Bug#1123337: rpy2: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13

[Santiago Vila]

Package: src:rpy2
Version: 3.6.4-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202512/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:rpy2, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --with python3 --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
   debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rfv .pybuild build */build src/*.egg-info */src/*.egg-info
find . -name __pycache__ | rm -rfv
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --with python3 --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild

[... snipped ...]

copying build/lib/rpy2/robjects/tests/robjects/test_packages.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/test_array.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/test_vector_datetime.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/test_rs4.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/test_dataframe.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/test_serialization.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/tests/robjects/test_robjects.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects/tests/robjects
copying build/lib/rpy2/robjects/packages.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects
copying build/lib/rpy2/robjects/methods.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects
copying build/lib/rpy2/robjects/pandas2ri.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects
copying build/lib/rpy2/robjects/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2/robjects
creating build/bdist.linux-x86_64/wheel/rpy2/interactive
copying build/lib/rpy2/interactive/packages.py -> build/bdist.linux-x86_64/wheel/./rpy2/interactive
copying build/lib/rpy2/interactive/process_revents.py -> build/bdist.linux-x86_64/wheel/./rpy2/interactive
copying build/lib/rpy2/interactive/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2/interactive
creating build/bdist.linux-x86_64/wheel/rpy2/ipython
copying build/lib/rpy2/ipython/rmagic.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython
creating build/bdist.linux-x86_64/wheel/rpy2/ipython/tests
copying build/lib/rpy2/ipython/tests/test_html.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython/tests
copying build/lib/rpy2/ipython/tests/test_ggplot.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython/tests
copying build/lib/rpy2/ipython/tests/test_rmagic.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython/tests
copying build/lib/rpy2/ipython/tests/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython/tests
copying build/lib/rpy2/ipython/ggplot.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython
copying build/lib/rpy2/ipython/html.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython
copying build/lib/rpy2/ipython/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2/ipython
running install_egg_info
Copying src/rpy2_robjects.egg-info to build/bdist.linux-x86_64/wheel/./rpy2_robjects-3.6.3.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/rpy2_robjects-3.6.3.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/.tmp-kfj92hxw/rpy2_robjects-3.6.3-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'rpy2/interactive/__init__.py'
adding 'rpy2/interactive/packages.py'
adding 'rpy2/interactive/process_revents.py'
adding 'rpy2/ipython/__init__.py'
adding 'rpy2/ipython/ggplot.py'
adding 'rpy2/ipython/html.py'
adding 'rpy2/ipython/rmagic.py'
adding 'rpy2/ipython/tests/__init__.py'
adding 'rpy2/ipython/tests/test_ggplot.py'
adding 'rpy2/ipython/tests/test_html.py'
adding 'rpy2/ipython/tests/test_rmagic.py'
adding 'rpy2/robjects/__init__.py'
adding 'rpy2/robjects/constants.py'
adding 'rpy2/robjects/conversion.py'
adding 'rpy2/robjects/environments.py'
adding 'rpy2/robjects/functions.py'
adding 'rpy2/robjects/help.py'
adding 'rpy2/robjects/language.py'
adding 'rpy2/robjects/methods.py'
adding 'rpy2/robjects/numpy2ri.py'
adding 'rpy2/robjects/packages.py'
adding 'rpy2/robjects/packages_utils.py'
adding 'rpy2/robjects/pandas2ri.py'
adding 'rpy2/robjects/robject.py'
adding 'rpy2/robjects/vectors.py'
adding 'rpy2/robjects/version.py'
adding 'rpy2/robjects/lib/__init__.py'
adding 'rpy2/robjects/lib/dbplyr.py'
adding 'rpy2/robjects/lib/dplyr.py'
adding 'rpy2/robjects/lib/ggplot2.py'
adding 'rpy2/robjects/lib/grdevices.py'
adding 'rpy2/robjects/lib/grid.py'
adding 'rpy2/robjects/lib/tidyr.py'
adding 'rpy2/robjects/tests/robjects/__init__.py'
adding 'rpy2/robjects/tests/robjects/test_array.py'
adding 'rpy2/robjects/tests/robjects/test_conversion.py'
adding 'rpy2/robjects/tests/robjects/test_conversion_numpy.py'
adding 'rpy2/robjects/tests/robjects/test_dataframe.py'
adding 'rpy2/robjects/tests/robjects/test_environment.py'
adding 'rpy2/robjects/tests/robjects/test_formula.py'
adding 'rpy2/robjects/tests/robjects/test_function.py'
adding 'rpy2/robjects/tests/robjects/test_help.py'
adding 'rpy2/robjects/tests/robjects/test_language.py'
adding 'rpy2/robjects/tests/robjects/test_methods.py'
adding 'rpy2/robjects/tests/robjects/test_packages.py'
adding 'rpy2/robjects/tests/robjects/test_packages_utils.py'
adding 'rpy2/robjects/tests/robjects/test_pandas_conversions.py'
adding 'rpy2/robjects/tests/robjects/test_robjects.py'
adding 'rpy2/robjects/tests/robjects/test_rs4.py'
adding 'rpy2/robjects/tests/robjects/test_serialization.py'
adding 'rpy2/robjects/tests/robjects/test_translated_function.py'
adding 'rpy2/robjects/tests/robjects/test_vector.py'
adding 'rpy2/robjects/tests/robjects/test_vector_datetime.py'
adding 'rpy2/robjects/tests/robjects/test_vector_extractdelegator.py'
adding 'rpy2/robjects/tests/robjects/test_vector_factor.py'
adding 'rpy2/robjects/tests/robjects/lib/__init__.py'
adding 'rpy2/robjects/tests/robjects/lib/test_dbplyr.py'
adding 'rpy2/robjects/tests/robjects/lib/test_dplyr.py'
adding 'rpy2/robjects/tests/robjects/lib/test_ggplot2.py'
adding 'rpy2/robjects/tests/robjects/lib/test_grdevices.py'
adding 'rpy2/robjects/tests/robjects/lib/test_grid.py'
adding 'rpy2/robjects/tests/robjects/lib/test_tidyr.py'
adding 'rpy2_robjects-3.6.3.dist-info/METADATA'
adding 'rpy2_robjects-3.6.3.dist-info/WHEEL'
adding 'rpy2_robjects-3.6.3.dist-info/top_level.txt'
adding 'rpy2_robjects-3.6.3.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built rpy2_robjects-3.6.3-py3-none-any.whl
I: pybuild plugin_pyproject:155: Unpacking wheel built for python3.13 with "installer" module
rm -fv .pybuild/*/*.whl
removed '.pybuild/cpython3_3.13/rpy2_robjects-3.6.3-py3-none-any.whl'
removed '.pybuild/cpython3_3.14/rpy2_robjects-3.6.3-py3-none-any.whl'
dh_auto_build
I: pybuild plugin_pyproject:131: Building wheel for python3.14 with "build" module
I: pybuild base:317: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14  
* Building wheel...
running bdist_wheel
running build
running build_py
creating build/lib/rpy2
copying src/rpy2/__init__.py -> build/lib/rpy2
running egg_info
creating src/rpy2.egg-info
writing src/rpy2.egg-info/PKG-INFO
writing dependency_links to src/rpy2.egg-info/dependency_links.txt
writing requirements to src/rpy2.egg-info/requires.txt
writing top-level names to src/rpy2.egg-info/top_level.txt
writing manifest file 'src/rpy2.egg-info/SOURCES.txt'
reading manifest file 'src/rpy2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README' anywhere in distribution
warning: no previously-included files matching '*patch*' found anywhere in distribution
warning: no previously-included files matching '*diff*' found anywhere in distribution
warning: no previously-included files matching '.hg' found anywhere in distribution
warning: no files found matching 'MANIFEST'
warning: no files found matching '_rinterface_cffi_build'
warning: no files found matching 'rpy/__init__.py'
warning: no files found matching 'rpy/situation.py'
warning: no files found matching '*.py' under directory 'rpy/robjects'
warning: no files found matching '*.py' under directory 'rpy/ipython'
warning: no files found matching '*.py' under directory 'rpy/interactive'
warning: no files found matching '*.py' under directory 'rpy/rlike'
no previously-included directories found matching 'dist'
warning: no files found matching 'doc/source/rpy2_logo.png'
adding license file 'LICENSE'
writing manifest file 'src/rpy2.egg-info/SOURCES.txt'
copying src/rpy2/py.typed -> build/lib/rpy2
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/rpy2
copying build/lib/rpy2/py.typed -> build/bdist.linux-x86_64/wheel/./rpy2
copying build/lib/rpy2/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2
running install_egg_info
Copying src/rpy2.egg-info to build/bdist.linux-x86_64/wheel/./rpy2-3.6.4.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/rpy2-3.6.4.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/.tmp-n4lktgd_/rpy2-3.6.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'rpy2/__init__.py'
adding 'rpy2/py.typed'
adding 'rpy2-3.6.4.dist-info/licenses/LICENSE'
adding 'rpy2-3.6.4.dist-info/METADATA'
adding 'rpy2-3.6.4.dist-info/WHEEL'
adding 'rpy2-3.6.4.dist-info/top_level.txt'
adding 'rpy2-3.6.4.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built rpy2-3.6.4-py3-none-any.whl
I: pybuild plugin_pyproject:155: Unpacking wheel built for python3.14 with "installer" module
I: pybuild plugin_pyproject:131: Building wheel for python3.13 with "build" module
I: pybuild base:317: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13  
* Building wheel...
running bdist_wheel
running build
running build_py
running egg_info
writing src/rpy2.egg-info/PKG-INFO
writing dependency_links to src/rpy2.egg-info/dependency_links.txt
writing requirements to src/rpy2.egg-info/requires.txt
writing top-level names to src/rpy2.egg-info/top_level.txt
reading manifest file 'src/rpy2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README' anywhere in distribution
warning: no previously-included files matching '*patch*' found anywhere in distribution
warning: no previously-included files matching '*diff*' found anywhere in distribution
warning: no previously-included files matching '.hg' found anywhere in distribution
warning: no files found matching 'MANIFEST'
warning: no files found matching '_rinterface_cffi_build'
warning: no files found matching 'rpy/__init__.py'
warning: no files found matching 'rpy/situation.py'
warning: no files found matching '*.py' under directory 'rpy/robjects'
warning: no files found matching '*.py' under directory 'rpy/ipython'
warning: no files found matching '*.py' under directory 'rpy/interactive'
warning: no files found matching '*.py' under directory 'rpy/rlike'
no previously-included directories found matching 'dist'
warning: no files found matching 'doc/source/rpy2_logo.png'
adding license file 'LICENSE'
writing manifest file 'src/rpy2.egg-info/SOURCES.txt'
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/rpy2
copying build/lib/rpy2/py.typed -> build/bdist.linux-x86_64/wheel/./rpy2
copying build/lib/rpy2/__init__.py -> build/bdist.linux-x86_64/wheel/./rpy2
running install_egg_info
Copying src/rpy2.egg-info to build/bdist.linux-x86_64/wheel/./rpy2-3.6.4.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/rpy2-3.6.4.dist-info/WHEEL
creating '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/.tmp-znzu5idf/rpy2-3.6.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'rpy2/__init__.py'
adding 'rpy2/py.typed'
adding 'rpy2-3.6.4.dist-info/licenses/LICENSE'
adding 'rpy2-3.6.4.dist-info/METADATA'
adding 'rpy2-3.6.4.dist-info/WHEEL'
adding 'rpy2-3.6.4.dist-info/top_level.txt'
adding 'rpy2-3.6.4.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built rpy2-3.6.4-py3-none-any.whl
I: pybuild plugin_pyproject:155: Unpacking wheel built for python3.13 with "installer" module
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
TZ=America/New_York LC_ALL=C.UTF-8 LANGUAGE=C.UTF-8 dh_auto_test
I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build; python3.14 -m pytest 
============================= test session starts ==============================
platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build
configfile: pyproject.toml
plugins: typeguard-4.4.4
collected 867 items / 1 error

==================================== ERRORS ====================================
______________ ERROR collecting rpy2/ipython/tests/test_rmagic.py ______________
rpy2/ipython/tests/test_rmagic.py:70: in <module>
    @pytest.mark.skipif(IPython is None,
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:401: in __call__
    store_mark(unwrapped_func, self.mark, stacklevel=3)
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:466: in store_mark
    warnings.warn(MARKED_FIXTURE, stacklevel=stacklevel)
E   pytest.PytestRemovedIn9Warning: Marks applied to fixtures have no effect
E   See docs: https://docs.pytest.org/en/stable/deprecations.html#applying-a-mark-to-a-fixture-function
=============================== warnings summary ===============================
rpy2/robjects/lib/ggplot2.py:76
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/rpy2/robjects/lib/ggplot2.py:76: UserWarning: This was designed against ggplot2 versions starting with 3.5. but you have 3.5.1.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR rpy2/ipython/tests/test_rmagic.py - pytest.PytestRemovedIn9Warning: Mar...
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
========================= 1 warning, 1 error in 8.24s ==========================
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build; python3.14 -m pytest 
I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest 
============================= test session starts ==============================
platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build
configfile: pyproject.toml
plugins: typeguard-4.4.4
collected 867 items / 1 error

==================================== ERRORS ====================================
______________ ERROR collecting rpy2/ipython/tests/test_rmagic.py ______________
rpy2/ipython/tests/test_rmagic.py:70: in <module>
    @pytest.mark.skipif(IPython is None,
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:401: in __call__
    store_mark(unwrapped_func, self.mark, stacklevel=3)
/usr/lib/python3/dist-packages/_pytest/mark/structures.py:466: in store_mark
    warnings.warn(MARKED_FIXTURE, stacklevel=stacklevel)
E   pytest.PytestRemovedIn9Warning: Marks applied to fixtures have no effect
E   See docs: https://docs.pytest.org/en/stable/deprecations.html#applying-a-mark-to-a-fixture-function
=============================== warnings summary ===============================
rpy2/robjects/lib/ggplot2.py:76
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/rpy2/robjects/lib/ggplot2.py:76: UserWarning: This was designed against ggplot2 versions starting with 3.5. but you have 3.5.1.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
ERROR rpy2/ipython/tests/test_rmagic.py - pytest.PytestRemovedIn9Warning: Mar...
!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
========================= 1 warning, 1 error in 4.56s ==========================
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest 
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13
make[1]: *** [debian/rules:33: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:20: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------