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>
View this message in rfc822 format
From: David Elsing <david.elsing <at> posteo.net> To: 77590 <at> debbugs.gnu.org Cc: David Elsing <david.elsing <at> posteo.net> Subject: [bug#77590] [PATCH v2 1/3] gnu: hdf5: Update to 1.14.6. Date: Mon, 7 Apr 2025 14:24:38 +0000
* 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 <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 +1834,187 @@ (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
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.