNGtfcSRz29nfyvhgLt75Pwi+xZl67IUMeU7phhKLUNtzP+9CX6LGdBk61nxM HR4a21BmDNbWOt1JLQcDjtUcsNUmu5ahVXk781Ms5aB2Ol7oDbRT2dWTvFuk2t+V3H U3fKyFoMHuhf2iXcADf0s+iO0yr0Vx+RbAXridil9Fu/EJGK+JW1M8LGYcSJWwgWD2 mLaRsV9HTo5eULEtOuYeEkulSgNiZBYBgv/eM7L+YlF1BsExABYNTBO87TE7qkMWpd g2zG0PXND7uDA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZYL8C4lkvz6ty6; Thu, 10 Apr 2025 15:22:19 +0200 (CEST) From: David Elsing To: Andreas Enge Subject: Re: [PATCH v2 1/3] gnu: hdf5: Update to 1.14.6. In-Reply-To: References: <22183d40b459566981fafe58e6e5e6124a28f861.1744035216.git.david.elsing@posteo.net> Date: Thu, 10 Apr 2025 13:22:19 +0000 Message-ID: <7yjz7sqhh0.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: rekado@elephly.net, bavier@posteo.net, sharlatanus@gmail.com, 77590@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hello, Andreas Enge writes: > I only had a very cursory look at your patches; they are not picked up > by QA, did you use "git send-email" for submitting them? Yes, I sent them as usual. > I do not think the hdf5-examples package makes sense if the examples are > not installed as some kind of documentation. What is its goal? We could > either drop it altogether. Or include its phases somehow into the main > hdf5 package so that its tests constitute an additional check phase. > Or also install the examples. I'm also not sure how useful installing the examples would be, as they are included in the source already, so I think we should just remove the package. > I suppose you wrote the reproducibility patch for hdf(5)-java yourself; > would it make sense to upstream it? No, I adapted the previous patch in Guix, which modifies the "configure" script, to change "configure.ac" instead. For hdf5-java, I added the 'strip-jar-timestamps phase. Anyway, I just noticed that upstream removed the Autotools build scripts (in favor of CMake) last month. :) I'll change the packages to already use CMake instead. Best, David From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 10 18:41:53 2025 Received: (at 77590) by debbugs.gnu.org; 10 Apr 2025 22:41:54 +0000 Received: from localhost ([127.0.0.1]:47481 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u30an-0002ZP-H3 for submit@debbugs.gnu.org; Thu, 10 Apr 2025 18:41:53 -0400 Received: from mout02.posteo.de ([185.67.36.66]:50437) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u30aj-0002Z6-2y for 77590@debbugs.gnu.org; Thu, 10 Apr 2025 18:41:51 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 909C8240103 for <77590@debbugs.gnu.org>; Fri, 11 Apr 2025 00:41:42 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744324902; bh=xkdNEUcCPhiiw7L7zV6kBnW+OprK4UWJzru4Z4b5upM=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=RHzsSIqzD7f/7vPgmXZm+ZL48VNySpcmpRq4/KwZTQVLZrOOJCNYvGlFQBhHkNvUo BiNRRjPqP7wlOvFYhrqG0KZfYIsLOMuAz57T4Q6QEST6Q36dCz6QZ5tScAJmvSFRBE BIvvh58bQFWqKfNMikXm+2EC7OabdUFCgz11F1bGCR9a3Uu4Kcjmoy6FuHzTr1wPlx gHuWmGNBiZWEU1GJNJp6ago7j4KixGSinkqaX8rgCeTl2VzBx2rxGVyjMVy26GCUXI Eal2V1XNTGaHNOQSu9DcUJm6PFEvi1M+IrQUEA4uZgsbgVoulRbP5RXCOp+u7VLtFk hcidRvPvA8Pmg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZYZYd6s3bz6tvq; Fri, 11 Apr 2025 00:41:41 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v3 0/2] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Date: Thu, 10 Apr 2025 22:41:23 +0000 Message-ID: In-Reply-To: <7yjz7sqhh0.fsf@posteo.net> References: <7yjz7sqhh0.fsf@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Because the Autotools scripts were removed in the development branch upstream, I changed the packages to cmake-build-system. Additionally, I did not include the example package and the examples are not installed, which does not seem to be intended by upstream anyway. They are also still included in the source. For hdf-java, I removed the installation of the external slf4j-*.jar files, as they are just copied to the lib directory. David Elsing (2): gnu: hdf5: Update to 1.14.6. gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. gnu/packages/maths.scm | 266 ++++++++++++++++++++++++++++------------- 1 file changed, 181 insertions(+), 85 deletions(-) -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 10 18:43:41 2025 Received: (at 77590) by debbugs.gnu.org; 10 Apr 2025 22:43:41 +0000 Received: from localhost ([127.0.0.1]:47485 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u30cP-0002ci-6M for submit@debbugs.gnu.org; Thu, 10 Apr 2025 18:43:40 -0400 Received: from mout01.posteo.de ([185.67.36.65]:52521) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u30cL-0002cL-R7 for 77590@debbugs.gnu.org; Thu, 10 Apr 2025 18:43:31 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id EB0E3240027 for <77590@debbugs.gnu.org>; Fri, 11 Apr 2025 00:43:22 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744325002; bh=wtw5RnFAT8r30LGdo0Pwy+8UGJE9+LHWSTSMuruxII8=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: Content-Transfer-Encoding:From; b=PB5LfsyqvwFzlJ5w/GZOoP09akpFPmReQ1xYPB0dGfDjSNv/DQn4e3iAtOS8ZuV6M pxFsjbvXQMwoI2cbTXe2s8VCJ7ZESzXeqo5jzwn8n8LltIFphQk5ZLPxNXQO5WQTZ9 cymvrF1RYN8i/GqxTzO8Cf5c+6chLsa02j4JdWQEkXuljX/V1/4raDmj9ypJr+CgfM XktlG4vW/Kw3yvjates1NnWeeNDualulGMgXH+MvVKT/THsk2Tsq8TRv70XuKjbHg1 jHakEdQkx9ZlvsV+HMIIUrWt+69a0u8yN6DtDWeTdWFnuBNzLSmWnDinguBI7ZWVLj OUQCTlwSSJQRg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZYZbY6RSQz6txj; Fri, 11 Apr 2025 00:43:21 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v3 1/2] gnu: hdf5: Update to 1.14.6. Date: Thu, 10 Apr 2025 22:42:55 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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/maths.scm | 152 ++++++++++++++++++++++++++++++++--------- 1 file changed, 119 insertions(+), 33 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 11a86216aa..5b7398756c 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 @@ -1834,44 +1834,130 @@ (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$") + (list "aclocal.m4" + "bin/compile" + "bin/config.guess" + "bin/config.sub" + "bin/depcomp" + "bin/install-sh" + "bin/ltmain.sh" + "bin/missing" + "bin/test-driver" + "configure" + "HDF5Examples/aclocal.m4" + "HDF5Examples/compile" + "HDF5Examples/configure" + "HDF5Examples/depcomp" + "HDF5Examples/missing" + "HDF5Examples/test-driver" + "hl/src/H5LTanalyze.c" + "hl/src/H5LTparse.c" + "hl/src/H5LTparse.h" + "hl/tools/gif2h5/testfiles/ex_image2.h5" + "hl/tools/gif2h5/testfiles/h52giftst.h5" + "m4/ax_prog_doxygen.m4" + "m4/libtool.m4" + "m4/lt~obsolete.m4" + "m4/ltoptions.m4" + "m4/ltsugar.m4" + "m4/ltversion.m4" + "src/H5config.h.in" + "src/H5Edefin.h" + "src/H5Einit.h" + "src/H5Epubgen.h" + "src/H5Eterm.h" + "src/H5overflow.h" + "src/H5version.h")))))) + (build-system cmake-build-system) + (inputs (list zlib)) + (native-inputs + (list bison + flex + gfortran + ;; Needed to generate some headers and for tests + perl + which)) (arguments - (substitute-keyword-arguments (package-arguments hdf5-1.8) - ((#:phases phases #~%standard-phases) - #~(modify-phases #$phases - (add-after 'configure 'skip-version-test - (lambda _ - ;; Skip test_check_version since the 'patch-settings' phase - ;; modifies the test reference. - (substitute* "test/test_check_version.sh.in" - (("TESTING\\(\\).*" all) - (string-append all "\nSKIP; exit 0\n"))))) - (add-after 'patch-configure 'patch-configure-build-settings - (lambda _ - (substitute* "src/H5build_settings.autotools.c.in" - ;; Don't record the build-time kernel version to make the - ;; library file reproducible. - (("@UNAME_INFO@") - "Linux")))))))))) + (list + ;; Some of the users, notably Flann, need the C++ interface. + #:configure-flags + ''("-DHD5F_ENABLE_THREADSAFE=ON" + "-DHDF5_BUILD_CPP_LIB=ON" + "-DHDF5_BUILD_DOC=ON" + "-DHDF5_BUILD_FORTRAN=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")))))) + (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 -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 10 18:43:42 2025 Received: (at 77590) by debbugs.gnu.org; 10 Apr 2025 22:43:42 +0000 Received: from localhost ([127.0.0.1]:47488 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u30cX-0002cx-1Y for submit@debbugs.gnu.org; Thu, 10 Apr 2025 18:43:42 -0400 Received: from mout01.posteo.de ([185.67.36.65]:33815) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u30cQ-0002cT-7J for 77590@debbugs.gnu.org; Thu, 10 Apr 2025 18:43:35 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 723D9240027 for <77590@debbugs.gnu.org>; Fri, 11 Apr 2025 00:43:27 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744325008; bh=kl5krvfco+1f2D4bm9NRimePTIyBySNWMaPwIgDgu5A=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=MApOp1woYP12byqHiDpwVixvBwzRc6XOpE580CqqLpIpcBeJxFaTWuu+RA1x5GcSO cYyWH64OXkfnYK4cZJHBIbuKEj7T5Y5qJW0qxKbuPt3oB4wfvzQ1KRnHknLg5X2YFU 5YTXU5TwceM1iRqXHPu6cuuqR7QIyAh1aHHFYU6OxdyLSgUw5oP881ypu+4j1W9UEa 4EjMnI0Xep/UkgRkrbhpDloTUQTPWphGk5O3ZEusciIo7HrkalGgKHPzkjQtpngfAC 43x2r6JMWn+Pxwj2lvI+8ZfzTeEbU3TgBbesBQSHw0dUlUvPXO3IA9kqONjSS7NB/J B+XIoRrqHWwSw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZYZbf6YKvz6txv; Fri, 11 Apr 2025 00:43:26 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v3 2/2] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Date: Thu, 10 Apr 2025 22:42:56 +0000 Message-ID: <114970ab28171e1588baf7653c50d990d866cbb9.1744324264.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 5b7398756c..e6e4008d53 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1959,33 +1959,24 @@ (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$"))))) - (build-system gnu-build-system) + (name "hdf5-java") + (version (package-version hdf5)) + (source (package-source hdf5)) + (build-system cmake-build-system) (arguments (list #:configure-flags - #~(list "--enable-java" - "--disable-tools") + #~(list "-DHDF5_BUILD_JAVA=ON" + "-DHDF5_BUILD_TOOLS=OFF") + #:modules + '((guix build cmake-build-system) + ((guix build ant-build-system) #:prefix ant:) + (guix build utils)) + #:imported-modules + `((guix build ant-build-system) + ,@%cmake-build-system-modules) #:phases #~(modify-phases %standard-phases (add-after 'unpack 'unbundle @@ -1996,27 +1987,35 @@ (define-public hdf-java (api (search-input-file inputs "/lib/m2/org/slf4j/slf4j-api/1.7.25/slf4j-api-1.7.25.jar")) + (nop + (search-input-file + inputs "/lib/m2/org/slf4j/slf4j-nop/1.7.25/slf4j-nop-1.7.25.jar")) (junit (search-input-file inputs "/lib/m2/junit/junit/4.12/junit-4.12.jar")) (hamcrest (search-input-file inputs "/lib/m2/org/hamcrest/hamcrest-core/1.3/hamcrest-core-1.3.jar"))) - (substitute* (append (find-files "java" "Makefile.am") - (find-files "java" "Makefile.in")) - (("\\$\\(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" @@ -2036,30 +2035,41 @@ (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 -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Apr 11 09:23:45 2025 Received: (at 77590) by debbugs.gnu.org; 11 Apr 2025 13:23:45 +0000 Received: from localhost ([127.0.0.1]:49553 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u3EMC-0005YY-Tw for submit@debbugs.gnu.org; Fri, 11 Apr 2025 09:23:45 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:37074) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u3EMA-0005Y7-Jk for 77590@debbugs.gnu.org; Fri, 11 Apr 2025 09:23:43 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id D6499283; Fri, 11 Apr 2025 15:23:34 +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 jewbV5o0cWIK; Fri, 11 Apr 2025 15:23:34 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 8AB3B1C0; Fri, 11 Apr 2025 15:23:32 +0200 (CEST) Date: Fri, 11 Apr 2025 15:23:30 +0200 From: Andreas Enge To: David Elsing Subject: Re: [PATCH v2 1/3] gnu: hdf5: Update to 1.14.6. Message-ID: References: <22183d40b459566981fafe58e6e5e6124a28f861.1744035216.git.david.elsing@posteo.net> <7yjz7sqhh0.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <7yjz7sqhh0.fsf@posteo.net> X-Rspamd-Server: hera X-Rspamd-Queue-Id: D6499283 X-Spamd-Bar: ++++++++ X-Spamd-Result: default: False [8.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_FIVE(0.00)[5]; ARC_NA(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; TO_DN_SOME(0.00)[]; FREEMAIL_CC(0.00)[debbugs.gnu.org,posteo.net,gmail.com,elephly.net] X-Spam-Level: ******** X-Rspamd-Action: add header X-Spam: Yes X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: rekado@elephly.net, bavier@posteo.net, sharlatanus@gmail.com, 77590@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Am Thu, Apr 10, 2025 at 01:22:19PM +0000 schrieb David Elsing: > Anyway, I just noticed that upstream removed the Autotools build scripts > (in favor of CMake) last month. :) > I'll change the packages to already use CMake instead. It fails like so: https://bordeaux.guix.gnu.org/build/fd03d80a-ba7b-4b60-b370-50f63edc2e84/log starting phase `configure' source directory: "/tmp/guix-build-hdf5-parallel-openmpi-1.14.6.drv-0/source" (relative from build: "../source") build directory: "/tmp/guix-build-hdf5-parallel-openmpi-1.14.6.drv-0/build" running 'cmake' with arguments ("../source" "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DCMAKE_INSTALL_PREFIX=/gnu/store/fmbv1qibdpvadm83wxkjlwbvab6pv862-hdf5-parallel-openmpi-1.14.6" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" "-DCMAKE_INSTALL_RPATH=/gnu/store/fmbv1qibdpvadm83wxkjlwbvab6pv862-hdf5-parallel-openmpi-1.14.6/lib" "-DCMAKE_VERBOSE_MAKEFILE=ON" "--enable-parallel" "-DHD5F_ENABLE_THREADSAFE=ON" "-DHDF5_BUILD_CPP_LIB=ON" "-DHDF5_BUILD_DOC=ON" "-DHDF5_BUILD_FORTRAN=ON") CMake Error: Unknown argument --enable-parallel CMake Error: Run 'cmake --help' for all supported options. Andreas From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 13:08:38 2025 Received: (at 77590) by debbugs.gnu.org; 14 Apr 2025 17:08:38 +0000 Received: from localhost ([127.0.0.1]:48735 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u4NIT-00079c-PW for submit@debbugs.gnu.org; Mon, 14 Apr 2025 13:08:38 -0400 Received: from mout01.posteo.de ([185.67.36.65]:39355) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u4NIQ-00079I-40 for 77590@debbugs.gnu.org; Mon, 14 Apr 2025 13:08:35 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id CA87B240027 for <77590@debbugs.gnu.org>; Mon, 14 Apr 2025 19:08:24 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1744650505; bh=wGZj0gTSKbRHTeR2f/HYMmvou88lLIaPPO3ZMjtJX5g=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=Ilp5wMS6r3fuoFpQ+sjf648V+OzXGNUABvQGti7zFDZGZ/Jb7R/EToJKqT/ublTgp IPuZwLeu9vMPXYzotIoVSwoQqanMCEP78sL3LQBvFTOQGpEud5EKl0EWhsY/VTKx8y 36KISK7BFgvlTX6uK0XI8252hcHilkFahmzpXNqRW2+lL9dYj2s/2iTadHOhIafzCa 2V/9YB5lsOBHY0e6erAiXoQdabmAEBGH/B6c+yHa7PrHXxnms9yDHjrPadt97K5y9B gAhpHxMEUws5MyjW/P6eKgIL1ZBMSBNN7qwz1UOO7Yh4Jw7tYqUGBmqd5lE7jef3uJ xoGWHsxOvJ8Qw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZbtzC5CqTz6tyf; Mon, 14 Apr 2025 19:08:23 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v4 0/5] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Date: Mon, 14 Apr 2025 17:07:56 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , andreas@enge.fr X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) I fixed the build of the reported new failures (hdf5-parallel-openmpi, insight-toolkit (all versions), itk-snap, netcdf-fortran and satdump) for x86_64-linux. For satdump, the issue was that because now the hdf5 installation is detected, an optional plugin is built, which has an incomplete RUNPATH. Also, I set the correct "-DHDF5_ENABLE_THREADSAFE=ON" flag and added some missing inputs. David Elsing (5): gnu: hdf5: Update to 1.14.6. gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. gnu: netcdf: Fix test. gnu: netcdf-fortran: Add missing inputs. gnu: satdump: Fix RUNPATH for a plugin. gnu/local.mk | 1 + gnu/packages/maths.scm | 314 ++++++++++++------ .../patches/hdf5-config-dependencies.patch | 31 ++ gnu/packages/radio.scm | 17 +- 4 files changed, 254 insertions(+), 109 deletions(-) create mode 100644 gnu/packages/patches/hdf5-config-dependencies.patch -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 13:10:20 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v4 1/5] gnu: hdf5: Update to 1.14.6. Date: Mon, 14 Apr 2025 17:09:24 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.3 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: 1.0 (+) * 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 () -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 13:10:46 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v4 2/5] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Date: Mon, 14 Apr 2025 17:09:25 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 13:11:21 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v4 3/5] gnu: netcdf: Fix test. 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 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 13:11:21 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v4 4/5] gnu: netcdf-fortran: Add missing inputs. Date: Mon, 14 Apr 2025 17:09:27 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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") -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 14 13:11:22 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v4 5/5] gnu: satdump: Fix RUNPATH for a plugin. 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 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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. -- 2.48.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 29 09:13:39 2025 Received: (at 77590) by debbugs.gnu.org; 29 Apr 2025 13:13:39 +0000 Received: from localhost ([127.0.0.1]:53388 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9kmF-0005Sh-A1 for submit@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:38 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:46416) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9kmB-0005Ra-Vh for 77590@debbugs.gnu.org; Tue, 29 Apr 2025 09:13:32 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 3DF46519; Tue, 29 Apr 2025 15:13:25 +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 Ux4Rw8LPu-PL; Tue, 29 Apr 2025 15:13:24 +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 A439D193; Tue, 29 Apr 2025 15:13:23 +0200 (CEST) From: Andreas Enge To: 77590@debbugs.gnu.org Subject: [PATCH v5 0/5] Small changes Date: Tue, 29 Apr 2025 15:07:51 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 3DF46519 X-Spamd-Result: default: False [-2.60 / 15.00]; BAYES_HAM(-3.00)[99.99%]; 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-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hello David, thanks for the updated patch series! QA shows a few package failures: https://qa.guix.gnu.org/issue/77590/package-changes?x86_64-linux-change=broken&x86_64-linux-change=still-failing&x86_64-linux-change=unknown-to-failing&x86_64-linux-change=new-failing hdf5-parallel-openmpi succeeds locally for me. gnudatalanguage does not find hdf5 any more. cdo does not find the nc_open symbol in netcdf anymore; I do not see how this could be related to the patch series. I even tried to not update hdf5 and to only apply the netcdf related patches, and this already caused a problem, which is very strange since the only changes are the additions of inputs. I am sending a slightly updated patch series; in particular I have added hdf-java as a deprecated alias for hdf5-java. So people's profiles do not break. Do you think you could have a look at the new failures? Andreas David Elsing (5): gnu: hdf5: Update to 1.14.6. gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. gnu: netcdf: Fix test. gnu: netcdf-fortran: Add missing inputs. gnu: satdump: Fix RUNPATH for a plugin. gnu/local.mk | 1 + gnu/packages/maths.scm | 312 ++++++++++++------ .../patches/hdf5-config-dependencies.patch | 31 ++ gnu/packages/radio.scm | 17 +- 4 files changed, 253 insertions(+), 108 deletions(-) create mode 100644 gnu/packages/patches/hdf5-config-dependencies.patch base-commit: 6ec4ed678fd9d1ead03cfb2860556dd8b17de755 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 29 09:13:47 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v5 3/5] gnu: netcdf: Fix test. 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-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Transfer-Encoding: 8bit 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-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 29 09:13:48 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v5 4/5] gnu: netcdf-fortran: Add missing inputs. 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-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Transfer-Encoding: 8bit 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-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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") -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 29 09:13:58 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v5 5/5] gnu: satdump: Fix RUNPATH for a plugin. 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 Content-Transfer-Encoding: 8bit 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-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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. -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 29 09:13:59 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v5 2/5] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. 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-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Transfer-Encoding: 8bit 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-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 29 09:14:06 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v5 1/5] gnu: hdf5: Update to 1.14.6. 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-Debbugs-Cc: Andreas Enge , Eric Bavier , Sharlatan Hellseher Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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-Level: ******* X-Spam: Yes X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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 () -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:23:30 2025 Received: (at 77590) by debbugs.gnu.org; 30 Apr 2025 16:23:30 +0000 Received: from localhost ([127.0.0.1]:44190 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAADZ-0007yV-Vr for submit@debbugs.gnu.org; Wed, 30 Apr 2025 12:23:30 -0400 Received: from mout01.posteo.de ([185.67.36.65]:41761) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAADW-0007yF-RT for 77590@debbugs.gnu.org; Wed, 30 Apr 2025 12:23:27 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id EB7E7240028 for <77590@debbugs.gnu.org>; Wed, 30 Apr 2025 18:23:18 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1746030198; bh=+U1mwDveJlQeprONjObE0/ZeGNkR5KzqSGi25E628zQ=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=RXeyORdG9PGjUkeHE9bY3dWbaa0nkcrrmFcjw6DH+1RdTBYW3SPpxqTNkybwn1Bec b5GOIV0QJk4aWByBkvLTwek5oH3W3ZusS+CHKaNs7sHDKY047w1EnVNUBFyIBYuGZr D7MRL1ObEdbwxHk2+hXCMncsOKbz54xhm49q7x8eUjnJA4Hyp3tMXAMnDRP+rtjVIC 24ylpoSCNhdc7rwL/bSFB3ZfPVZ+kBkE3O7D+l2dxf/3/PiowSYHfo+jAg3iwS67Dz au55Kzj0ucSdZGEo2yH8tIRyK5CQ8VGmL0p/YbQpJUoi8s7hr6c2aZBcygqPS6MF5E pxcWtE1w/nKQw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjCp2cFlz9rxM; Wed, 30 Apr 2025 18:23:18 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v6 0/7] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Date: Wed, 30 Apr 2025 16:21:43 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , andreas@enge.fr X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) Hello Andreas, thank you for looking at the updated patches. I cannot see the old QA results anymore, so I don't know whether there were failures other than the ones you mentioned. The HDF5 compiler wrappers (e.g. h5cc) when built with CMake depend on pkg-config, so adding it to the native-inputs fixed the build for gnudatalanguage. Regarding cdo, I did not see the error you mentioned, but the build failed because the libsz library was not found, which happens because I added libaec (which provides libsz.so) to the native-inputs (but now moved to the inputs) of netcdf. I forgot to mention hdf5-parallel-openmpi in the commit message, which is included now. Cheers, David David Elsing (7): gnu: hdf5: Update to 1.14.6. gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. gnu: netcdf: Build with libaec. gnu: netcdf-fortran: Add missing inputs. gnu: satdump: Fix RUNPATH for a plugin. gnu: gnudatalanguage: Fix build. gnu: cdo: Fix build. gnu/local.mk | 1 + gnu/packages/data-language.scm | 3 +- gnu/packages/geo.scm | 2 +- gnu/packages/maths.scm | 313 ++++++++++++------ .../patches/hdf5-config-dependencies.patch | 31 ++ gnu/packages/radio.scm | 17 +- 6 files changed, 257 insertions(+), 110 deletions(-) create mode 100644 gnu/packages/patches/hdf5-config-dependencies.patch -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:08 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v6 2/7] gnu: hdf-java: Update to 1.14.6 and rename to hdf5-java. Date: Wed, 30 Apr 2025 16:27:04 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:09 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v6 3/7] gnu: netcdf: Build with libaec. Date: Wed, 30 Apr 2025 16:27:05 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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 -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:18 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v6 1/7] gnu: hdf5: Update to 1.14.6. Date: Wed, 30 Apr 2025 16:27:03 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * 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 () -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:18 2025 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>; 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=IIJeXlJ2Oe2XQv3Ugy+UEVM60yfP+ivjPHub89D7XrE=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=g+HTYjbwLUMAEJXgg/Az8U8uLfz/2++Y/IXGxMnNq4pbGyc/Hv7z4NqHe+N3+H2M5 UXkR6MmEtYWb6Yy5lEVBZWVYob5vo8Cm6n+VGkeTOgYyZZb1JWceuee2no98uIFogJ X5PeeC/m/Rq2Ub7v2r9Es1hnPQ5yKQ96xgGNp+rWNHn4j0sORPt30UyuvQ/w64DMZ6 QYU5CdVYatZYE1+xVoK7Z4U6Ue+THHrE6l7aCbSjq6D7pBYtOL2HPloxlThbGSyjA/ vQqMl523vn/d8NJmQ4Jv/SwH/CRoGOxlv8L/lvrsroF3XszX6bG/GoIhbIBQ7khuF3 VqdQg9c9WbKgg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZnjK93qVKz6tw5; Wed, 30 Apr 2025 18:27:57 +0200 (CEST) From: David Elsing To: 77590@debbugs.gnu.org Subject: [PATCH v6 6/7] gnu: gnudatalanguage: Fix build. Date: Wed, 30 Apr 2025 16:27:08 +0000 Message-ID: <46294c72cf7dea26c1d86cccd97f75ed25b5424f.1746029810.git.david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * gnu/packages/data-language.scm (gnudatalanguage)[native-inputs]: Add pkg-config. --- gnu/packages/data-language.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/data-language.scm b/gnu/packages/data-language.scm index e779832dd3..aad8df72a0 100644 --- a/gnu/packages/data-language.scm +++ b/gnu/packages/data-language.scm @@ -31,6 +31,7 @@ (define-module (gnu packages data-language) #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) #:use-module (gnu packages onc-rpc) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages plotutils) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) @@ -53,7 +54,7 @@ (define-public gnudatalanguage (base32 "1bb3nin3qrzx2dwdk08vffp4bblrcpv6vv1ybaj499qhqcpqpc12")))) (build-system cmake-build-system) (native-inputs - (list python python-numpy)) + (list pkg-config python python-numpy)) (inputs (list eccodes eigen -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:18 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v6 7/7] gnu: cdo: Fix build. 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 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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") -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:19 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v6 5/7] gnu: satdump: Fix RUNPATH for a plugin. Date: Wed, 30 Apr 2025 16:27:07 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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. -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 12:28:19 2025 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 To: 77590@debbugs.gnu.org Subject: [PATCH v6 4/7] gnu: netcdf-fortran: Add missing inputs. Date: Wed, 30 Apr 2025 16:27:06 +0000 Message-ID: In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing , Andreas Enge X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) * 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") -- 2.49.0 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 30 13:59:27 2025 Received: (at 77590-done) by debbugs.gnu.org; 30 Apr 2025 17:59:27 +0000 Received: from localhost ([127.0.0.1]:36072 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uABiR-0000W7-9Z for submit@debbugs.gnu.org; Wed, 30 Apr 2025 13:59:27 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:52886) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uABiP-0000Vp-7V for 77590-done@debbugs.gnu.org; Wed, 30 Apr 2025 13:59:25 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 20E7A5D3; Wed, 30 Apr 2025 19:51:24 +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 WPzSbBeJPGEH; Wed, 30 Apr 2025 19:51:23 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 064A9291; Wed, 30 Apr 2025 19:51:22 +0200 (CEST) Date: Wed, 30 Apr 2025 19:51:21 +0200 From: Andreas Enge To: David Elsing Subject: Re: [PATCH v6 0/7] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Queue-Id: 20E7A5D3 X-Spamd-Result: default: False [-9.59 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[99.98%]; NEURAL_HAM(-2.99)[-0.998]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_TWO(0.00)[2]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: --------- X-Rspamd-Server: hera X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77590-done Cc: 77590-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thanks, David, for your patience in repairing the hdf5 dependencies! I trust the previous QA run, have verified that gnudatalanguage and cdo compile now, and pushed your patches. Andreas From debbugs-submit-bounces@debbugs.gnu.org Mon May 19 17:11:26 2025 Received: (at 77590) by debbugs.gnu.org; 19 May 2025 21:11:26 +0000 Received: from localhost ([127.0.0.1]:46224 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uH7ld-00055R-KK for submit@debbugs.gnu.org; Mon, 19 May 2025 17:11:26 -0400 Received: from mailgate4.ufz.de ([141.65.7.211]:46436 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uH7la-00054w-E6 for 77590@debbugs.gnu.org; Mon, 19 May 2025 17:11:23 -0400 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate4-UFZ) with ESMTP id 4BE0F160280 for <77590@debbugs.gnu.org>; Mon, 19 May 2025 23:11:20 +0200 (CEST) MIME-version: 1.0 Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0SWI00J00ZAI5C00@imap.intranet.ufz.de> for 77590@debbugs.gnu.org; Mon, 19 May 2025 23:11:20 +0200 (CEST) Received: from smtp1.ufz.de ([141.65.7.216]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0SWJ001X91IWUZA0@imap.intranet.ufz.de> for 77590@debbugs.gnu.org; Mon, 19 May 2025 23:11:20 +0200 (CEST) Received: from [100.99.158.7] (unknown [141.65.34.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp1.ufz.de (smtp1-UFZ) with ESMTPSA id 0B8C78007B for <77590@debbugs.gnu.org>; Mon, 19 May 2025 23:11:20 +0200 (CEST) Date: Mon, 19 May 2025 23:11:19 +0200 From: Lars Bilke Subject: [PATCH 0/3] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. To: 77590@debbugs.gnu.org Message-id: <047385C2-9EB6-4F0F-AA3F-F57083172B40@ufz.de> X-Mailer: MailMate (2.0r6203) Content-type: multipart/signed; boundary="=_MailMate_6D14136E-5726-4F9E-BE84-06CCF0A4CCD7_="; micalg=sha-256; protocol="application/pkcs7-signature" X-Scanned-By: MIMEDefang 2.84 on 127.0.0.1 X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 77590 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) This is an S/MIME signed message (RFC 5652 and 8551). --=_MailMate_6D14136E-5726-4F9E-BE84-06CCF0A4CCD7_= Content-Type: text/plain; markup=markdown Content-Transfer-Encoding: quoted-printable Dear David, it looks like netcdf-cxx4-parallel-openmpi is not building (https://ci.gu= ix.gnu.org/build/10639292/details) since this patch was merged: CMake Error at /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-= 3.24.2/share/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:230 (= message): Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR) Call Stack (most recent call first): /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/share/= cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILUR= E_MESSAGE) /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/share/= cmake-3.24/Modules/FindZLIB.cmake:166 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)= /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/share/= cmake-3.24/Modules/CMakeFindDependencyMacro.cmake:47 (find_package) /gnu/store/gh7m8a9ivnbav6pkwni124j2mjmqykly-hdf5-parallel-openmpi-1.14.= 6/cmake/hdf5-config.cmake:173 (find_dependency) /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/share/= cmake-3.24/Modules/FindHDF5.cmake:502 (find_package) CMakeLists.txt:402 (FIND_PACKAGE) I guess this is related to the patch in hdf5-config.cmake.in. Do you have= any idea how this can be solved? Thanks! 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submit@debbugs.gnu.org; Tue, 20 May 2025 05:24:43 -0400 Received: from mailgate5.ufz.de ([141.65.7.212]:32948 helo=mailgate.ufz.de) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uHJCo-0003in-0e for 77590@debbugs.gnu.org; Tue, 20 May 2025 05:24:15 -0400 Received: from imap.intranet.ufz.de (dcs1.intranet.ufz.de [141.65.125.135]) by mailgate.ufz.de (Mailgate5-UFZ) with ESMTP id 3B44E1602B7 for <77590@debbugs.gnu.org>; Tue, 20 May 2025 11:24:12 +0200 (CEST) MIME-version: 1.0 Received: from conversion-daemon.imap.intranet.ufz.de by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) id <0SWJ00H00YT6SP00@imap.intranet.ufz.de> for 77590@debbugs.gnu.org; Tue, 20 May 2025 11:24:12 +0200 (CEST) Received: from smtp2.ufz.de ([141.65.7.217]) by imap.intranet.ufz.de (Oracle Communications Messaging Server 8.0.2.6.20200227 64bit (built Feb 27 2020)) with ESMTPS id <0SWJ00I0SZGCDP10@imap.intranet.ufz.de> for 77590@debbugs.gnu.org; Tue, 20 May 2025 11:24:12 +0200 (CEST) Received: from [100.99.158.7] (unknown [141.65.34.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp2.ufz.de (smtp2-UFZ) with ESMTPSA id 055AAE004D for <77590@debbugs.gnu.org>; Tue, 20 May 2025 11:24:12 +0200 (CEST) Date: Tue, 20 May 2025 11:24:11 +0200 From: Lars Bilke Subject: Re: [PATCH 0/3] Update hdf5 to 1.14.6, fix wrappers and remove generated source files. In-reply-to: <047385C2-9EB6-4F0F-AA3F-F57083172B40@ufz.de> To: 77590@debbugs.gnu.org Message-id: <5C9CEA65-FCA3-4FAD-8ADE-5CAA9BF31E7B@ufz.de> X-Mailer: MailMate (2.0r6203) Content-type: multipart/signed; boundary="=_MailMate_F6B93892-5ED4-487D-BF94-A0A6BFA58B36_="; micalg=sha-256; protocol="application/pkcs7-signature" X-Scanned-By: MIMEDefang 2.84 on 127.0.1.1 References: <047385C2-9EB6-4F0F-AA3F-F57083172B40@ufz.de> X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -3.3 (---) This is an S/MIME signed message (RFC 5652 and 8551). --=_MailMate_F6B93892-5ED4-487D-BF94-A0A6BFA58B36_= Content-Type: text/plain; markup=markdown Content-Transfer-Encoding: quoted-printable Never mind, on current master (e7d73a08d569904f8a71db5b84f5fafaf0dff188) = netcdf-cxx4-parallel-openmpi builds fine. On 19 May 2025, at 23:11, Lars Bilke wrote: > Dear David, > > it looks like netcdf-cxx4-parallel-openmpi is not building (https://ci.= guix.gnu.org/build/10639292/details) since this patch was merged: > > CMake Error at /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minima= l-3.24.2/share/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:230= (message): > Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR) > Call Stack (most recent call first): > /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/shar= e/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAIL= URE_MESSAGE) > /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/shar= e/cmake-3.24/Modules/FindZLIB.cmake:166 (FIND_PACKAGE_HANDLE_STANDARD_ARG= S) > /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/shar= e/cmake-3.24/Modules/CMakeFindDependencyMacro.cmake:47 (find_package) > /gnu/store/gh7m8a9ivnbav6pkwni124j2mjmqykly-hdf5-parallel-openmpi-1.1= 4.6/cmake/hdf5-config.cmake:173 (find_dependency) > /gnu/store/8wkkxkgkiqaddpn2al8khxnaaanici26-cmake-minimal-3.24.2/shar= e/cmake-3.24/Modules/FindHDF5.cmake:502 (find_package) > CMakeLists.txt:402 (FIND_PACKAGE) > > I guess this is related to the patch in hdf5-config.cmake.in. Do you ha= ve any idea how this can be solved? > > Thanks! > Lars --=_MailMate_F6B93892-5ED4-487D-BF94-A0A6BFA58B36_= Content-Description: S/MIME digital signature Content-Disposition: attachment; filename=smime.p7s Content-Type: application/pkcs7-signature; name=smime.p7s Content-Transfer-Encoding: base64 MIAGCSqGSIb3DQEHAqCAMIACAQExDzANBglghkgBZQMEAgEFADCABgkqhkiG9w0BBwEAAKCCEacw ggUSMIID+qADAgECAgkA4wvV+K8l2YEwDQYJKoZIhvcNAQELBQAwgYIxCzAJBgNVBAYTAkRFMSsw KQYDVQQKDCJULVN5c3RlbXMgRW50ZXJwcmlzZSBTZXJ2aWNlcyBHbWJIMR8wHQYDVQQLDBZULVN5 c3RlbXMgVHJ1c3QgQ2VudGVyMSUwIwYDVQQDDBxULVRlbGVTZWMgR2xvYmFsUm9vdCBDbGFzcyAy MB4XDTE2MDIyMjEzMzgyMloXDTMxMDIyMjIzNTk1OVowgZUxCzAJBgNVBAYTAkRFMUUwQwYDVQQK EzxWZXJlaW4genVyIEZvZXJkZXJ1bmcgZWluZXMgRGV1dHNjaGVuIEZvcnNjaHVuZ3NuZXR6ZXMg ZS4gVi4xEDAOBgNVBAsTB0RGTi1QS0kxLTArBgNVBAMTJERGTi1WZXJlaW4gQ2VydGlmaWNhdGlv biBBdXRob3JpdHkgMjCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAMtg1/9moUHN0vqH l4pzq5lN6mc5WqFggEcVToyVsuXPztNXS43O+FZsFVV2B+pG/cgDRWM+cNSrVICxI5y+NyipCf8F 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