Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Sun, 6 Apr 2025 23:25:01 UTC
Severity: normal
Tags: patch
Done: Andreas Enge <andreas <at> enge.fr>
Message #38 received at 77590 <at> debbugs.gnu.org (full text, mbox):
From: David Elsing <david.elsing <at> posteo.net> To: 77590 <at> debbugs.gnu.org Cc: David Elsing <david.elsing <at> posteo.net> Subject: [PATCH v3 1/2] gnu: hdf5: Update to 1.14.6. Date: Thu, 10 Apr 2025 22:42:55 +0000
* gnu/packages/maths.scm (hdf5): Update to 1.14.6. Do not inherit from
hdf5-1.8.
[name, version]: New field.
[source]: Switch to git-fetch. Add modules and snippet fields. Use different
patch file.
[build-system]: New field. Use CMake.
[inputs]: New field.
[native-inputs]: New field. Add bison, flex and which.
[arguments]: Do not inherit from hdf5-1.8.
<#:configure-flags>: New field.
<#:phases>: New field. Use gexps. Remove 'patch-configure, 'patch-settings,
'patch-references, 'split, 'skip-version-test and
'patch-configure-build-settings phases. Add 'make-gen-deterministic,
'generate-flexbison, 'patch-trace-shebang, 'fix-fortran-i686-test and
'generate-headers phases.
[home-page, synopsis, description]: New fields.
[license]: New field. Adjust URL.
---
gnu/packages/maths.scm | 152 ++++++++++++++++++++++++++++++++---------
1 file changed, 119 insertions(+), 33 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 11a86216aa..5b7398756c 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -62,7 +62,7 @@
;;; Copyright © 2022 Roman Scherer <roman.scherer <at> burningswell.com>
;;; Copyright © 2023 Jake Leporte <jakeleporte <at> outlook.com>
;;; Copyright © 2023 Camilo Q.S. (Distopico) <distopico <at> riseup.net>
-;;; Copyright © 2023 David Elsing <david.elsing <at> posteo.net>
+;;; Copyright © 2023, 2025 David Elsing <david.elsing <at> posteo.net>
;;; Copyright © 2024 Herman Rimm <herman <at> rimm.ee>
;;; Copyright © 2024 Foundation Devices, Inc. <hello <at> foundation.xyz>
;;; Copyright © 2024, 2025 Artyom V. Poptsov <poptsov.artyom <at> gmail.com>
@@ -1834,44 +1834,130 @@ (define-public hdf5-1.10
(base32 "14gih7kmjx4h3lc7pg4fwcl28hf1qqkf2x7rljpxqvzkjrqbxi00"))
(patches (search-patches "hdf5-config-date.patch"))))))
-;; When updating this package, please also update hdf-java.
(define-public hdf5
(package
- (inherit hdf5-1.8)
- (version "1.14.3")
+ (name "hdf5")
+ (version "1.14.6")
(source
(origin
- (method url-fetch)
- (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
- "hdf5-" (version-major+minor version)
- "/hdf5-" version "/src/hdf5-"
- version ".tar.bz2")
- (string-append "https://support.hdfgroup.org/ftp/HDF5/"
- "current"
- (apply string-append
- (take (string-split version #\.) 2))
- "/src/hdf5-" version ".tar.bz2")))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/HDFGroup/hdf5")
+ (commit (string-append "hdf5_" version))))
+ (file-name (git-file-name name version))
(sha256
- (base32 "05zr11y3bivfwrbvzbky1q2gjf6r7n92cvvdnh5jilbmxljg49cl"))
- (patches (search-patches "hdf5-config-date.patch"))))
+ (base32
+ "1f7yv0xra465c3qy8c79fzddib653wzj5dsakb0bs02nwp3xm54q"))
+ (modules '((guix build utils)))
+ (snippet
+ '(for-each
+ delete-file
+ (append
+ (find-files "." "Makefile\\.in$")
+ (find-files "java/lib" "\\.jar$")
+ (list "aclocal.m4"
+ "bin/compile"
+ "bin/config.guess"
+ "bin/config.sub"
+ "bin/depcomp"
+ "bin/install-sh"
+ "bin/ltmain.sh"
+ "bin/missing"
+ "bin/test-driver"
+ "configure"
+ "HDF5Examples/aclocal.m4"
+ "HDF5Examples/compile"
+ "HDF5Examples/configure"
+ "HDF5Examples/depcomp"
+ "HDF5Examples/missing"
+ "HDF5Examples/test-driver"
+ "hl/src/H5LTanalyze.c"
+ "hl/src/H5LTparse.c"
+ "hl/src/H5LTparse.h"
+ "hl/tools/gif2h5/testfiles/ex_image2.h5"
+ "hl/tools/gif2h5/testfiles/h52giftst.h5"
+ "m4/ax_prog_doxygen.m4"
+ "m4/libtool.m4"
+ "m4/lt~obsolete.m4"
+ "m4/ltoptions.m4"
+ "m4/ltsugar.m4"
+ "m4/ltversion.m4"
+ "src/H5config.h.in"
+ "src/H5Edefin.h"
+ "src/H5Einit.h"
+ "src/H5Epubgen.h"
+ "src/H5Eterm.h"
+ "src/H5overflow.h"
+ "src/H5version.h"))))))
+ (build-system cmake-build-system)
+ (inputs (list zlib))
+ (native-inputs
+ (list bison
+ flex
+ gfortran
+ ;; Needed to generate some headers and for tests
+ perl
+ which))
(arguments
- (substitute-keyword-arguments (package-arguments hdf5-1.8)
- ((#:phases phases #~%standard-phases)
- #~(modify-phases #$phases
- (add-after 'configure 'skip-version-test
- (lambda _
- ;; Skip test_check_version since the 'patch-settings' phase
- ;; modifies the test reference.
- (substitute* "test/test_check_version.sh.in"
- (("TESTING\\(\\).*" all)
- (string-append all "\nSKIP; exit 0\n")))))
- (add-after 'patch-configure 'patch-configure-build-settings
- (lambda _
- (substitute* "src/H5build_settings.autotools.c.in"
- ;; Don't record the build-time kernel version to make the
- ;; library file reproducible.
- (("@UNAME_INFO@")
- "Linux"))))))))))
+ (list
+ ;; Some of the users, notably Flann, need the C++ interface.
+ #:configure-flags
+ ''("-DHD5F_ENABLE_THREADSAFE=ON"
+ "-DHDF5_BUILD_CPP_LIB=ON"
+ "-DHDF5_BUILD_DOC=ON"
+ "-DHDF5_BUILD_FORTRAN=ON")
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; XXX: src/H5private.h includes <fenv.h> and fails to find the
+ ;; stdlib types when the gfortran header is used. Remove gfortran
+ ;; from CPLUS_INCLUDE_PATH as a workaround.
+ (add-after 'set-paths 'hide-gfortran
+ (lambda _
+ (let ((gfortran #$(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))))))
+ ;; This is a known issue on i686, see
+ ;; https://github.com/HDFGroup/hdf5/issues/4926
+ (add-after 'unpack 'fix-fortran-i686-test
+ (lambda _
+ (substitute* "fortran/test/tH5R.F90"
+ (((string-append
+ "CALL h5rget_obj_name_f\\(C_LOC\\(ref_ptr\\(2\\)\\),"
+ " \"\", error, name_len=buf_size \\)"))
+ (string-append
+ "CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)),"
+ " \"xxxxxxxxxxxxxx\", error, name_len=buf_size)")))))
+ (add-after 'unpack 'generate-headers
+ (lambda _
+ (invoke "perl" "bin/make_err" "src/H5err.txt")
+ (invoke "perl" "bin/make_vers" "src/H5vers.txt")
+ (invoke "perl" "bin/make_overflow" "src/H5overflow.txt"))))))
+ (home-page "https://www.hdfgroup.org")
+ (synopsis "Management suite for extremely large and complex data")
+ (description "HDF5 is a suite that makes possible the management of
+extremely large and complex data collections.")
+ (license (license:x11-style
+ "https://support.hdfgroup.org/ftp/HDF5/releases/COPYING.html"))))
;; Keep this in sync with the current hdf5 package.
(define-public hdf-java
--
2.48.1
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Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.