Your message dated Mon, 23 Oct 2023 23:03:59 +0000
with message-id <e1qv3xn-00ccqe...@fasolo.debian.org>
and subject line Bug#1042198: fixed in unifrac 1.3-1
has caused the Debian Bug report #1042198,
regarding unifrac: FTBFS: AssertionError: 0.9999999403953552 != 1.0
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.)
--
1042198: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042198
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: unifrac
Version: 1.2-3
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20230726 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> 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
> I: pybuild base:240: python3.11 setup.py config
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the
> future `np.bool` will be defined as the corresponding NumPy scalar.
> if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the
> future `np.bytes` will be defined as the corresponding NumPy scalar.
> obj = getattr(themodule, elem)
> Compiling unifrac/_api.pyx because it changed.
> [1/1] Cythonizing unifrac/_api.pyx
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:240: /usr/bin/python3 setup.py build
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the
> future `np.bool` will be defined as the corresponding NumPy scalar.
> if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the
> future `np.bytes` will be defined as the corresponding NumPy scalar.
> obj = getattr(themodule, elem)
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac
> copying unifrac/_methods.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac
> copying unifrac/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac
> copying unifrac/_meta.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests
> copying unifrac/tests/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests
> copying unifrac/tests/test_methods.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests
> copying unifrac/tests/test_api.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests
> creating
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/test.faith.exp ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/crawford.biom ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/e2.biom ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/e1.biom ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/crawford.tre ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/t1.newick ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> copying unifrac/tests/data/t2.newick ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/data
> running build_ext
> Compiling SSU
> building 'unifrac._api' extension
> INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2
> -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv
> -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
> -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
>
> creating build
> creating build/temp.linux-x86_64-cpython-311
> creating build/temp.linux-x86_64-cpython-311/unifrac
> INFO: compile options: '-I/usr/lib/python3/dist-packages/numpy/core/include
> -I/usr/include/python3.11 -c'
> INFO: x86_64-linux-gnu-gcc: unifrac/_api.c
> In file included from
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
> from
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
> from
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
> from unifrac/_api.c:780:
> /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2:
> warning: #warning "Using deprecated NumPy API, disable it with " "#define
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> 17 | #warning "Using deprecated NumPy API, disable it with " \
> | ^~~~~~~
> unifrac/_api.c: In function
> ‘__pyx_f_7unifrac_4_api_result_to_skbio_distance_matrix’:
> unifrac/_api.c:5912:33: warning: comparison of integer expressions of
> different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
> 5912 | for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_14; __pyx_t_7+=1) {
> | ^
> unifrac/_api.c: In function ‘__pyx_f_7unifrac_4_api_construct_support_bptree’:
> unifrac/_api.c:8449:32: warning: assignment to ‘_Bool *’ from incompatible
> pointer type ‘__pyx_t_7unifrac_4_api_bool *’ {aka ‘unsigned char *’}
> [-Wincompatible-pointer-types]
> 8449 | __pyx_v_sp_bptree->structure = __pyx_v_structure;
> | ^
> INFO: x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g
> -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2
> -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
> build/temp.linux-x86_64-cpython-311/unifrac/_api.o
> -L/usr/lib/x86_64-linux-gnu -lssu -o
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/_api.cpython-311-x86_64-linux-gnu.so
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:240: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build; python3.11 -m unittest
> discover -v
> test_ssu_table_not_subset_tree
> (unifrac.tests.test_api.EdgeCasesTests.test_ssu_table_not_subset_tree) ... ok
> test_unweighted_extra_tips
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_extra_tips) ... ok
> test_unweighted_minimal_trees
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_minimal_trees) ... FAIL
> test_unweighted_otus_out_of_order
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_otus_out_of_order) ...
> ok
> test_unweighted_root_not_observed
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_root_not_observed) ...
> ok
> test_unweighted_unifrac
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_unifrac) ... ok
> test_unweighted_unifrac_identity
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_unifrac_identity) ...
> ok
> test_unweighted_unifrac_non_overlapping
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_unifrac_non_overlapping)
> ... ok
> test_unweighted_unifrac_symmetry
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_unifrac_symmetry) ...
> ok
> test_weighted_extra_tips
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_extra_tips) ... ok
> test_weighted_normalized_root_not_observed
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_normalized_root_not_observed)
> ... ok
> test_weighted_otus_out_of_order
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_otus_out_of_order) ... ok
> test_weighted_root_not_observed
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_root_not_observed) ... ok
> test_weighted_unifrac
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac) ... ok
> test_weighted_unifrac_identity
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_identity) ... ok
> test_weighted_unifrac_identity_normalized
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_identity_normalized)
> ... ok
> test_weighted_unifrac_non_overlapping
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_non_overlapping)
> ... ok
> test_weighted_unifrac_non_overlapping_normalized
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_non_overlapping_normalized)
> ... ok
> test_weighted_unifrac_normalized
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_normalized) ...
> ok
> test_weighted_unifrac_symmetry
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_symmetry) ... ok
> test_weighted_unifrac_symmetry_normalized
> (unifrac.tests.test_api.EdgeCasesTests.test_weighted_unifrac_symmetry_normalized)
> ... ok
> test_faith_pd (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd)
> ... ok
> test_faith_pd_all_observed
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_all_observed) ...
> ok
> test_faith_pd_biom_table_empty
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_biom_table_empty)
> ... ok
> test_faith_pd_extra_tips
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_extra_tips) ... ok
> test_faith_pd_invalid_input
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_invalid_input)
> ... ok
> test_faith_pd_minimal
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_minimal) ... ok
> test_faith_pd_none_observed
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_none_observed)
> ... ERROR
> test_faith_pd_root_not_observed
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_root_not_observed)
> ... ok
> test_faith_pd_series_name
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_series_name) ...
> ok
> test_faith_pd_table_not_subset_tree
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_table_not_subset_tree)
> ... ok
> test_faith_pd_zero_branches_omitted
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_zero_branches_omitted)
> ... ok
> test_meta_unifrac (unifrac.tests.test_api.UnifracAPITests.test_meta_unifrac)
> ... ok
> test_ssu_bad_method
> (unifrac.tests.test_api.UnifracAPITests.test_ssu_bad_method) ... ok
> test_ssu_bad_table
> (unifrac.tests.test_api.UnifracAPITests.test_ssu_bad_table) ... ok
> test_ssu_bad_tree (unifrac.tests.test_api.UnifracAPITests.test_ssu_bad_tree)
> ... ok
> test_unweighted_fp32_inmem
> (unifrac.tests.test_api.UnifracAPITests.test_unweighted_fp32_inmem) ... ok
> test_unweighted_fp64_inmem
> (unifrac.tests.test_api.UnifracAPITests.test_unweighted_fp64_inmem) ... ok
> test_unweighted_inmem
> (unifrac.tests.test_api.UnifracAPITests.test_unweighted_inmem) ... ok
> test_unweighted_root_eval_issue_46
> (unifrac.tests.test_api.UnifracAPITests.test_unweighted_root_eval_issue_46)
> ... ok
> test_meta_unifrac
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac)
> meta_unifrac should give correct result on sample trees ... ok
> test_meta_unifrac_alpha_not_generalized
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_alpha_not_generalized)
> ... ok
> test_meta_unifrac_bad_consolidation
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_bad_consolidation)
> ... ok
> test_meta_unifrac_bad_method
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_bad_method)
> ... ok
> test_meta_unifrac_missing
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_missing) ...
> ok
> test_meta_unifrac_no_method
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_no_method)
> ... ok
> test_meta_unifrac_unbalanced
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_unbalanced)
> ... ok
> test_meta_unifrac_unbalanced_weights
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_unifrac_unbalanced_weights)
> ... ok
> test_meta_validation
> (unifrac.tests.test_methods.StateUnifracTests.test_meta_validation) ... ok
>
> ======================================================================
> ERROR: test_faith_pd_none_observed
> (unifrac.tests.test_api.FaithPDEdgeCasesTests.test_faith_pd_none_observed)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/test_api.py",
> line 717, in test_faith_pd_none_observed
> self.assertAlmostEqual(actual.values, expected)
> File "/usr/lib/python3.11/unittest/case.py", line 918, in assertAlmostEqual
> if round(diff, places) == 0:
> ^^^^^^^^^^^^^^^^^^^
> TypeError: type numpy.ndarray doesn't define __round__ method
>
> ======================================================================
> FAIL: test_unweighted_minimal_trees
> (unifrac.tests.test_api.EdgeCasesTests.test_unweighted_minimal_trees)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File
> "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build/unifrac/tests/test_api.py",
> line 296, in test_unweighted_minimal_trees
> self.assertEqual(actual, expected)
> AssertionError: 0.9999999403953552 != 1.0
>
> ----------------------------------------------------------------------
> Ran 49 tests in 9.651s
>
> FAILED (failures=1, errors=1)
> E: pybuild pybuild:388: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_unifrac/build; python3.11 -m unittest
> discover -v
> dh_auto_test: error: pybuild --test -i python{version} -p 3.11 returned exit
> code 13
The full build log is available from:
http://qa-logs.debian.net/2023/07/26/unifrac_1.2-3_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230726;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
--- Begin Message ---
Source: unifrac
Source-Version: 1.3-1
Done: Nilesh Patra <nil...@debian.org>
We believe that the bug you reported is fixed in the latest version of
unifrac, 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 1042...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <nil...@debian.org> (supplier of updated unifrac 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: SHA256
Format: 1.8
Date: Tue, 24 Oct 2023 04:20:14 +0530
Source: unifrac
Architecture: source
Version: 1.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <nil...@debian.org>
Closes: 1042198
Changes:
unifrac (1.3-1) unstable; urgency=medium
.
[ Andreas Tille ]
* Team Upload.
* New upstream version
* Bump versioned Build-Depends: libssu-dev (>= 1.3.2-1~)
.
[ Nilesh Patra ]
* Relax test conditions on test_unweighted_minimal_trees to get
tests passing (Closes: #1042198)
* Add versioned dep on libssu-dev (1.4-2~) to get faith_pd test fixed
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Files:
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5b9f4c8ff4caf738771a7c467ce6e043 65918 science optional unifrac_1.3.orig.tar.gz
81435caa1764410bd78b3f9966995b66 7168 science optional
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unifrac_1.3-1_amd64.buildinfo
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