Bug#1139554: xmds2: FTBFS against HDF5 2.1.0 - The waf toolchain has to be adapted
Gilles Filippini
pini at debian.org
Mon Jun 22 15:58:53 BST 2026
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.
-------------- next part --------------
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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