Bug#1139554: xmds2: FTBFS against HDF5 2.1.0 - The waf toolchain has to be adapted
pini at debian.org
pini at debian.org
Tue Jun 23 14:34:52 BST 2026
Hi Rafaël,
Le 2026-06-23 13:43, Rafael Laboissière a écrit :
> 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.
I use a local repo for the rebuilt reverse-depedencies.
Plus a dedicated sbuild chroot with unstable + experimental + local
repo, and HDF5 packages in experimental Priority-Pined, as well as all
the packages in the local repo.
I rebuild all the reverse dependencies in the order given by the ben
file and upload them into the local repo. So xmds2 is rebuilt against:
* hdf5 2.1.0 in experimental
* h5py rebuilt against hdf5 2.1.0
* octave rebuilt against hdf5 2.1.0
Best,
_g.
> 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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