Control: tags -1 + patch Hi,
Gilles Filippini a écrit le 09/06/2026 à 14:57 :
Source: xmds2
Version: 3.1.0+dfsg2-13
Severity: important
Tags: ftbfs
Hi,
During a test rebuild of HDF5's reverse dependcies against HDF5 2.1.0
currently in experimental, xmds2 FTBFS with:
Checking for program 'h5cc' : /usr/bin/h5cc
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/bin-test/xmds2", line 4, in <module>
sys.exit(parser2.main())
~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/xpdeint/parser2.py", line 219, in main
return Configuration.run_reconfig(includePaths, libPaths)
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/xpdeint/Configuration.py", line 145, in run_reconfig
return run_config(includePaths = includePaths, libPaths = libPaths)
File "/<<PKGBUILDDIR>>/xpdeint/Configuration.py", line 119, in run_config
ret = ctx.execute()
File "/<<PKGBUILDDIR>>/xpdeint/waf/waflib/Configure.py", line 159, in execute
super(ConfigurationContext, self).execute()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/xpdeint/waf/waflib/Context.py", line 204, in execute
self.recurse([os.path.dirname(g_module.root_path)])
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/xpdeint/Configuration.py", line 56, in <lambda>
lambda x, y: getattr(Context.g_module, x.cmd or x.fun, Utils.nada)(x)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
File "/<<PKGBUILDDIR>>/xpdeint/Configuration.py", line 85, in _
return f(ctx, *args, **kw)
File "/<<PKGBUILDDIR>>/xpdeint/support/wscript", line 754, in configure
configure_compiler()
~~~~~~~~~~~~~~~~~~^^
File "/<<PKGBUILDDIR>>/xpdeint/support/wscript", line 411, in
configure_compiler
hdf5_libpath = re.search(r'\s-L(\S+)', h5cc_shared_flags).group(1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'group'
I tried to poke into the xpdeint/support/wscript file; but while xmds2 seems
to build successfully many tests fail then. So I let it to the maintainer of
the package :)
Don't hesitate to reach if needed, as I am in touch with HDF5 devs and
they are willing to help.
Best, _g.
diff -Nru xmds2-3.1.0+dfsg2/debian/changelog xmds2-3.1.0+dfsg2/debian/changelog --- xmds2-3.1.0+dfsg2/debian/changelog 2026-03-26 13:48:46.000000000 +0100 +++ xmds2-3.1.0+dfsg2/debian/changelog 2026-06-22 16:17:06.000000000 +0200 @@ -1,3 +1,10 @@ +xmds2 (3.1.0+dfsg2-13.1) UNRELEASED; urgency=medium + + * Non-maintainer upload. + * New patch to add support for HDF5 2.1.0 (closes: #1139554) + + -- Gilles Filippini <[email protected]> Mon, 22 Jun 2026 16:17:06 +0200 + xmds2 (3.1.0+dfsg2-13) unstable; urgency=medium * Upload to unstable diff -Nru xmds2-3.1.0+dfsg2/debian/patches/hdf5-2.1.0.patch xmds2-3.1.0+dfsg2/debian/patches/hdf5-2.1.0.patch --- xmds2-3.1.0+dfsg2/debian/patches/hdf5-2.1.0.patch 1970-01-01 01:00:00.000000000 +0100 +++ xmds2-3.1.0+dfsg2/debian/patches/hdf5-2.1.0.patch 2026-06-22 16:17:06.000000000 +0200 @@ -0,0 +1,58 @@ +Index: xmds2-3.1.0+dfsg2/xpdeint/support/wscript +=================================================================== +--- xmds2-3.1.0+dfsg2.orig/xpdeint/support/wscript ++++ xmds2-3.1.0+dfsg2/xpdeint/support/wscript +@@ -400,22 +400,31 @@ def configure(conf): + if conf.env['ENVIRONMENT_NAME'] == 'default': + hdf5_helper = 'h5cc' + hdf5_helper_var = 'H5CC' ++ hdf5_lib = 'hdf5_serial' ++ hdf5_hl_lib = 'hdf5_serial_hl' + else: + hdf5_helper = 'h5pcc' + hdf5_helper_var = 'H5PCC' ++ helper_implementation = "/usr/bin/h5pcc" ++ while os.path.islink(helper_implementation): ++ helper_implementation = os.readlink(helper_implementation) ++ hdf5_mpi_flavor = os.path.splitext(helper_implementation)[1][1:] ++ hdf5_lib = f'hdf5_{hdf5_mpi_flavor}' ++ hdf5_hl_lib = f'hdf5_{hdf5_mpi_flavor}_hl' + + if conf.find_program(f'{hdf5_helper}', var=hdf5_helper_var, mandatory = False): + h5cc_shared_flags = conf.cmd_and_log([conf.env[hdf5_helper_var][0], '-show', '-shlib']) + h5cc_static_flags = conf.cmd_and_log([conf.env[hdf5_helper_var][0], '-show', '-noshlib']) + +- hdf5_libpath = re.search(r'\s-L(\S+)', h5cc_shared_flags).group(1) +- +- conf.env.append_unique("LIBPATH_hdf5", hdf5_libpath) ++ re_res = re.search(r'\s-L(\S+)', h5cc_shared_flags) ++ if re_res: ++ hdf5_libpath = re_res.group(1) ++ conf.env.append_unique("LIBPATH_hdf5", hdf5_libpath) + + # h5cc uses absolute paths to the static libraries. This interferes with how waf likes to link + # against static libraries. Let's remove the absolute paths to the libraries, and add the static libraries + # again later. +- h5cc_static_flags = re.sub(re.escape(hdf5_libpath) + r"/libhdf5\S*\.a", "", h5cc_static_flags) ++ h5cc_static_flags = re.sub(r" /[^ ]*/lib(hdf5\S*)\.a", r" -l\1", h5cc_static_flags) + + conf.parse_flags(h5cc_shared_flags, 'hdf5_shared') + conf.parse_flags(h5cc_static_flags, 'hdf5_static') +@@ -423,7 +432,7 @@ def configure(conf): + conf.env['uselib'].extend(['hdf5_shared', 'hdf5_static']) + + check_cxx( +- lib='hdf5', ++ lib=hdf5_lib, + header_name='hdf5.h', + #function_name='H5check_version', + fragment=''' +@@ -444,7 +453,7 @@ def configure(conf): + if 'hdf5' in conf.env['uselib']: + + check_cxx( +- lib='hdf5_hl', ++ lib=hdf5_hl_lib, + defines='HAVE_HDF5_HL', + header_name=['hdf5.h', 'hdf5_hl.h'], + fragment=''' diff -Nru xmds2-3.1.0+dfsg2/debian/patches/series xmds2-3.1.0+dfsg2/debian/patches/series --- xmds2-3.1.0+dfsg2/debian/patches/series 2026-03-26 13:48:46.000000000 +0100 +++ xmds2-3.1.0+dfsg2/debian/patches/series 2026-06-22 16:17:06.000000000 +0200 @@ -16,3 +16,4 @@ wscript-hdf5-cmake-support.patch wscript-hdf5-mpi-support.patch auto-gitignore +hdf5-2.1.0.patch
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