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From: David Elsing <david.elsing@HIDDEN>
To: 77590 <at> 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
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* 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
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From: David Elsing <david.elsing@HIDDEN>
To: 77590 <at> debbugs.gnu.org
Subject: [PATCH v2 2/3] gnu: Add hdf5-examples.
Date: Mon, 7 Apr 2025 14:24:39 +0000
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* 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
Full text available.
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From: David Elsing <david.elsing@HIDDEN>
To: 77590 <at> debbugs.gnu.org
Subject: [PATCH v2 1/3] gnu: hdf5: Update to 1.14.6.
Date: Mon, 7 Apr 2025 14:24:38 +0000
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* 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 <roman.scherer@HIDDEN>
;;; Copyright © 2023 Jake Leporte <jakeleporte@HIDDEN>
;;; Copyright © 2023 Camilo Q.S. (Distopico) <distopico@HIDDEN>
-;;; Copyright © 2023 David Elsing <david.elsing@HIDDEN>
+;;; Copyright © 2023, 2025 David Elsing <david.elsing@HIDDEN>
;;; Copyright © 2024 Herman Rimm <herman@HIDDEN>
;;; Copyright © 2024 Foundation Devices, Inc. <hello@HIDDEN>
;;; Copyright © 2024, 2025 Artyom V. Poptsov <poptsov.artyom@HIDDEN>
@@ -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 <fenv.h> 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
Full text available.Received: (at 77590) by debbugs.gnu.org; 7 Apr 2025 14:25:06 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Apr 07 10:25:06 2025 Received: from localhost ([127.0.0.1]:56090 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u1nPN-0007r7-G8 for submit <at> 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 <david.elsing@HIDDEN>) id 1u1nPJ-0007pR-A5 for 77590 <at> 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 <at> 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 <david.elsing@HIDDEN> To: 77590 <at> 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: <cover.1744035216.git.david.elsing@HIDDEN> In-Reply-To: <cover.1743980993.git.david.elsing@HIDDEN> References: <cover.1743980993.git.david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 77590 Cc: David Elsing <david.elsing@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
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From: David Elsing <david.elsing@HIDDEN>
To: 77590 <at> 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
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* 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
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From: David Elsing <david.elsing@HIDDEN>
To: 77590 <at> debbugs.gnu.org
Subject: [PATCH 1/3] gnu: hdf5: Update to 1.14.6.
Date: Sun, 6 Apr 2025 23:26:40 +0000
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* 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 <roman.scherer@HIDDEN>
;;; Copyright © 2023 Jake Leporte <jakeleporte@HIDDEN>
;;; Copyright © 2023 Camilo Q.S. (Distopico) <distopico@HIDDEN>
-;;; Copyright © 2023 David Elsing <david.elsing@HIDDEN>
+;;; Copyright © 2023, 2025 David Elsing <david.elsing@HIDDEN>
;;; Copyright © 2024 Herman Rimm <herman@HIDDEN>
;;; Copyright © 2024 Foundation Devices, Inc. <hello@HIDDEN>
;;; Copyright © 2024, 2025 Artyom V. Poptsov <poptsov.artyom@HIDDEN>
@@ -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 <fenv.h> 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
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From: David Elsing <david.elsing@HIDDEN>
To: 77590 <at> debbugs.gnu.org
Subject: [PATCH 2/3] gnu: Add hdf5-examples.
Date: Sun, 6 Apr 2025 23:26:41 +0000
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* 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
guix-patches@HIDDEN:bug#77590; Package guix-patches.
Full text available.Received: (at submit) by debbugs.gnu.org; 6 Apr 2025 23:24:41 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Apr 06 19:24:41 2025 Received: from localhost ([127.0.0.1]:50104 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1u1ZM1-0004hU-3w for submit <at> 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 <david.elsing@HIDDEN>) id 1u1ZLz-0004gy-3c for submit <at> 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 <david.elsing@HIDDEN>) id 1u1ZLt-00079j-Ee for guix-patches@HIDDEN; 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 <david.elsing@HIDDEN>) id 1u1ZLr-0002PC-16 for guix-patches@HIDDEN; 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 <guix-patches@HIDDEN>; 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 <david.elsing@HIDDEN> To: guix-patches@HIDDEN 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: <cover.1743980993.git.david.elsing@HIDDEN> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=david.elsing@HIDDEN; 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 <david.elsing@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> 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
David Elsing <david.elsing@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#77590; Package guix-patches.
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