Bug#1144001: bitshuffle: FTBFS: ValueError: list.remove(x): x not in list

Gilles Filippini <[email protected]> Mon, 17 Aug 2026 12:58:08 +0200

Newsgroups	gmane.linux.debian.devel.bugs.rc
Message-ID	<[email protected]>

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: [email protected]
> 
> 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.

bitshuffle.debdiff (text/plain, 1.7 KB)

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 <[email protected]>  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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