Bug#1139554: xmds2: FTBFS against HDF5 2.1.0 - The waf toolchain has to be adapted
Rafael Laboissière
rafael at debian.org
Tue Jun 23 12:43:22 BST 2026
Salut Gilles,
Thanks for the bug report and for the patch.
Which build-dependencies do you use to build the xmds2 package, in order to reproduce the FTBFS issue? The package builds fine against the libhdf5-dev and libhdf5-mpi-dev packages currently in experimental.
Best,
Rafael
* Gilles Filippini <pini at debian.org> [2026-06-22 16:58]:
> 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.
> Please review the attached patch. I've tested it with both HDF5 1.14.6 in
> unstable and HDF5 2.1.0 in experimental.
>
> 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 <pini at debian.org> 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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