Your message dated Thu, 08 May 2025 03:04:25 +0000
with message-id <e1ucryf-00h0bb...@fasolo.debian.org>
and subject line Bug#1100292: fixed in r-cran-fastcluster 1.3.0-1
has caused the Debian Bug report #1100292,
regarding r-cran-fastcluster: FTBFS: FAIL: test_vector
(tests.fastcluster_test.test_vector)
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1100292: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1100292
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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: â#pragma message: Use fenv header.â
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.
--- End Message ---
--- Begin Message ---
Source: r-cran-fastcluster
Source-Version: 1.3.0-1
Done: Charles Plessy <ple...@debian.org>
We believe that the bug you reported is fixed in the latest version of
r-cran-fastcluster, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1100...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Charles Plessy <ple...@debian.org> (supplier of updated r-cran-fastcluster
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 08 May 2025 11:42:23 +0900
Source: r-cran-fastcluster
Architecture: source
Version: 1.3.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net>
Changed-By: Charles Plessy <ple...@debian.org>
Closes: 1100292
Changes:
r-cran-fastcluster (1.3.0-1) unstable; urgency=medium
.
* Team upload.
* New upstream version. Closes: #1100292
* Standards-Version: 4.7.2 (routine-update)
* Add missing build dependency on python3-numpy-dev for command dh_numpy3.
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