From unknown Thu Jun 19 14:10:49 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#64448 <64448@debbugs.gnu.org> To: bug#64448 <64448@debbugs.gnu.org> Subject: Status: [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Reply-To: bug#64448 <64448@debbugs.gnu.org> Date: Thu, 19 Jun 2025 21:10:49 +0000 retitle 64448 [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated sourc= e files from all hdf5 versions. reassign 64448 guix-patches submitter 64448 David Elsing severity 64448 normal tag 64448 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 03 17:59:01 2023 Received: (at submit) by debbugs.gnu.org; 3 Jul 2023 21:59:01 +0000 Received: from localhost ([127.0.0.1]:34581 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGRZU-00075a-Mq for submit@debbugs.gnu.org; Mon, 03 Jul 2023 17:59:01 -0400 Received: from lists.gnu.org ([209.51.188.17]:46676) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGRZQ-00075O-BN for submit@debbugs.gnu.org; Mon, 03 Jul 2023 17:58:59 -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 1qGRZQ-0002Ab-1Z for guix-patches@gnu.org; Mon, 03 Jul 2023 17:58:56 -0400 Received: from mout02.posteo.de ([185.67.36.66]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qGRZN-0003Qv-QO for guix-patches@gnu.org; Mon, 03 Jul 2023 17:58:55 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 0CCE5240101 for ; Mon, 3 Jul 2023 23:58:49 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1688421530; bh=XRasyfLG5emYUI48C2zO9uiZ41iRvjuh5loJJFBeMXI=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=CqnhD/1WRCR179v2FteuyvJ8TbjKQT/rUb0XCIpWbNlw7o3jCc0vls6LXD+wFB8jW g9/JOG0cu9vNCg/gTj3j+p8DDljAmC4FCEka11nejHemXwZAS0PkRiUv5iLshV0RTv Qs4Es3em7azr+vkL7cLiKJRilsIUC/0+856kcyiXU0c8jqayIC/HO4sGz1PjR/ghHf 1LiORvs0lEIqEr+uZCXP9xez49EFzDNXgFblfTtr6JxtsmMsjhsBBaWtETLlkYGFZk +8mge7Li41lDaVIzY2AC7EmiKsDpmx9mGdknjRSb+gFUrGe/NYyCB3SiOQDP2jemNa lYy8g7Uz0uj5w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Qw0Dn3zdKz6tvt; Mon, 3 Jul 2023 23:58:49 +0200 (CEST) From: David Elsing To: guix-patches@gnu.org Subject: [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Date: Mon, 3 Jul 2023 21:58:45 +0000 Message-Id: MIME-Version: 1.0 X-Debbugs-Cc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.66; envelope-from=david.elsing@posteo.net; helo=mout02.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_H5=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) 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: -2.3 (--) When using hdf5 with CMake, I noticed that it does not work for the 1.14 version, because the h5cc and h5c++ wrappers contain the flag "-I/tmp/guix-build-hdf5-1.14.0.drv-0/hdf5-1.14.0/src/H5FDsubfiling". It is required in the 'configure phase, but can be removed afterwards. Additionally, I noticed that the hdf5 source tarballs contain many autogenerated files, so I also removed them. Somehow, the 1.8.23 release is missing two m4 scripts (which are included in later releases, but different from this one), so they are copied from the 1.8.21 tarball (the latest earlier release which includes them). The genparser script is missing as well, which is copied from the 1.10.9 release. David Elsing (2): gnu: hdf5-1.8: Remove generated files from source gnu: hdf5-1.14: Remove spurious include directories. gnu/packages/maths.scm | 234 +++++++++++++++----- gnu/packages/patches/hdf5-config-date.patch | 14 +- 2 files changed, 188 insertions(+), 60 deletions(-) base-commit: 76e39909e886bb51cf9b2fa03a1523545faca880 -- 2.40.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 03 18:01:04 2023 Received: (at 64448) by debbugs.gnu.org; 3 Jul 2023 22:01:04 +0000 Received: from localhost ([127.0.0.1]:34592 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGRbT-0007BV-7B for submit@debbugs.gnu.org; Mon, 03 Jul 2023 18:01:04 -0400 Received: from mout01.posteo.de ([185.67.36.65]:56959) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGRbP-0007Am-K5 for 64448@debbugs.gnu.org; Mon, 03 Jul 2023 18:01:02 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 55C36240028 for <64448@debbugs.gnu.org>; Tue, 4 Jul 2023 00:00:53 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1688421653; bh=/SJT2S2HACA28SK/isW8I+C8clfxHxMq0LWofHiyUeg=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=Jj2CdqpNHfzjQThDezIPlMmWk7nCT/oYOtqfVXzQZ6lL0Ea4f2flKujgfv6Ozv1FS LZsCemwTK5kYl4CcnKyj+y0DOQeP1uYlCEJwKFPfyCpQZno+GhsJiFS4Yrlk+CD2yQ 7KYSjMXs2w7kD9dWzB6FXyo49bD5V0oUAF4Xx5QwGJugRw5iBwebE5w4kBjFV8kTf+ xxxEqFvKkSBTzI4pMeG7hhHwfo2492zPkriwzPF+hFOtwhPQM8ZdxEti/Q3VF+MttI eyxbDVMss53PxiuYqjs0apMk9so4f8hgnbnmrPPYtR/aC1UlF0IRRCJxclq5MnUtO/ 0kY0jEycZgTQA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Qw0H8526zz9rxM; Tue, 4 Jul 2023 00:00:52 +0200 (CEST) From: David Elsing To: 64448@debbugs.gnu.org Subject: [PATCH 1/2] gnu: hdf5-1.8: Remove generated files from source Date: Mon, 3 Jul 2023 22:00:46 +0000 Message-Id: In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64448 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-snippet): New variable. (hdf5-1.8.21-source): New variable. (hdf5-1.8)[source](modules, snippet): New fields. [native-inputs]: Add autoconf, automake, bison, flex, libtool and which. [arguments] Use Gexps. <#:phases>: Add 'copy-scripts, 'make-gen-deterministic, 'generate-flexbison and 'generate-headers phases. (hdf5-1.10)[source](modules, snippet): New fields. [arguments]<#:phases>: Use 'substitute-keyword-arguments' and delete 'copy-scripts phase. (hdf5-1.12): Inherit from hdf5-1.10. [source](modules, snippet): New fields. (hdf5-1.14): Inherit from hdf5-1.10. [source](modules, snippet): New fields. * gnu/packages/patches/hdf5-config-date.patch: Apply to configure.ac instead of configure. --- gnu/packages/maths.scm | 221 +++++++++++++++----- gnu/packages/patches/hdf5-config-date.patch | 14 +- 2 files changed, 176 insertions(+), 59 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 653e76027a..b2029db615 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -60,6 +60,7 @@ ;;; Copyright © 2022 Akira Kyle ;;; Copyright © 2022 Roman Scherer ;;; Copyright © 2023 Jake Leporte +;;; Copyright © 2023 David Elsing ;;; ;;; This file is part of GNU Guix. ;;; @@ -1376,12 +1377,48 @@ (define-public hdf4-alt (synopsis "HDF4 without netCDF API, can be combined with the regular netCDF library"))) -(define-public hdf5-1.8 - (package - (name "hdf5") - (version "1.8.23") - (source - (origin +(define hdf5-snippet + #~(begin + (for-each delete-file (find-files "." "Makefile\\.in$")) + (when (file-exists? "autom4te.cache") + (delete-file-recursively "autom4te.cache")) + (for-each (lambda (file) + (when (file-exists? file) + (delete-file file))) + (list + "configure" + "bin/ltmain.sh" + "bin/compile" + "bin/config.guess" + "bin/config.sub" + "bin/install-sh" + "bin/missing" + "bin/test-driver" + "bin/depcomp" + "src/H5config.h.in" + "src/H5Epubgen.h" + "src/H5Einit.h" + "src/H5Eterm.h" + "src/H5Edefin.h" + "src/H5version.h" + "src/H5overflow.h" + "aclocal.m4" + "hl/tools/gif2h5/testfiles/ex_image2.h5" + "hl/tools/gif2h5/testfiles/5giftst.h5" + "hl/src/H5LTparse.h" + "hl/src/H5LTparse.c" + "hl/src/H5LTanalyze.c" + ;; In later releases + "m4/libtool.m4" + "m4/ltoptions.m4" + "m4/ltsugar.m4" + "m4/ltversion.m4" + "m4/lt~obsolete.m4")))) + +;; In the 1.8.22 and 1.8.23 release, some m4 scripts are missing +(define hdf5-1.8.21-source + (let ((version "1.8.21")) + (origin (method url-fetch) (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" "hdf5-" (version-major+minor version) @@ -1394,18 +1431,53 @@ (define-public hdf5-1.8 (string-append major minor))) "/src/hdf5-" version ".tar.bz2"))) (sha256 - (base32 "0km65mr6dgk4ia2dqr1b9dzw9qg15j5z35ymbys9cnny51z1zb39")) - (patches (search-patches "hdf5-config-date.patch")))) + (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5")) + (modules '((guix build utils))) + (snippet hdf5-snippet) + (patches (search-patches "hdf5-config-date.patch"))))) + +(define-public hdf5-1.8 + (package + (name "hdf5") + (version "1.8.23") + (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" + (match (string-split version #\.) + ((major minor _ ...) + (string-append major minor))) + "/src/hdf5-" version ".tar.bz2"))) + (sha256 + (base32 "0km65mr6dgk4ia2dqr1b9dzw9qg15j5z35ymbys9cnny51z1zb39")) + (modules '((guix build utils))) + (snippet hdf5-snippet) + (patches (search-patches "hdf5-config-date.patch")))) (build-system gnu-build-system) (inputs (list zlib)) (native-inputs - (list gfortran perl)) ;part of the test machinery needs Perl + (list autoconf + automake + bison + flex + gfortran + libtool + ;; Needed to generate some headers and for tests + perl + which)) (outputs '("out" ; core library "fortran")) ; fortran interface (arguments - `(;; Some of the users, notably Flann, need the C++ interface. - #:configure-flags '("--enable-cxx" + (list + ;; Some of the users, notably Flann, need the C++ interface. + #:configure-flags #~(list + "--enable-cxx" "--enable-fortran" "--enable-fortran2003" @@ -1418,44 +1490,71 @@ (define-public hdf5-1.8 "--enable-threadsafe" "--with-pthread" "--enable-unsupported") - ;; Use -fPIC to allow the R bindings to link with the static libraries - #:make-flags (list "CFLAGS=-fPIC" - "CXXFLAGS=-fPIC") - #:phases - (modify-phases %standard-phases - (add-before 'configure 'patch-configure - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "configure" - (("/bin/mv") "mv")) - (substitute* "fortran/src/Makefile.in" - (("libhdf5_fortran_la_LDFLAGS =") - (string-append "libhdf5_fortran_la_LDFLAGS = -Wl,-rpath=" - (assoc-ref outputs "fortran") "/lib"))) - (substitute* "hl/fortran/src/Makefile.in" - (("libhdf5hl_fortran_la_LDFLAGS =") - (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath=" - (assoc-ref outputs "fortran") "/lib"))))) - (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/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:.*") - "Uname information: Linux\n")))) - (add-after 'install 'patch-references - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (zlib (assoc-ref inputs "zlib"))) - (substitute* (find-files bin "h5p?cc") - (("-lz" lib) - (string-append "-L" zlib "/lib " lib)))))) - (add-after 'install 'split + ;; Use -fPIC to allow the R bindings to link with the static libraries + #:make-flags #~(list "CFLAGS=-fPIC" + "CXXFLAGS=-fPIC") + #:phases + #~(modify-phases %standard-phases + ;; These scripts are missing in this release + (add-after 'unpack 'copy-scripts + (lambda _ + (invoke "tar" "-xf" #$hdf5-1.8.21-source + "-C" "m4" "--strip-components=2" + "hdf5-1.8.21/m4/aclocal_fc.m4" + "hdf5-1.8.21/m4/aclocal_cxx.m4") + (invoke "tar" "-xf" #$(package-source hdf5-1.10) + "-C" "bin" "--strip-components=2" + "hdf5-1.10.9/bin/genparser"))) + (add-after 'copy-scripts '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 'copy-scripts 'generate-flexbison + (lambda _ + (invoke "bash" "bin/genparser" "hl/src"))) + (add-before 'configure 'patch-configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "configure" + (("/bin/mv") "mv")) + (substitute* "fortran/src/Makefile.in" + (("libhdf5_fortran_la_LDFLAGS =") + (string-append "libhdf5_fortran_la_LDFLAGS = -Wl,-rpath=" + (assoc-ref outputs "fortran") "/lib"))) + (substitute* "hl/fortran/src/Makefile.in" + (("libhdf5hl_fortran_la_LDFLAGS =") + (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath=" + (assoc-ref outputs "fortran") "/lib"))))) + (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/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:.*") + "Uname information: Linux\n")))) + (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"))) + (add-after 'install 'patch-references + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (zlib (assoc-ref inputs "zlib"))) + (substitute* (find-files bin "h5p?cc") + (("-lz" lib) + (string-append "-L" zlib "/lib " lib)))))) + (add-after 'install 'split (lambda* (#:key inputs outputs #:allow-other-keys) ;; Move all fortran-related files (let* ((out (assoc-ref outputs "out")) @@ -1515,11 +1614,25 @@ (define-public hdf5-1.10 "/src/hdf5-" version ".tar.bz2"))) (sha256 (base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00")) - (patches (search-patches "hdf5-config-date.patch")))))) + (modules '((guix build utils))) + (snippet hdf5-snippet) + (patches (search-patches "hdf5-config-date.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments hdf5-1.8) + ((#:phases phases) + #~(modify-phases #$phases + (delete 'copy-scripts) + (add-after 'unpack 'patch-trace-shebang + (lambda _ + (for-each + patch-shebang + (find-files "bin" + (lambda (file stat) + (executable-file? file)))))))))))) (define-public hdf5-1.12 (package - (inherit hdf5-1.8) + (inherit hdf5-1.10) (version "1.12.2") (source (origin @@ -1535,11 +1648,13 @@ (define-public hdf5-1.12 "/src/hdf5-" version ".tar.bz2"))) (sha256 (base32 "1zlawdzb0gsvcxif14fwr5ap2gk4b6j02wirr2hcx8hkcbivp20s")) + (modules '((guix build utils))) + (snippet hdf5-snippet) (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf5-1.14 (package - (inherit hdf5-1.8) + (inherit hdf5-1.10) (version "1.14.0") (source (origin @@ -1555,6 +1670,8 @@ (define-public hdf5-1.14 "/src/hdf5-" version ".tar.bz2"))) (sha256 (base32 "181bdh8hp7v9xqwcby3lknr92lxlicc2hqscba3f5nhf8lrr9rz4")) + (modules '((guix build utils))) + (snippet hdf5-snippet) (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf5 diff --git a/gnu/packages/patches/hdf5-config-date.patch b/gnu/packages/patches/hdf5-config-date.patch index c105435dc2..d9710f91e9 100644 --- a/gnu/packages/patches/hdf5-config-date.patch +++ b/gnu/packages/patches/hdf5-config-date.patch @@ -1,14 +1,14 @@ Honor SOURCE_DATE_EPOCH when exporting configuration date. Autoconf-level patch submitted upstream on Wed Apr 13 17:03:23 UTC 2016 ---- a/configure -+++ b/configure -@@ -27737,7 +28573,14 @@ - +--- a/configure.ac ++++ b/configure.ac +@@ -3566,7 +3566,14 @@ + AC_SUBST([H5_VERSION]) ## Configuration date -- CONFIG_DATE="`date`" -+ CONFIG_DATE="`date -u`" +-AC_SUBST([CONFIG_DATE]) CONFIG_DATE="`date`" ++AC_SUBST([CONFIG_DATE]) CONFIG_DATE="`date -u`" +if test -n "$SOURCE_DATE_EPOCH"; then + CONFIG_DATE=`date -u -d "@$SOURCE_DATE_EPOCH" 2>/dev/null \ + || date -u -r "$SOURCE_DATE_EPOCH" 2>/dev/null` @@ -18,4 +18,4 @@ Autoconf-level patch submitted upstream on Wed Apr 13 17:03:23 UTC 2016 +fi ## User doing the configuration - CONFIG_USER="`whoami`@`hostname`" + AC_SUBST([CONFIG_USER]) CONFIG_USER="`whoami`@`hostname`" \ No newline at end of file -- 2.40.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 03 18:01:04 2023 Received: (at 64448) by debbugs.gnu.org; 3 Jul 2023 22:01:04 +0000 Received: from localhost ([127.0.0.1]:34594 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGRbU-0007Bd-6S for submit@debbugs.gnu.org; Mon, 03 Jul 2023 18:01:04 -0400 Received: from mout01.posteo.de ([185.67.36.65]:53965) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGRbS-0007At-V7 for 64448@debbugs.gnu.org; Mon, 03 Jul 2023 18:01:03 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id 6F2BB240027 for <64448@debbugs.gnu.org>; Tue, 4 Jul 2023 00:00:57 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1688421657; bh=lZUbEeBIFSoiWxy2EBNNKwvP5ExvDr5wqYjE+Zj5GGM=; h=From:To:Cc:Subject:Date:Message-Id:MIME-Version: Content-Transfer-Encoding:From; b=bm17PCq3gy9F6BMv+2ceOwnS6AYPdpOu+vDWJ4gVMz7Hk3d3BBOO/fIo/kY4asl1Z 8Sb0czm5Fyf45euMSa2cS0llO6K5han87qFwN0tBE1ezB/BIhQtnfrZIhRaNMzRKOy EDVYBUQYcB2iERrjLVHd1z7fDPKNIPpXh8obLuxISyL5zIjWdYICzJ6x7qXrNt381d TjTOCBuBt4Pk8rHUM0A0WI1qsM+j/+Q+l6BsZWhG3qecduyKUtgkgOck0JUxwD9bt8 GI/7eKiEbgF/VfGvyXksZVhrczXRgW4RH99EfMkN5UD4OcBLXnSFiKawPL9QXGg6++ ScIrI8Da/RGSw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4Qw0HF0T6tz6tvy; Tue, 4 Jul 2023 00:00:56 +0200 (CEST) From: David Elsing To: 64448@debbugs.gnu.org Subject: [PATCH 2/2] gnu: hdf5-1.14: Remove spurious include directories. Date: Mon, 3 Jul 2023 22:00:47 +0000 Message-Id: In-Reply-To: References: MIME-Version: 1.0 X-Debbugs-Cc: andreas@enge.fr, efraim@flashner.co.il, bavier@posteo.net Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64448 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 (hdf5-1.14)[arguments]: Use 'substitute-keyword-arguments' to add 'remove-subfiling-cppflags phase. --- gnu/packages/maths.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b2029db615..5ba9e07058 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1672,7 +1672,18 @@ (define-public hdf5-1.14 (base32 "181bdh8hp7v9xqwcby3lknr92lxlicc2hqscba3f5nhf8lrr9rz4")) (modules '((guix build utils))) (snippet hdf5-snippet) - (patches (search-patches "hdf5-config-date.patch")))))) + (patches (search-patches "hdf5-config-date.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments hdf5-1.10) + ((#:phases phases) + #~(modify-phases #$phases + ;; Remove include flag to directory in source tree + (add-after 'configure 'remove-subfiling-cppflags + (lambda _ + (substitute* '("src/libhdf5.settings" + "bin/h5cc" + "c++/src/h5c++") + (("-I.*/src/H5FDsubfiling") "")))))))))) (define-public hdf5 ;; Default version of HDF5. -- 2.40.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 04 17:14:12 2023 Received: (at 64448) by debbugs.gnu.org; 4 Jul 2023 21:14:12 +0000 Received: from localhost ([127.0.0.1]:36700 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGnLf-0002ZF-Oa for submit@debbugs.gnu.org; Tue, 04 Jul 2023 17:14:12 -0400 Received: from mout02.posteo.de ([185.67.36.66]:54075) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qGnLc-0002Yz-8e for 64448@debbugs.gnu.org; Tue, 04 Jul 2023 17:14:10 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 28B7D240105 for <64448@debbugs.gnu.org>; Tue, 4 Jul 2023 23:14:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1688505242; bh=/bAmEuY0Cc1ZomSwO6PZ8hMES3zFjfc6YR7XQwflNdk=; h=From:To:Subject:Date:Message-ID:MIME-Version:From; b=d3FNXKtK/xgVU3JPx6baTKWEn6sAbQKV7OLysQ/n2nYkE7DClueYFZ0ajkp5wjr2m h+xAJN3gg/JmOkxvdqPxw64WpL2jgfBiVJa7ihkOSRqrAYgsgGcK7oB0p/HjBet6bf qH0qUvPs8wGx4tvLJ4L9N/7/U8Ana5LWMVK6tLz6obs6BDha7PTOKfexn5NVvlxL6q x2T/17gldEIk3c0+mahkEtD453i66lI9fcISmZ+kbOi7Fe7lqnM/JnJvrGxTM5N4zz 7kF5nVsWubBxqp15zuegZ6hQhBFyuk3kAQy8wdMqpt1YDYHl88KESxL5hDXmxHydKP +hECix4tJKaJQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4QwbBd56Jwz9rxD for <64448@debbugs.gnu.org>; Tue, 4 Jul 2023 23:14:01 +0200 (CEST) From: David Elsing To: 64448@debbugs.gnu.org Subject: Re: [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. In-Reply-To: References: Date: Tue, 04 Jul 2023 21:14:01 +0000 Message-ID: <86fs63wfae.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64448 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 saw that the Git repository is also available, with the releases as tags: https://github.com/HDFGroup/hdf5. Would it be preferred to use them instead and make the snippet shorter? The missing scripts are also included for the 1.8.23 release. From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 24 09:50:02 2023 Received: (at 64448) by debbugs.gnu.org; 24 Jul 2023 13:50:02 +0000 Received: from localhost ([127.0.0.1]:42202 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNvwn-0008IU-Oi for submit@debbugs.gnu.org; Mon, 24 Jul 2023 09:50:02 -0400 Received: from hera.aquilenet.fr ([2a0c:e300::1]:54648) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNvwl-0008I2-AN for 64448@debbugs.gnu.org; Mon, 24 Jul 2023 09:50:00 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 92A201B4F; Mon, 24 Jul 2023 15:49:51 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id R-JPg5dWmisf; Mon, 24 Jul 2023 15:49:51 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id EC25619D; Mon, 24 Jul 2023 15:49:50 +0200 (CEST) Date: Mon, 24 Jul 2023 15:49:49 +0200 From: Andreas Enge To: David Elsing Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: bavier@posteo.net, 64448@debbugs.gnu.org, Gerd Heber , efraim@flashner.co.il 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, adding Gerd Heber in cc, who seems to be the last person having worked on these packages. I am not competent at all about them, so commenting more as an outsider. Using "guix package -A hdf": hdf4 4.2.14 out gnu/packages/maths.scm:1289:2 hdf4-alt 4.2.14 out gnu/packages/maths.scm:1372:2 hdf5 1.8.23 out,fortran gnu/packages/maths.scm:1382:2 hdf5 1.14.0 out,fortran gnu/packages/maths.scm:1543:2 hdf5 1.12.2 out,fortran gnu/packages/maths.scm:1523:2 hdf5 1.10.9 out,fortran gnu/packages/maths.scm:1503:2 hdf5-blosc 1.0.0 out gnu/packages/maths.scm:1807:2 hdf5-parallel-openmpi 1.10.9 out,fortran gnu/packages/maths.scm:1775:2 and a lot of packages in other languages, for instance: cl-hdf5-cffi 1.8.18-1.5b5c88f out gnu/packages/lisp-xyz.scm:12238:4 ecl-hdf5-cffi 1.8.18-1.5b5c88f out gnu/packages/lisp-xyz.scm:12238:4 (apparently based on 1.8.18? but it has hdf5-1.10 as input). So there are lots of versions, and in the middle of them, (define-public hdf5 ;; Default version of HDF5. hdf5-1.10) And hdf5-parallel-openmpi 1.10.9 out,fortran gnu/packages/maths.scm:1775:2 which inherits like this: (package/inherit hdf5-1.10 ;use the latest but takes inputs like this: (inputs `(("mpi" ,openmpi) ,@(package-inputs hdf5))) which, I suppose, works by chance since currently hdf5-1.10 and hdf5 are the same (but not "the latest"). Are all of these needed? If only the latest version 1.14.0 could be kept, this would make the patch for 1.8.23 obsolete, for instance. Andreas From debbugs-submit-bounces@debbugs.gnu.org Tue Aug 08 05:31:36 2023 Received: (at 64448) by debbugs.gnu.org; 8 Aug 2023 09:31:36 +0000 Received: from localhost ([127.0.0.1]:35213 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qTJ3w-00056v-74 for submit@debbugs.gnu.org; Tue, 08 Aug 2023 05:31:36 -0400 Received: from hera.aquilenet.fr ([2a0c:e300::1]:47586) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qTJ3u-00056g-QQ for 64448@debbugs.gnu.org; Tue, 08 Aug 2023 05:31:35 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 710A5390 for <64448@debbugs.gnu.org>; Tue, 8 Aug 2023 11:31:27 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id NdpKE1__5MVK for <64448@debbugs.gnu.org>; Tue, 8 Aug 2023 11:31:26 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id C877E170 for <64448@debbugs.gnu.org>; Tue, 8 Aug 2023 11:31:26 +0200 (CEST) Resent-From: Andreas Enge Resent-Date: Tue, 8 Aug 2023 11:31:25 +0200 Resent-Message-ID: Resent-To: 64448@debbugs.gnu.org Delivered-To: andreas.enge@aquilenet.fr Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 6B166C36; Mon, 24 Jul 2023 16:00:25 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id EYp9g6ly8iST; Mon, 24 Jul 2023 16:00:24 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id B496C298; Mon, 24 Jul 2023 16:00:24 +0200 (CEST) Date: Mon, 24 Jul 2023 16:00:23 +0200 From: Andreas Enge To: David Elsing Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 64448 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 Mon, Jul 24, 2023 at 03:49:49PM +0200 schrieb Andreas Enge: > Are all of these needed? Partial answer at https://portal.hdfgroup.org/display/support/HDF5+1.8.23 : "Future of HDF5-1.8 Please be aware that this will be the last release for HDF5 1.8. We encourage users to move to HDF5 1.10 or HDF5 1.14. Please refer to the release schedule for future releases of these versions." The schedule at https://github.com/HDFGroup/hdf5#release-schedule shows that 1.10 and 1.12 should see their last release this autumn, so probably we should really move to 1.14. $ guix refresh -l hdf5@1.8 Building the following 9 packages would ensure 16 dependent packages are rebuilt: pigx-sars-cov-2@0.0.9 pigx@0.0.3 nip2@8.7.1 python-pyvips@2.2.1 gnss-sdr@0.0.17 hdf-eos5@1.15 scilab@5.5.0 hdf-java@3.3.2 h5check@2.0.1 $ guix refresh -l hdf5@1.10 Building the following 210 packages would ensure 411 dependent packages are rebuilt: ... $ guix refresh -l hdf5@1.12 No dependents other than itself: hdf5@1.12.2 So this could probably be dropped immediately. $ guix refresh -l hdf5@1.14 Building the following 2 packages would ensure 2 dependent packages are rebuilt: ecl-hdf5-cffi@1.8.18-1.5b5c88f cl-hdf5-cffi@1.8.18-1.5b5c88f I suppose that the many dependencies on 1.10 come from the definition of the variable hd5 as hdf5-10; it is quite possible we could simply upgrade this to hdf5-14. Someone™ should give it a try... Andreas From debbugs-submit-bounces@debbugs.gnu.org Sun Aug 20 20:37:10 2023 Received: (at 64448) by debbugs.gnu.org; 21 Aug 2023 00:37:10 +0000 Received: from localhost ([127.0.0.1]:55078 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qXsus-0006xB-9F for submit@debbugs.gnu.org; Sun, 20 Aug 2023 20:37:10 -0400 Received: from mail-oo1-xc32.google.com ([2607:f8b0:4864:20::c32]:60641) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qXsuq-0006wx-LE for 64448@debbugs.gnu.org; Sun, 20 Aug 2023 20:37:09 -0400 Received: by mail-oo1-xc32.google.com with SMTP id 006d021491bc7-56ea1d3335cso1461066eaf.0 for <64448@debbugs.gnu.org>; Sun, 20 Aug 2023 17:37:06 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20221208; t=1692578221; x=1693183021; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:from:to:cc:subject:date:message-id:reply-to; bh=kLtch5EHRS4yO7M6Hxhc9urvyCjPBYSUqVhzcb2SXuA=; b=QsuUiKcahrgp0XEmf2dPfJKBWGv5onqZDbsurV48xK3O2HTE9TjwDF6vHP15yicZli vc2Y4F+fBlZK6WFfo8/ddc8+aMocFSANxwk5/g478SxDQdz3Fky5dOE/y8qfmcigrZDf IHfUQXLT3kxAlI1Sgm3noJiXaj30TsRwFhEuWIYRu1xTKOg+4CplJKS19wrpb77EsHwt Nj8QCysgVOn3Vbhk/1RrJUkKf75eiF44zHBsocHFy40uXcxqZhVqa0nc2WSLMV9Lfj8P DJces0nHPvjiM0riuMAuVeIqUozI/EdGLwE5f7HhMJoNApReFoQGXLEyEHYfMAggV8JL qGFw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20221208; t=1692578221; x=1693183021; h=cc:to:subject:message-id:date:from:in-reply-to:references :mime-version:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=kLtch5EHRS4yO7M6Hxhc9urvyCjPBYSUqVhzcb2SXuA=; b=E2tHXBdH1rVX6DA/O572GdBoPL4u3H1ljdw513+gM2K0orrUwuidDmlMCa+JmGJwCx 4Fx8E8fhmhVGv8oTwjDt4/XgZTtssD7UH+FRCGdM88fVEji45qeOLhw9LAErlcU/eK8V JFKwJT/B8WkU+9JwvnjuLEaOVrrIVh0IOLjn9dK03YGir44dXFP8YaZnFJSgg32lzish LbgVrkCvsiqzph0kX07CK1WNCycShcODQpQIZp+Z3rMsjS+KbsC1NqQvgf3uPgz+A1iM A1vcG7ttF/5q/RBunRiSBXRITBeQfRqb7KjQQUxEyhytz16c2sfECtXgj2sifiyx+Jcg SuNA== X-Gm-Message-State: AOJu0YzXSPPXIWATfx1Siqx/XIXQYwJclCpHOrMUa8Wn2r84pxorQoNh AmhvwXHFwb2X2t0JeC8zGxV0LFfRGOLGp4fIiBo= X-Google-Smtp-Source: AGHT+IHETvqQ6F7C0si8mhT79VAHJi8sXTGsbuwymUziJ/ZJ8w11rNgz1Oe7U687ncWKj+oIatSIgDc/kRJ84ZULiOs= X-Received: by 2002:a4a:2708:0:b0:56c:e4b7:2c0d with SMTP id l8-20020a4a2708000000b0056ce4b72c0dmr5611431oof.1.1692578220909; Sun, 20 Aug 2023 17:37:00 -0700 (PDT) MIME-Version: 1.0 References: In-Reply-To: From: Gerd Heber Date: Sun, 20 Aug 2023 19:36:50 -0500 Message-ID: Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. To: Andreas Enge Content-Type: multipart/alternative; boundary="0000000000009ca9b40603641393" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: David Elsing , bavier@posteo.net, 64448@debbugs.gnu.org, efraim@flashner.co.il 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 (-) --0000000000009ca9b40603641393 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Only HDF5 1.14.x (currently, 1.14.2) should be kept. However, hdf5 and hdf5-parallel should be kept separate. Aside from the MPI dependence, the parallel build is NOT a superset of the sequential version. There could be even two versions of hdf5: a non-threadsafe build (hdf5) and a threadsafe build (hdf5-ts? hdf5-mt?). For HDF4, 4.2.16-2 is the latest HDF4 release. We are maintaining that indefinitely (for NASA). Best, G. On Mon, Jul 24, 2023 at 8:49=E2=80=AFAM Andreas Enge wrot= e: > Hello, > > adding Gerd Heber in cc, who seems to be the last person having worked on > these packages. > > I am not competent at all about them, so commenting more as an outsider. > Using "guix package -A hdf": > hdf4 4.2.14 out > gnu/packages/maths.scm:1289:2 > hdf4-alt 4.2.14 out > gnu/packages/maths.scm:1372:2 > hdf5 1.8.23 out,fortran > gnu/packages/maths.scm:1382:2 > hdf5 1.14.0 out,fortran > gnu/packages/maths.scm:1543:2 > hdf5 1.12.2 out,fortran > gnu/packages/maths.scm:1523:2 > hdf5 1.10.9 out,fortran > gnu/packages/maths.scm:1503:2 > hdf5-blosc 1.0.0 out > gnu/packages/maths.scm:1807:2 > hdf5-parallel-openmpi 1.10.9 out,fortran > gnu/packages/maths.scm:1775:2 > > and a lot of packages in other languages, for instance: > cl-hdf5-cffi 1.8.18-1.5b5c88f out > gnu/packages/lisp-xyz.scm:12238:4 > ecl-hdf5-cffi 1.8.18-1.5b5c88f out > gnu/packages/lisp-xyz.scm:12238:4 > (apparently based on 1.8.18? but it has hdf5-1.10 as input). > > So there are lots of versions, and in the middle of them, > (define-public hdf5 > ;; Default version of HDF5. > hdf5-1.10) > > And > hdf5-parallel-openmpi 1.10.9 out,fortran > gnu/packages/maths.scm:1775:2 > which inherits like this: > (package/inherit hdf5-1.10 ;use the latest > but takes inputs like this: > (inputs > `(("mpi" ,openmpi) > ,@(package-inputs hdf5))) > which, I suppose, works by chance since currently hdf5-1.10 and hdf5 are > the same (but not "the latest"). > > Are all of these needed? If only the latest version 1.14.0 could be kept, > this would make the patch for 1.8.23 obsolete, for instance. > > Andreas > > --0000000000009ca9b40603641393 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Only HDF5 1.14.x (currently, 1.14.2) should be kept. However, h= df5 and hdf5-parallel should be kept separate. Aside from the MPI dependenc= e,
the parallel build is NOT a superset of the sequential version. There co= uld be even two versions of hdf5: a non-threadsafe build (hdf5) and a threa= dsafe build (hdf5-ts? hdf5-mt?).

For HDF4, 4.2.16-2 is the latest HDF4= release. We are maintaining that indefinitely (for NASA).

Best, G= .

On Mon, Jul 24, 2023 at 8:49=E2=80=AFAM Andreas Enge <andreas@enge.fr> wrote:
Hello,

adding Gerd Heber in cc, who seems to be the last person having worked on these packages.

I am not competent at all about them, so commenting more as an outsider. Using "guix package -A hdf":
hdf4=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4= .2.14=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 out=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1289:2<= br> hdf4-alt=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 4.2.14=C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 out=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1372:2
hdf5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1= .8.23=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 out,for= tran=C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1382:2
hdf5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1= .14.0=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 out,for= tran=C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1543:2
hdf5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1= .12.2=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 out,for= tran=C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1523:2
hdf5=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1= .10.9=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 out,for= tran=C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1503:2
hdf5-blosc=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.0.0=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0out=C2=A0 =C2=A0= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0gnu/packages/maths.scm:1807:2
hdf5-parallel-openmpi=C2=A0 =C2=A01.10.9=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 out,fortran=C2=A0 =C2=A0 =C2=A0gnu/packages/mat= hs.scm:1775:2

and a lot of packages in other languages, for instance:
cl-hdf5-cffi=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 1.8.18-1.5b5c88f=C2= =A0 =C2=A0 =C2=A0 =C2=A0 out=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0gnu/packages/lisp-xyz.scm:12238:4
ecl-hdf5-cffi=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A01.8.18-1.5b5c88f=C2= =A0 =C2=A0 =C2=A0 =C2=A0 out=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2= =A0gnu/packages/lisp-xyz.scm:12238:4
(apparently based on 1.8.18? but it has hdf5-1.10 as input).

So there are lots of versions, and in the middle of them,
(define-public hdf5
=C2=A0 ;; Default version of HDF5.
=C2=A0 hdf5-1.10)

And
hdf5-parallel-openmpi=C2=A0 =C2=A01.10.9=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 out,fortran=C2=A0 =C2=A0 =C2=A0gnu/packages/mat= hs.scm:1775:2
which inherits like this:
=C2=A0 (package/inherit hdf5-1.10=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 ;use the latest
but takes inputs like this:
=C2=A0 =C2=A0 (inputs
=C2=A0 =C2=A0 =C2=A0`(("mpi" ,openmpi)
=C2=A0 =C2=A0 =C2=A0 =C2=A0,@(package-inputs hdf5)))
which, I suppose, works by chance since currently hdf5-1.10 and hdf5 are the same (but not "the latest").

Are all of these needed? If only the latest version 1.14.0 could be kept, this would make the patch for 1.8.23 obsolete, for instance.

Andreas

--0000000000009ca9b40603641393-- From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 21 16:24:51 2023 Received: (at 64448) by debbugs.gnu.org; 21 Aug 2023 20:24:51 +0000 Received: from localhost ([127.0.0.1]:57997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qYBSE-0005GO-Ux for submit@debbugs.gnu.org; Mon, 21 Aug 2023 16:24:51 -0400 Received: from hera.aquilenet.fr ([2a0c:e300::1]:57642) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qYBSD-0005G9-1U for 64448@debbugs.gnu.org; Mon, 21 Aug 2023 16:24:49 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id C415BE0D; Mon, 21 Aug 2023 22:24:38 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id ramvbgYxpLFH; Mon, 21 Aug 2023 22:24:38 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 2D0492D7; Mon, 21 Aug 2023 22:24:38 +0200 (CEST) Date: Mon, 21 Aug 2023 22:24:36 +0200 From: Andreas Enge To: Gerd Heber Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: David Elsing , bavier@posteo.net, 64448@debbugs.gnu.org, efraim@flashner.co.il 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 Sun, Aug 20, 2023 at 07:36:50PM -0500 schrieb Gerd Heber: > Only HDF5 1.14.x (currently, 1.14.2) should be kept. However, hdf5 and > hdf5-parallel should be kept separate. Aside from the MPI dependence, > the parallel build is NOT a superset of the sequential version. There could be > even two versions of hdf5: a non-threadsafe build (hdf5) and a threadsafe build > (hdf5-ts? hdf5-mt?). > > For HDF4, 4.2.16-2 is the latest HDF4 release. We are maintaining that > indefinitely (for NASA). Thanks for the info, which helps us set a target! I am trying to update hdf4, see https://issues.guix.gnu.org/65443 Andreas From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 21 16:38:30 2023 Received: (at 64448) by debbugs.gnu.org; 21 Aug 2023 20:38:30 +0000 Received: from localhost ([127.0.0.1]:58006 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qYBfR-0005aM-RB for submit@debbugs.gnu.org; Mon, 21 Aug 2023 16:38:30 -0400 Received: from hera.aquilenet.fr ([2a0c:e300::1]:59238) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qYBfP-0005a5-C0 for 64448@debbugs.gnu.org; Mon, 21 Aug 2023 16:38:27 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 3BBCFE0D; Mon, 21 Aug 2023 22:38:18 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id mb75oIWgtR3m; Mon, 21 Aug 2023 22:38:17 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 9A79916C; Mon, 21 Aug 2023 22:38:17 +0200 (CEST) Date: Mon, 21 Aug 2023 22:38:16 +0200 From: Andreas Enge To: Gerd Heber Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: David Elsing , bavier@posteo.net, 64448@debbugs.gnu.org, efraim@flashner.co.il 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 (-) And I have removed hdf5@1.12, which had no dependent packages. Andreas From debbugs-submit-bounces@debbugs.gnu.org Mon Sep 25 18:06:34 2023 Received: (at 64448) by debbugs.gnu.org; 25 Sep 2023 22:06:34 +0000 Received: from localhost ([127.0.0.1]:46851 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qktir-0001sC-Ug for submit@debbugs.gnu.org; Mon, 25 Sep 2023 18:06:34 -0400 Received: from mout02.posteo.de ([185.67.36.66]:52215) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qktio-0001rs-Bu for 64448@debbugs.gnu.org; Mon, 25 Sep 2023 18:06:32 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id 287DA240101 for <64448@debbugs.gnu.org>; Tue, 26 Sep 2023 00:06:11 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1695679571; bh=RaGJGTFBV9+SmkvnG4748J5lCTOFEcUXUB+DQbBsMrs=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:From; b=ipd52zvjSOJedIgClTXjAcyAZt/hVR08C/DBIyzmZNfM1SiPdrT1LfgxW13+Y825w o3IJYqCbTSx9E3zTytWiMkGp40lD6cELQCWDO/X6+3sReC9fw6Sl0NkJFibjiWA0ha ma+Nn8y8xQS8nVJrSwjxBX8JFBKl2+PhTAShz9nwED5m2F6KQYvZhIGSHXJsovihWM QQl+h5bDA0z1HdhhQVe+8+Qj1HkJpqbEategwfoCFf3GjnkLF6tRs2UuEUC3q9wdwE cXq10HhZbeYSAVVXjxuamNFVNfDdrpEsy9FO45EuBOTe7QP5VmOxFoMQT0K4kfOhAQ jRBcGClNZjudg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4RvcQV3ySLz9rxL; Tue, 26 Sep 2023 00:06:10 +0200 (CEST) From: David Elsing To: Andreas Enge Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. In-Reply-To: References: Date: Mon, 25 Sep 2023 22:06:10 +0000 Message-ID: <7yo7hpzz59.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64448 Cc: 64448@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, > $ guix refresh -l hdf5@1.8 > Building the following 9 packages would ensure 16 dependent packages are rebuilt: pigx-sars-cov-2@0.0.9 pigx@0.0.3 nip2@8.7.1 python-pyvips@2.2.1 gnss-sdr@0.0.17 hdf-eos5@1.15 scilab@5.5.0 hdf-java@3.3.2 h5check@2.0.1 Currently, 5 packages depend directly on hdf5@1.8 (from guix graph -t reverse-package): -scilab, for which the latest version can be built with hdf5@1.14: https://issues.guix.gnu.org/66201 -hdf5-eos, for which the latest version can also be built with hdf5@1.14: https://issues.guix.gnu.org/66204 -java-cisd-jhdf5, where newer versions seem to be built only with Gradle: https://sissource.ethz.ch/sispub/jhdf5. It has fastqc and pigx(-*) as dependencies. -hdf-java, where the latest version is from 2017. Maybe it can be built with a newer HDF5 version? No other packages depend on it. -h5check, where the latest version is from 2014. When I tried to compile it with hdf5@1.14, some tests failed because the file format is not accepted anymore. No other packages depend on it. Cheers, David From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 26 12:06:12 2025 Received: (at 64448) by debbugs.gnu.org; 26 Mar 2025 16:06:12 +0000 Received: from localhost ([127.0.0.1]:44014 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1txTGd-0006ky-O2 for submit@debbugs.gnu.org; Wed, 26 Mar 2025 12:06:12 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:38852) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1txTGX-0006kH-K4 for 64448@debbugs.gnu.org; Wed, 26 Mar 2025 12:06:09 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 1B4F6DBB; Wed, 26 Mar 2025 17:05:58 +0100 (CET) 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 9Qx_y2F0Xd-z; Wed, 26 Mar 2025 17:05:57 +0100 (CET) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 1BEF9172; Wed, 26 Mar 2025 17:05:56 +0100 (CET) Date: Wed, 26 Mar 2025 17:05:53 +0100 From: Andreas Enge To: David Elsing Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: <7yo7hpzz59.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <7yo7hpzz59.fsf@posteo.net> X-Rspamd-Queue-Id: 1B4F6DBB X-Spamd-Result: default: False [-5.60 / 15.00]; BAYES_HAM(-3.00)[99.99%]; NEURAL_HAM(-3.00)[-1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCPT_COUNT_THREE(0.00)[3]; FROM_EQ_ENVFROM(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(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: 64448 Cc: Ricardo Wurmus , 64448@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, I have submitted two new issues with the goal of getting closer to removing hdf5@1.8 and hdf5@1.10, see https://issues.guix.gnu.org/77285 https://issues.guix.gnu.org/77287 Ricardo, since you seem to be interested in this package, your input there would be very welcome. And here also; after the proposed removal of h5check (which, I just see, does not even build any more), the only remaining direct dependency of hdf5@1.8 is java-cisd-jhdf5 and "guix refresh -l hdf5@1.8" lists pigx-sars-cov-2@0.0.9 trinityrnaseq@2.13.2 pigx@0.0.3 as leaf packages. Andreas From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 26 13:29:53 2025 Received: (at 64448) by debbugs.gnu.org; 26 Mar 2025 17:29:53 +0000 Received: from localhost ([127.0.0.1]:44233 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1txUZd-0002XU-2n for submit@debbugs.gnu.org; Wed, 26 Mar 2025 13:29:53 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21193) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1txUZa-0002XK-Q6 for 64448@debbugs.gnu.org; Wed, 26 Mar 2025 13:29:51 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1743010186; cv=none; d=zohomail.com; s=zohoarc; b=PcgGnXBY12pw9OxiBTJCOZt2J4jUdXwYZNZznAIaamDilFaTIn4VWBb7wzqNciKztiNs2o4vxniXkaisiGlM5ipy/HBbhDJVpOIn4F37B1fbwdhEhJyVlyQRzWNOzhEISsOQY8GqEKIK/MLdZj+PcGiUIUaqRcH0b8r/zfXOiX0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1743010186; h=Content-Type:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=rkJ+FJQWzLo2xnwt8nGgDW8JtuzEsfmmpyKrml4xR+E=; b=MnuKgYumV4QT+eEa3njpQ7ONrA08+DaqshFWD97P4RZYoqNcmRJb35glrvsV2b3LDiTIABxxFcC61t7UHtCCewrxBOmjeVTa4QE9ziUM2Jrzw5wJ0nWbLknqeIae/4rb6Kg2KDxnLEvMnSNjrhlv0bjGQvwjPdJzfaCjQFNBQs4= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1743010186; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:In-Reply-To:References:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=rkJ+FJQWzLo2xnwt8nGgDW8JtuzEsfmmpyKrml4xR+E=; b=BKJ/E4VHMSAfKCJAcSpb5jquCSuCANdW1LM6BkDp5b6IcAMwaKSIsZxoBNBQ0X98 uDyXmp6FJ9sb8EZTsgNDmcHZQdluNyy0FzmxOPdMXyCylS4qtKkOxOnrUH/+UF58vFG 4BV5qfxOP4Tyn/J4sLUEqdh4exhz5nz5wawgSGaU= Received: by mx.zohomail.com with SMTPS id 1743010183276894.5613536865442; Wed, 26 Mar 2025 10:29:43 -0700 (PDT) From: Ricardo Wurmus To: Andreas Enge Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. In-Reply-To: (Andreas Enge's message of "Wed, 26 Mar 2025 17:05:53 +0100") References: <7yo7hpzz59.fsf@posteo.net> User-Agent: mu4e 1.12.9; emacs 29.4 Date: Wed, 26 Mar 2025 18:29:39 +0100 Message-ID: <874izfhf98.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; format=flowed X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: David Elsing , 64448@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 (-) Hi Andreas, > I have submitted two new issues with the goal of getting closer > to > removing hdf5@1.8 and hdf5@1.10, see > https://issues.guix.gnu.org/77285 > https://issues.guix.gnu.org/77287 > > Ricardo, since you seem to be interested in this package, your > input > there would be very welcome. And here also; after the proposed > removal > of h5check (which, I just see, does not even build any more), > the only > remaining direct dependency of hdf5@1.8 is > java-cisd-jhdf5 > and "guix refresh -l hdf5@1.8" lists > pigx-sars-cov-2@0.0.9 trinityrnaseq@2.13.2 pigx@0.0.3 > as leaf packages. On the python-team branch the only user of java-cisd-jhdf5 is fastqc, which should be updated to a more recent version. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 28 16:39:18 2025 Received: (at 64448) by debbugs.gnu.org; 28 Mar 2025 20:39:18 +0000 Received: from localhost ([127.0.0.1]:55654 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tyGU1-0006O5-OJ for submit@debbugs.gnu.org; Fri, 28 Mar 2025 16:39:18 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:52294) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tyGTx-0006Nl-Fu for 64448@debbugs.gnu.org; Fri, 28 Mar 2025 16:39:16 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id D846F278; Fri, 28 Mar 2025 21:39:05 +0100 (CET) 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 fY2eShX6xz2e; Fri, 28 Mar 2025 21:39:05 +0100 (CET) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 102D623B; Fri, 28 Mar 2025 21:39:01 +0100 (CET) Date: Fri, 28 Mar 2025 21:38:57 +0100 From: Andreas Enge To: Ricardo Wurmus Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: <7yo7hpzz59.fsf@posteo.net> <874izfhf98.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <874izfhf98.fsf@elephly.net> X-Rspamd-Queue-Id: D846F278 X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(3.00)[1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCPT_COUNT_THREE(0.00)[3]; FROM_EQ_ENVFROM(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; ARC_NA(0.00)[] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spamd-Bar: +++++ X-Rspamd-Server: hera X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: David Elsing , 64448@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 Ricardo, Am Wed, Mar 26, 2025 at 06:29:39PM +0100 schrieb Ricardo Wurmus: > On the python-team branch the only user of java-cisd-jhdf5 is fastqc, which > should be updated to a more recent version. looking at its git repository, fastqc still requires java-cisd-jhdf5 (there is an eight year old jar file), so it does not look as if updating fastqc will help us get rid of java-cisd-jhdf5 and then hdf5@1.8. Andreas From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 31 06:24:24 2025 Received: (at 64448) by debbugs.gnu.org; 31 Mar 2025 10:24:24 +0000 Received: from localhost ([127.0.0.1]:39965 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzCJb-00087G-Oa for submit@debbugs.gnu.org; Mon, 31 Mar 2025 06:24:24 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:45288) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzCJX-00086O-Ga for 64448@debbugs.gnu.org; Mon, 31 Mar 2025 06:24:20 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id BBAEE240; Mon, 31 Mar 2025 12:24:11 +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 qXMB3C8WVR0d; Mon, 31 Mar 2025 12:24:11 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 79B56111; Mon, 31 Mar 2025 12:24:09 +0200 (CEST) Date: Mon, 31 Mar 2025 12:24:07 +0200 From: Andreas Enge To: David Elsing Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. Message-ID: References: <7yo7hpzz59.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Queue-Id: BBAEE240 X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(3.00)[1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCPT_COUNT_THREE(0.00)[3]; FROM_EQ_ENVFROM(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; ARC_NA(0.00)[] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spamd-Bar: +++++ X-Rspamd-Server: hera X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 64448 Cc: Ricardo Wurmus , 64448@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, with a lot of work on hdf5 unrelated to your original issue, this bug report has become a bit unwieldy (sorry for that, but I think we made good progress around this package complex!). So I wonder whether you would be okay closing this issue and opening new ones with updated patches? Useful remaining work would be updating hdf5@1.14 to its latest version; working towards getting rid of hdf5@1.8 and hdf5@1.10; and your original issue about generated files, which maybe could be combined with an update to hdf5@1.14 (I think there is no point in spending much work on the outdated versions that we would prefer to remove). For testing updates, it might make sense to wait until the non-building dependencies have been removed in about a month. What do you think? Andreas From debbugs-submit-bounces@debbugs.gnu.org Sun Apr 06 19:34:08 2025 Received: (at 64448-done) by debbugs.gnu.org; 6 Apr 2025 23:34:08 +0000 Received: from localhost ([127.0.0.1]:50138 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u1ZV9-0005Tp-SE for submit@debbugs.gnu.org; Sun, 06 Apr 2025 19:34:08 -0400 Received: from mout02.posteo.de ([185.67.36.66]:44847) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u1ZV4-0005St-Ta for 64448-done@debbugs.gnu.org; Sun, 06 Apr 2025 19:34:05 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id C1296240101 for <64448-done@debbugs.gnu.org>; Mon, 7 Apr 2025 01:33:56 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743982436; bh=29skx3NpIWaZ2aR14KPJq4SIqUX0GgyCq1NPL/Z+Vuc=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version:Content-Type: From; b=kZZV7I6yjdNOPPqo8qP5jMVOZNilurqDiwxUUPPb1xWqsph767jP7OqvygV9ehuDi mMmxvILjjz+IkGAHYr0to7Lhi0qoHXZ41Qj1TIFTsRA9dNrv8PKPlbX5GHDM2SbB3p +uZqdvtC5/Bs9dngAbGOws8IdGON3FpUcNb3m8anDryrm8xYNMgf07HCUwRW4RT3Zr 280WtDdcLMQTlnFwTRtnTnqlgBKonlgu2ODRlP3DnyaMPRDcA2uUAriaRxaejvWl5u GfCiheCqWmEzpkHRAJ20b6b9RRF5JgfZVHiOnJm1+uD6/2dIBm0Dnd8D02pQjmdvYJ TpgihPAMYJjQg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZW7vm113Tz6tw4; Mon, 7 Apr 2025 01:33:55 +0200 (CEST) From: David Elsing To: Andreas Enge Subject: Re: [bug#64448] [PATCH 0/2] Fix hdf5-1.14 wrappers and remove generated source files from all hdf5 versions. In-Reply-To: References: <7yo7hpzz59.fsf@posteo.net> Date: Sun, 06 Apr 2025 23:33:55 +0000 Message-ID: <7y34eksw4c.fsf@posteo.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 64448-done Cc: Ricardo Wurmus , 64448-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: -3.3 (---) Hi Andreas, Andreas Enge writes: > So I wonder whether you would be okay closing this issue and opening > new ones with updated patches? Sure, I'm closing it now. > Useful remaining work would be updating hdf5@1.14 to its latest version; > working towards getting rid of hdf5@1.8 and hdf5@1.10; > and your original issue about generated files, which maybe could be > combined with an update to hdf5@1.14 (I think there is no point in > spending much work on the outdated versions that we would prefer to > remove). Yes, that's a good suggestion, I made a new patch series which only changes hdf5@1.14 and hdf-java: https://issues.guix.gnu.org/77590 Thanks, David From unknown Thu Jun 19 14:10:49 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Mon, 05 May 2025 11:24:08 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator