[R-pkg-team] Bug#1100292: r-cran-fastcluster: FTBFS: FAIL: test_vector (tests.fastcluster_test.test_vector)
Santiago Vila
sanvila at debian.org
Wed Mar 12 16:33:32 GMT 2025
Package: src:r-cran-fastcluster
Version: 1.2.6-2
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild --sourcedirectory=src/python
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean || true
I: pybuild base:311: python3.13 setup.py clean
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
Fastcluster version: 1.2.6
Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0]
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
if test -d src; then \
find src -name "*.o" -delete ; \
find src -name "*.so" -delete ; \
fi
rm -f config.log config.status
rm -rf tmp-install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean -O--buildsystem=pybuild -O--sourcedirectory=src/python
dh_clean -O--buildsystem=pybuild -O--sourcedirectory=src/python
debian/rules binary
dh binary --buildsystem=pybuild --sourcedirectory=src/python
dh_update_autotools_config -O--buildsystem=pybuild -O--sourcedirectory=src/python
dh_autoreconf -O--buildsystem=pybuild -O--sourcedirectory=src/python
dh_auto_configure -O--buildsystem=pybuild -O--sourcedirectory=src/python
I: pybuild base:311: python3.13 setup.py config
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
Fastcluster version: 1.2.6
Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0]
running config
dh_auto_build -O--buildsystem=pybuild -O--sourcedirectory=src/python
I: pybuild base:311: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
Fastcluster version: 1.2.6
Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0]
running build
running build_py
copying fastcluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build
running build_ext
building '_fastcluster' extension
creating build/temp.linux-x86_64-cpython-313
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c fastcluster_python.cpp -o build/temp.linux-x86_64-cpython-313/fastcluster_python.o
In file included from fastcluster_python.cpp:38:
../fastcluster.cpp:53:35: note: ‘#pragma message: Use fenv header.’
53 | #pragma message("Use fenv header.")
| ^
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/fastcluster_python.o -L/usr/lib/x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build/_fastcluster.cpython-313-x86_64-linux-gnu.so
dh_auto_test -O--buildsystem=pybuild -O--sourcedirectory=src/python
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build; python3.13 -m unittest discover -v
test (tests.fastcluster_test.test) ... ok
test_nan (tests.fastcluster_test.test_nan) ... ok
test_vector (tests.fastcluster_test.test_vector) ... FAIL
======================================================================
FAIL: test_vector (tests.fastcluster_test.test_vector)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build/tests/__init__.py", line 14, in test_vector
test(10)
~~~~^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build/tests/vectortest.py", line 236, in test
test_all(n,dim)
~~~~~~~~^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build/tests/vectortest.py", line 115, in test_all
check(Z2, method, D)
~~~~~^^^^^^^^^^^^^^^
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build/tests/vectortest.py", line 142, in check
raise AssertionError(
'Not the global minimum in step {2}: {0}, {1}'.
format(Z2[i,2], gmin,i), squareform(D))
AssertionError: ('Not the global minimum in step 0: 0.42857142857142855, 0.0', array([[0. , 0.28571429, 0.14285714, ..., 0.33333333, 0.14285714,
0.14285714],
[0.28571429, 0. , 0.14285714, ..., 0.57142857, 0.14285714,
0.14285714],
[0.14285714, 0.14285714, 0. , ..., 0.42857143, 0. ,
0. ],
...,
[0.33333333, 0.57142857, 0.42857143, ..., 0. , 0.42857143,
0.42857143],
[0.14285714, 0.14285714, 0. , ..., 0.42857143, 0. ,
0. ],
[0.14285714, 0.14285714, 0. , ..., 0.42857143, 0. ,
0. ]], shape=(62, 62)))
----------------------------------------------------------------------
Ran 3 tests in 1.095s
FAILED (failures=1)
Test program for the 'fastcluster' package.
Copyright:
* Until package version 1.1.23: (c) 2011 Daniel Müllner <https://danifold.net>
* All changes from version 1.1.24 on: (c) Google Inc. <https://www.google.com>
Dimension: 8
Number of points: 28
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 17
Number of points: 20
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 6
Number of points: 6
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 14
Number of points: 57
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 12
Number of points: 78
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 10
Number of points: 7
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 18
Number of points: 7
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 11
Number of points: 42
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 12
Number of points: 31
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Dimension: 12
Number of points: 5
Real distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Integer distance values:
Method: single...OK.
Method: complete...OK.
Method: average...OK.
Method: weighted...OK.
Method: ward...OK.
Method: centroid...OK.
Method: median...OK.
Test program for the 'fastcluster' package.
Copyright:
* Until package version 1.1.23: (c) 2011 Daniel Müllner <https://danifold.net>
* All changes from version 1.1.24 on: (c) Google Inc. <https://www.google.com>
Test program for the 'fastcluster' package.
Copyright:
* Until package version 1.1.23: (c) 2011 Daniel Müllner <https://danifold.net>
* All changes from version 1.1.24 on: (c) Google Inc. <https://www.google.com>
Seed: 62465845
Dimension: 7
Number of points: 62
Metric: hamming...Method: single...OK.
Metric: jaccard...Method: single...OK.
Metric: yule...Method: single...OK.
Metric: matching...Method: single...OK.
Metric: dice...Method: single...OK.
Metric: rogerstanimoto...Method: single...OK.
Metric: russellrao...Method: single...OK.
Metric: sokalsneath...Method: single...OK.
Metric: euclidean...Method: single...OK.
Metric: sqeuclidean...Method: single...OK.
Metric: cityblock...Method: single...OK.
Metric: chebychev...Method: single...OK.
Metric: minkowski...p: 2.8385464125577693...Method: single...OK.
Metric: cosine...Method: single...OK.
Metric: correlation...Method: single...OK.
Metric: hamming...Method: single...OK.
Metric: jaccard...Method: single...Seed: 62465845
Seed: 986035629
Seed: 858259965
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_fastcluster/build; python3.13 -m unittest discover -v
dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --dir src/python returned exit code 13
make: *** [debian/rules:14: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202503/
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 could not 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:r-cran-fastcluster, so that this is still
visible in the BTS web page for this package.
Thanks.
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