[Debian-pan-maintainers] Bug#1144001: bitshuffle: FTBFS: ValueError: list.remove(x): x not in list
Gilles Filippini
pini at debian.org
Mon Aug 17 11:58:08 BST 2026
Control: tags -1 + patch
Hi,
Sebastian Ramacher a écrit le 09/08/2026 à 17:27 :
> Source: bitshuffle
> Version: 0.5.2-1
> Severity: serious
> Tags: ftbfs
> Justification: fails to build from source (but built successfully in the past)
> X-Debbugs-Cc: sramacher at debian.org
>
> Dear maintainer,
>
> bitshuffle FTBFS:
>
> make[1]: Entering directory '/build/reproducible-path/bitshuffle-0.5.2'
> CC=mpicc dh_auto_build
> pybuild --build -i python{version} -p "3.13 3.14" --parallel=6
> I: pybuild plugin_pyproject:142: Building wheel for python3.13 with "build" module
> I: pybuild base:385: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/bitshuffle-0.5.2/.pybuild/cpython3_3.13_bitshuffle
> * Building wheel...
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
> main()
> ~~~~^^
> File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in main
> json_out["return_val"] = hook(**hook_input["kwargs"])
> ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
> return _build_backend().build_wheel(
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
> wheel_directory, config_settings, metadata_directory
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> )
> ^
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 435, in build_wheel
> return _build(['bdist_wheel'])
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 426, in _build
> return self._build_with_temp_dir(
> ~~~~~~~~~~~~~~~~~~~~~~~~~^
> cmd,
> ^^^^
> ...<3 lines>...
> self._arbitrary_args(config_settings),
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> )
> ^
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
> self.run_setup()
> ~~~~~~~~~~~~~~^^
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 320, in run_setup
> exec(code, locals())
> ~~~~^^^^^^^^^^^^^^^^
> File "<string>", line 169, in <module>
> ValueError: list.remove(x): x not in list
>
> TIP pass --env-dir and --sdist-extract-dir to keep the build environment and sources, then see https://build.pypa.io/en/stable/how-to/troubleshooting.html#debug-a-failed-build for help debugging a failed build
> ERROR Backend subprocess exited when trying to invoke build_wheel
> E: pybuild pybuild:485: build: plugin pyproject failed with: exit code=1: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/bitshuffle-0.5.2/.pybuild/cpython3_3.13_bitshuffle
> I: pybuild plugin_pyproject:142: Building wheel for python3.14 with "build" module
> I: pybuild base:385: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/bitshuffle-0.5.2/.pybuild/cpython3_3.14_bitshuffle
> * Building wheel...
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
> main()
> ~~~~^^
> File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in main
> json_out["return_val"] = hook(**hook_input["kwargs"])
> ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
> File "/usr/lib/python3/dist-packages/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
> return _build_backend().build_wheel(
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
> wheel_directory, config_settings, metadata_directory
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> )
> ^
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 435, in build_wheel
> return _build(['bdist_wheel'])
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 426, in _build
> return self._build_with_temp_dir(
> ~~~~~~~~~~~~~~~~~~~~~~~~~^
> cmd,
> ^^^^
> ...<3 lines>...
> self._arbitrary_args(config_settings),
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> )
> ^
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line 407, in _build_with_temp_dir
> self.run_setup()
> ~~~~~~~~~~~~~~^^
> File "/usr/lib/python3/dist-packages/setuptools/build_meta.py", line
> 320, in run_setup
> exec(code, locals())
> ~~~~^^^^^^^^^^^^^^^^
> File "<string>", line 169, in <module>
> ValueError: list.remove(x): x not in list
>
> TIP pass --env-dir and --sdist-extract-dir to keep the build environment and sources, then see https://build.pypa.io/en/stable/how-to/troubleshooting.html#debug-a-failed-build for help debugging a failed build
> ERROR Backend subprocess exited when trying to invoke build_wheel
> E: pybuild pybuild:485: build: plugin pyproject failed with: exit code=1: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/bitshuffle-0.5.2/.pybuild/cpython3_3.14_bitshuffle
> dh_auto_build: error: pybuild --build -i python{version} -p "3.13 3.14" --parallel=6 returned exit code 13
> make[1]: *** [debian/rules:34: override_dh_auto_build] Error 25
>
> See
> https://buildd.debian.org/status/fetch.php?pkg=bitshuffle&arch=amd64&ver=0.5.2-1%2Bb5&stamp=1786283965&raw=0
> for details.
Patch proposal attached.
Best,
_g.
-------------- next part --------------
diff -Nru bitshuffle-0.5.2/debian/changelog bitshuffle-0.5.2/debian/changelog
--- bitshuffle-0.5.2/debian/changelog 2024-11-19 12:15:44.000000000 +0100
+++ bitshuffle-0.5.2/debian/changelog 2026-05-28 21:46:46.000000000 +0200
@@ -1,3 +1,10 @@
+bitshuffle (0.5.2-1.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Fix FTBFS against HDF5 >= 2.1.0 (closes: #1144001)
+
+ -- Gilles Filippini <pini at debian.org> Thu, 28 May 2026 21:46:46 +0200
+
bitshuffle (0.5.2-1) unstable; urgency=medium
* New upstream version 0.5.2
diff -Nru bitshuffle-0.5.2/debian/patches/hdf5-2.patch bitshuffle-0.5.2/debian/patches/hdf5-2.patch
--- bitshuffle-0.5.2/debian/patches/hdf5-2.patch 1970-01-01 01:00:00.000000000 +0100
+++ bitshuffle-0.5.2/debian/patches/hdf5-2.patch 2026-05-28 21:46:46.000000000 +0200
@@ -0,0 +1,14 @@
+Index: bitshuffle-0.5.2/setup.py
+===================================================================
+--- bitshuffle-0.5.2.orig/setup.py
++++ bitshuffle-0.5.2/setup.py
+@@ -166,7 +166,8 @@ h5filter = Extension(
+
+ if not sys.platform.startswith("win"):
+ h5filter.sources.append("src/hdf5_dl.c")
+- h5filter.libraries.remove("hdf5")
++ if "hdf5" in h5filter.libraries:
++ h5filter.libraries.remove("hdf5")
+
+ filter_plugin = Extension(
+ "bitshuffle.plugin.libh5bshuf",
diff -Nru bitshuffle-0.5.2/debian/patches/series bitshuffle-0.5.2/debian/patches/series
--- bitshuffle-0.5.2/debian/patches/series 2024-11-19 12:15:44.000000000 +0100
+++ bitshuffle-0.5.2/debian/patches/series 2026-05-28 21:46:46.000000000 +0200
@@ -3,3 +3,4 @@
0003-link-with-libzstd.patch
0004-cython-and-setuptools-are-not-runtime-dependencies.patch
0005-remove-march-and-mcpu-to-avoid-FTBFS.patch
+hdf5-2.patch
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