Your message dated Sun, 08 Sep 2024 11:19:15 +0000
with message-id <e1snfwp-008rhd...@fasolo.debian.org>
and subject line Bug#1075607: fixed in unifrac 1.3-4
has caused the Debian Bug report #1075607,
regarding unifrac: ftbfs with GCC-14
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.
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--
1075607: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075607
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:unifrac
Version: 1.3-3
Severity: important
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-14
[This bug is targeted to the upcoming trixie release]
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/unifrac_1.3-3_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-14/porting_to.html
[...]
running build_ext
Compiling SSU
building 'unifrac._api' extension
creating build
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/unifrac
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g
-Werror=implicit-function-declaration -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g
-O2 -Werror=implicit-function-declaration -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/python3/dist-packages/numpy/core/include -I/usr/include/python3.11
-c unifrac/_api.c -o build/temp.linux-x86_64-cpython-311/unifrac/_api.o
In file included from
/usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
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:1255:
/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:23770:33: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
23770 | 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:27151:32: error: assignment to ‘_Bool *’ from incompatible
pointer type ‘__pyx_t_7unifrac_4_api_bool *’ {aka ‘unsigned char *’}
[-Wincompatible-pointer-types]
27151 | __pyx_v_sp_bptree->structure = __pyx_v_structure;
| ^
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1:
/usr/bin/python3.11 setup.py build
I: pybuild base:311: /usr/bin/python3 setup.py build
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
copying unifrac/_methods.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
copying unifrac/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
copying unifrac/_meta.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
copying unifrac/tests/test_api.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
copying unifrac/tests/test_methods.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
copying unifrac/tests/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/e1.biom ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/t1.newick ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/crawford.group.tsv ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/e2.biom ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/crawford.tre ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/test.faith.exp ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/crawford.biom ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
copying unifrac/tests/data/t2.newick ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_unifrac/build/unifrac/tests/data
running build_ext
Compiling SSU
building 'unifrac._api' extension
creating build/temp.linux-x86_64-cpython-312
creating build/temp.linux-x86_64-cpython-312/unifrac
x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall
-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac
-I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12
-c unifrac/_api.c -o build/temp.linux-x86_64-cpython-312/unifrac/_api.o
In file included from
/usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929,
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:1255:
/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:23770:33: warning: comparison of integer expressions of
different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
23770 | 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:27151:32: error: assignment to ‘_Bool *’ from incompatible
pointer type ‘__pyx_t_7unifrac_4_api_bool *’ {aka ‘unsigned char *’}
[-Wincompatible-pointer-types]
27151 | __pyx_v_sp_bptree->structure = __pyx_v_structure;
| ^
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1:
/usr/bin/python3 setup.py build
dh_auto_build: error: pybuild --build -i python{version} -p "3.11 3.12"
returned exit code 13
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: unifrac
Source-Version: 1.3-4
Done: Michael R. Crusoe <cru...@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 1075...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <cru...@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: SHA512
Format: 1.8
Date: Sun, 08 Sep 2024 12:56:59 +0200
Source: unifrac
Architecture: source
Version: 1.3-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <cru...@debian.org>
Closes: 1075607
Changes:
unifrac (1.3-4) unstable; urgency=medium
.
* Team upload.
* d/rules: add workaround for https://bugs.debian.org/1077205. Closes:
#1075607
* d/rules: move cleanup to d/clean
* Switch to pytest, and using pybuild-autopkgtest
* Standards-Version: 4.6.2 (routine-update)
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