[R-pkg-team] Bug#1100292: r-cran-fastcluster: FTBFS: FAIL: test_vector (tests.fastcluster_test.test_vector)

[Charles Plessy]

Control: tag -1 help

Hi all,

I had a look at the build failure and could reproduce it locally.  Here 
is an extract from Santiago's report.

The test failure looks relevant and probably should not ignored. 
Unfortunately, the combination of C++ and Python is very, very far from 
my expertise.  If somebody else can have a look that would be great.

The alternative is to release without the package and its reverse 
dependencies, unless we know that there is no risk to inflict erroneous 
computations on our users.

Have a nice day,

Charles

==================================================================================================================
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

==================================================================================================================

-- 
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.plessy at oist.jp
Okinawa  Institute  of  Science  and  Technology  Graduate  University
Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu
Toots from work - ~~ ~~~~ ~~ - https://fediscience.org/@charles_plessy